Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/percolator.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.nksnzd5p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.nksnzd5p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '9f8697053cc1474083740b67ca2ef9a0', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.nksnzd5p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/percolator.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658448000 Wrote: /builddir/build/SRPMS/percolator-3.05-10.fc38.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/percolator.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.nksnzd5p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.nksnzd5p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '65f335fb382d42a187c03d2c60a5598e', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.nksnzd5p:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/percolator.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658448000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.2DdFkb + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf percolator-rel-3-05 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-05.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd percolator-rel-3-05 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + tar -xvf /builddir/build/SOURCES/yeast-01.sqt.tar.gz yeast-01.shuffled2.sqt yeast-01.shuffled.sqt yeast-01.sqt + find . -type f -name '*.cpp' -exec chmod 0644 '{}' ';' + find . -type f -name '*.h' -exec chmod 0644 '{}' ';' + find . -type f -name '*.xx' -exec chmod 0644 '{}' ';' + find . -type f -name '*.txt' -exec chmod 0644 '{}' ';' + chmod a-x src/converters/MSToolkit/RAMP/README + mv src/converters/MSToolkit/RAMP/README src/converters/MSToolkit/RAMP/RAMP-README + mv src/converters/MSToolkit/RAMP/Readme.Mike.txt src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt + cp -p /builddir/build/SOURCES/percolator-RAMP_license_lgpl-2.1.txt RAMP_license_lgpl-2.1.txt + sed -e 's|./bin|bin|g' -i src/qvality/CMakeLists.txt + sed -e 's|${ELUDE_MODELS_PATH}..|${ELUDE_MODELS_PATH}|g' -i src/elude_tool/CMakeLists.txt + sed -e 's|${CMAKE_INSTALL_PREFIX}/share/elude/models/|${CMAKE_INSTALL_PREFIX}/share/elude|g' -i src/elude_tool/CMakeLists.txt + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.RQ5F4u + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH ~/build/BUILD/percolator-rel-3-05/percolator ~/build/BUILD/percolator-rel-3-05 + CC=gcc + export CC + CXX=g++ + export CXX + cd percolator-rel-3-05 + export 'CXXFLAGS=-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + mkdir -p percolator + pushd percolator + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=x86_64 .. -- The C compiler identification is GNU 13.0.0 -- The CXX compiler identification is GNU 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- -- ------------------------------------------------------------------------------- -- Building PERCOLATOR: -- change a configuration variable with: cmake -D= -- CMAKE_INSTALL_PREFIX = /usr -- CMAKE_BUILD_TYPE = Release -- CMAKE_PREFIX_PATH = ../ -- XML_SUPPORT = ON -- GOOGLE_TEST = -- GOOGLE_TEST_PATH = -- TARGET_ARCH = x86_64 -- TOOL CHAIN FILE = -- PROFILING = -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages: -- Found Xerces-C: /usr/lib64/libxerces-c.so -- : /usr/include -- Version: 3.2.3 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Locating CodeSynthesis library with XSDDIR set to -- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx -- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.46.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/percolator + cd src + xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../../src/xml/percolator_in.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../../src/xml/percolator_out.xsd + cd .. + /usr/bin/make -O -j2 V=1 VERBOSE=1 /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05 -B/builddir/build/BUILD/percolator-rel-3-05/percolator --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/percolator//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend /usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build /usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 2%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 4%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 5%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 6%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 8%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp: In member function 'void PercolatorCrux::Database::print(FILE*)': /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp:206:12: warning: unused variable 'protein' [-Wunused-variable] 206 | Protein* protein = NULL; | ^~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 9%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Peptide.cpp /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Peptide.cpp:375:13: warning: 'bool equal_peptides(char*, PercolatorCrux::Peptide*)' defined but not used [-Wunused-function] 375 | static bool equal_peptides( | ^~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 10%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PeptideConstraint.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 12%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PeptideSrc.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 2%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/percolator/src/percolator_in.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 13%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp: In member function 'bool PickedProteinCaller::getProteinFragmentsAndDuplicates(std::map, std::__cxx11::basic_string >&, std::map, std::__cxx11::basic_string >&, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp:365:8: warning: unused variable 'success' [-Wunused-variable] 365 | bool success = true; | ^~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 16%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::shuffle(PercolatorCrux::DECOY_TYPE_T)': /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:529:9: warning: enumeration value 'PEPTIDE_REVERSE_DECOYS' not handled in switch [-Wswitch] 529 | switch(decoy_type){ | ^ In function 'PercolatorCrux::Protein::readRawSequence(_IO_FILE*, char*, unsigned int, char*, unsigned int*)', inlined from 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)' at /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:366:23: /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 505 | raw_sequence[i_seq] = '\0'; | ~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)': /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)::buffer' of size 40000 355 | static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in. | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 17%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/ProteinPeptideIterator.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 18%] Linking CXX static library libpicked_protein.a cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1 /usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o /usr/bin/ranlib libpicked_protein.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 18%] Built target picked_protein make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/blas /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 20%] Building C object src/blas/CMakeFiles/blas.dir/daxpy.c.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/daxpy.c.o -MF CMakeFiles/blas.dir/daxpy.c.o.d -o CMakeFiles/blas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/daxpy.c make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 21%] Building C object src/blas/CMakeFiles/blas.dir/ddot.c.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/ddot.c.o -MF CMakeFiles/blas.dir/ddot.c.o.d -o CMakeFiles/blas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/ddot.c make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 22%] Building C object src/blas/CMakeFiles/blas.dir/dgemv.c.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dgemv.c.o -MF CMakeFiles/blas.dir/dgemv.c.o.d -o CMakeFiles/blas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c /builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c: In function 'dgemv_': /builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c:59:45: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 59 | if (*m == 0 || *n == 0 || *alpha == 0.0 && *beta == 1.0) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 24%] Building C object src/blas/CMakeFiles/blas.dir/dnrm2.c.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dnrm2.c.o -MF CMakeFiles/blas.dir/dnrm2.c.o.d -o CMakeFiles/blas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/dnrm2.c make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 25%] Building C object src/blas/CMakeFiles/blas.dir/dscal.c.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dscal.c.o -MF CMakeFiles/blas.dir/dscal.c.o.d -o CMakeFiles/blas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/dscal.c make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 26%] Linking C static library libblas.a cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/cmake -P CMakeFiles/blas.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/cmake -E cmake_link_script CMakeFiles/blas.dir/link.txt --verbose=1 /usr/bin/ar rcv libblas.a CMakeFiles/blas.dir/daxpy.c.o CMakeFiles/blas.dir/ddot.c.o CMakeFiles/blas.dir/dgemv.c.o CMakeFiles/blas.dir/dnrm2.c.o CMakeFiles/blas.dir/dscal.c.o a - CMakeFiles/blas.dir/daxpy.c.o a - CMakeFiles/blas.dir/ddot.c.o a - CMakeFiles/blas.dir/dgemv.c.o a - CMakeFiles/blas.dir/dnrm2.c.o a - CMakeFiles/blas.dir/dscal.c.o /usr/bin/ranlib libblas.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 26%] Built target blas make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 28%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o -MF CMakeFiles/fido.dir/BasicBigraph.cpp.o.d -o CMakeFiles/fido.dir/BasicBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/StringTable.h:9, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:6: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:8: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 14%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/percolator/src/percolator_out.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.cxx.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/parser.cxx.o -MF CMakeFiles/perclibrary.dir/parser.cxx.o.d -o CMakeFiles/perclibrary.dir/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In constructor 'parser_impl::parser_impl()': /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder] 106 | std::auto_ptr gp_; // (new XMLGrammarPoolImpl (mm)); | ^~~ /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:102:22: warning: 'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder] 102 | DOMImplementation& dom_impl_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:144:1: warning: when initialized here [-Wreorder] 144 | parser_impl::parser_impl() : clean_(true), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In member function 'xsd::cxx::xml::dom::auto_ptr parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable] 178 | size_t n(s.size()); | ^ /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable] 170 | int i(1); | ^ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/serializer.cxx.o -MF CMakeFiles/perclibrary.dir/serializer.cxx.o.d -o CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/src/serializer.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 29%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o -MF CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o.d -o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o -MF CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o.d -o CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/DescriptionOfCorrect.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/DescriptionOfCorrect.cpp:23: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=] 39 | void Array::add(const T & element) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note: by 'void Set::add(int)' 14 | void add(int el); | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 37%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MassHandler.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:21: /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()': /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder] 92 | double pI_, massDiff_, predictedTime_, retentionTime_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning: 'double PSMDescriptionDOC::predictedTime_' [-Wreorder] 92 | double pI_, massDiff_, predictedTime_, retentionTime_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:26:1: warning: when initialized here [-Wreorder] 26 | PSMDescriptionDOC::PSMDescriptionDOC() : | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)': /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder] 92 | double pI_, massDiff_, predictedTime_, retentionTime_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning: 'double PSMDescriptionDOC::predictedTime_' [-Wreorder] 92 | double pI_, massDiff_, predictedTime_, retentionTime_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:30:1: warning: when initialized here [-Wreorder] 30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) : | ^~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ResultHolder.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 36%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o -MF CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o.d -o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 44%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Numerical.cpp.o -MF CMakeFiles/fido.dir/Numerical.cpp.o.d -o CMakeFiles/fido.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Numerical.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 45%] Building CXX object src/fido/CMakeFiles/fido.dir/Random.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Random.cpp.o -MF CMakeFiles/fido.dir/Random.cpp.o.d -o CMakeFiles/fido.dir/Random.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Random.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 46%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Set.cpp.o -MF CMakeFiles/fido.dir/Set.cpp.o.d -o CMakeFiles/fido.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:29, from /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h: In constructor 'XMLInterface::XMLInterface(const std::string&, bool, bool, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:99:8: warning: 'XMLInterface::reportUniquePeptides_' will be initialized after [-Wreorder] 99 | bool reportUniquePeptides_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:93:8: warning: 'bool XMLInterface::printDecoys_' [-Wreorder] 93 | bool printDecoys_, printExpMass_; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:58:1: warning: when initialized here [-Wreorder] 58 | XMLInterface::XMLInterface(const std::string& outputFN, | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp: In member function 'int XMLInterface::readAndScorePin(std::istream&, std::vector&, Scores&, const std::string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)': /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:257:26: warning: unused variable 'numFeatures' [-Wunused-variable] 257 | const unsigned int numFeatures = FeatureNames::getNumFeatures(); | ^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 48%] Building CXX object src/fido/CMakeFiles/fido.dir/Vector.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Vector.cpp.o -MF CMakeFiles/fido.dir/Vector.cpp.o.d -o CMakeFiles/fido.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 50%] Linking CXX static library libfido.a cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1 /usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.cpp.o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o CMakeFiles/fido.dir/Numerical.cpp.o CMakeFiles/fido.dir/Random.cpp.o CMakeFiles/fido.dir/Set.cpp.o CMakeFiles/fido.dir/Vector.cpp.o /usr/bin/ranlib libfido.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 50%] Built target fido make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/StdvNormalizer.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 49%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'int SetHandler::getNumFeatures(const std::string&, int)': /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:158:10: warning: variable 'a' set but not used [-Wunused-but-set-variable] 158 | double a = reader.readDouble(); | ^ /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'void SetHandler::readPSMs(std::istream&, std::string&, bool, bool&, std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:290:18: warning: unused variable 'targetIdx' [-Wunused-variable] 290 | unsigned int targetIdx = 0u, decoyIdx = 0u; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:290:34: warning: unused variable 'decoyIdx' [-Wunused-variable] 290 | unsigned int targetIdx = 0u, decoyIdx = 0u; | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'int SetHandler::readAndScoreTab(std::istream&, std::vector&, Scores&, SanityCheck*&)': /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:489:46: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 489 | if (hasDefaultValues && init_values.size() > numFeatures) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:28, from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39, from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:29: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h: In constructor 'CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, int, bool, int, bool, unsigned int, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:101:8: warning: 'CrossValidation::trainBestPositive_' will be initialized after [-Wreorder] 101 | bool trainBestPositive_; | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:90:16: warning: 'unsigned int CrossValidation::numThreads_' [-Wreorder] 90 | unsigned int numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:32:1: warning: when initialized here [-Wreorder] 32 | CrossValidation::CrossValidation(bool quickValidation, | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)': /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:106:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 106 | for (int set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:107:39: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 107 | for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:141:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 141 | for (int set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:145:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 145 | for (int set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::doStep(bool, Normalizer*, double)': /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:263:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 263 | for (int set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:269:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 269 | for (int set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:291:26: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 291 | for (int set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:303:42: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 303 | for (int nestedFold = 0; nestedFold < nestedXvalBins_; ++nestedFold) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:318:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 318 | for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++){ | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'void CrossValidation::trainCpCnPair(candidateCposCfrac&, options*, AlgIn*)': /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:343:16: warning: unused variable 'set' [-Wunused-variable] 343 | unsigned int set = cpCnFold.set; | ^~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:344:16: warning: unused variable 'nestedFold' [-Wunused-variable] 344 | unsigned int nestedFold = cpCnFold.nestedSet; | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:356:7: warning: unused variable 'tp' [-Wunused-variable] 356 | int tp = 0; | ^~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::mergeCpCnPairs(doubmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' le, options*, std::vector >&, const std::vector&, const std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:399:21: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 399 | for (set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:439:23: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 439 | for (set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:474:21: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 474 | for (set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'void CrossValidation::postIterationProcessing(Scores&, SanityCheck*)': /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:483:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 483 | for (int set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:21: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:24: /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h: In constructor 'SanityCheck::SanityCheck()': /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h:87:8: warning: 'SanityCheck::concatenatedSearch_' will be initialized after [-Wreorder] 87 | bool concatenatedSearch_; | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h:72:10: warning: 'double SanityCheck::test_fdr_' [-Wreorder] 72 | double test_fdr_, initial_train_fdr_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:31:1: warning: when initialized here [-Wreorder] 31 | SanityCheck::SanityCheck() : | ^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp: In member function 'void DataSet::print_features()': /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 69 | for (int i = 0; i < getSize(); i++) { | ~~^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/FeatureNames.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:36, from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h: In constructor 'Caller::Caller()': /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:103:48: warning: 'Caller::trainBestPositive_' will be initialized after [-Wreorder] 103 | bool reportEachIteration_, quickValidation_, trainBestPositive_, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:101:59: warning: 'unsigned int Caller::numThreads_' [-Wreorder] 101 | unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:35:1: warning: when initialized here [-Wreorder] 35 | Caller::Caller() : | ^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp: In member function 'bool Caller::parseOptions(int, char**)': /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:694:7: warning: label 'std' defined but not used [-Wunused-label] 694 | std:cerr << "Error: the --static option requires the --init-weights " | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h: In constructor 'ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)': /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:238:16: warning: 'ProteinProbEstimator::absenceRatio_' will be initialized after [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:238:10: warning: 'double ProteinProbEstimator::pi0_' [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:242:16: warning: 'ProteinProbEstimator::numberTargetProteins_' will be initialized after [-Wreorder] 242 | unsigned int numberTargetProteins_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:237:8: warning: 'bool ProteinProbEstimator::usePi0_' [-Wreorder] 237 | bool usePi0_; | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:243:15: warning: 'ProteinProbEstimator::decoyPattern_' will be initialized after [-Wreorder] 243 | std::string decoyPattern_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:240:10: warning: 'double ProteinProbEstimator::fdr_' [-Wreorder] 240 | double fdr_; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp:37: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp: In static member function 'static void PosteriorEstimator::getQValuesFromPEP(const std::vector&, std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp:468:21: warning: unused variable 'queue' [-Wunused-variable] 468 | int nP = 1, queue = 0; | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ProteinFDRestimator.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 74%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PseudoRandom.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/SqtSanityCheck.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/SqtSanityCheck.cpp:17: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'void cglsFun2(int, int*, const double*, double*, int, int, double*, double*, double*, double*, double, double)': /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:86:7: warning: unused variable 'ind' [-Wunused-variable] 86 | int ind = 0; | ^~~ /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:87:10: warning: unused variable 'temp' [-Wunused-variable] 87 | double temp = 0.0; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'int CGLS(const AlgIn&, double, int, double, const vector_int*, vector_double*, vector_double*, double, double)': /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:117:19: warning: unused variable 'j' [-Wunused-variable] 117 | register int i, j; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'int L2_SVM_MFN(const AlgIn&, options*, vector_double*, vector_double*, double, double)': /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:251:10: warning: unused variable 't' [-Wunused-variable] 251 | double t = 0.0; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'double line_search(double*, double*, double, double*, double*, const double*, int, int, double, double)': /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:364:7: warning: unused variable 'inc' [-Wunused-variable] 364 | int inc = 1; | ^~~ In function 'Clear(options*)', inlined from 'Clear(options*)' at /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:440:6: /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:442:12: warning: pointer 'opt_2(D)' used after 'operator delete[](void*)' [-Wuse-after-free] 442 | delete[] opt; | ^~~ /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:441:12: note: call to 'operator delete[](void*)' here 441 | delete[] opt; | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/EludeModel.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/EludeModel.cpp.o -MF CMakeFiles/perclibrary.dir/EludeModel.cpp.o.d -o CMakeFiles/perclibrary.dir/EludeModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/EludeModel.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/EludeModel.cpp:34: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.cpp:8: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PackedMatrix.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedMatrix.h:11, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedMatrix.cpp:8: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:32: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp: In member function 'void Scores::populateWithPSMs(SetHandler&)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:292:29: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 292 | if (totalNumberOfTargets_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:295:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 295 | if (totalNumberOfDecoys_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 84%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 85%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 82%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Matrix.cpp.o -MF CMakeFiles/perclibrary.dir/Matrix.cpp.o.d -o CMakeFiles/perclibrary.dir/Matrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Matrix.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/Matrix.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/Matrix.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 88%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h: In constructor 'ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)': /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h:108:8: warning: 'ProteinScoreHolder::isDecoy_' will be initialized after [-Wreorder] 108 | bool isDecoy_; | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h:106:7: warning: 'int ProteinScoreHolder::groupId_' [-Wreorder] 106 | int groupId_; | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp:20:1: warning: when initialized here [-Wreorder] 20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide, | ^~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 86%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o -MF CMakeFiles/perclibrary.dir/FidoInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34, from /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:20, from /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h: In constructor 'FidoInterface::FidoInterface(double, double, double, bool, bool, bool, unsigned int, double, double, double, double, bool, std::string, bool, double)': /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:110:10: warning: 'FidoInterface::mseThreshold_' will be initialized after [-Wreorder] 110 | double mseThreshold_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:106:8: warning: 'bool FidoInterface::doGridSearch_' [-Wreorder] 106 | bool doGridSearch_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:76:1: warning: when initialized here [-Wreorder] 76 | FidoInterface::FidoInterface(double alpha, double beta, double gamma, | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp: In member function 'double FidoInterface::estimatePriors(Scores&)': /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:132:10: warning: variable 'prior' set but not used [-Wunused-but-set-variable] 132 | double prior, prior2, prior3, prior4; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp: In member function 'void FidoInterface::getEstimated_and_Empirical_FDR(const std::vector > >&, const std::vector&, std::vector&, std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:556:12: warning: unused variable 'prob' [-Wunused-variable] 556 | double prob = probabilities[k]; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:558:14: warning: unused variable 'fpChange' [-Wunused-variable] 558 | unsigned fpChange = proteinNames[k].size() - tpChange; | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 90%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/FeatureMemoryPool.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 89%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:27, from /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h: In constructor 'PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)': /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:86:10: warning: 'PickedProteinInterface::maxPeptidePval_' will be initialized after [-Wreorder] 86 | double maxPeptidePval_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:85:8: warning: 'bool PickedProteinInterface::reportFragmentProteins_' [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:85:33: warning: 'PickedProteinInterface::reportDuplicateProteins_' will be initialized after [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:83:26: warning: 'ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_' [-Wreorder] 83 | ProteinInferenceMethod protInferenceMethod_; | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp: In member function 'virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)': /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:165:36: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 165 | if (total_non_enzymatic_flanks > peptideScores.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp: In member function 'virtual void PickedProteinInterface::computeProbabilities(const std::string&)': /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:344:13: warning: unused variable 'significantPeptides' [-Wunused-variable] 344 | int significantPeptides = 0; | ^~~~~~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 92%] Linking CXX static library libperclibrary.a cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1 /usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/percolator_in.cxx.o CMakeFiles/perclibrary.dir/percolator_out.cxx.o CMakeFiles/perclibrary.dir/parser.cxx.o CMakeFiles/perclibrary.dir/serializer.cxx.o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/EludeModel.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Matrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o /usr/bin/ranlib libperclibrary.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 94%] Built target perclibrary make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend /usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build /usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 97%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/qvality/qvality_main.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 96%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/main.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31, from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:36, from /builddir/build/BUILD/percolator-rel-3-05/src/main.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 98%] Linking CXX executable qvality cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality -L/builddir/build/BUILD/percolator-rel-3-05/percolator/src ../libperclibrary.a ../fido/libfido.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [100%] Built target qvality make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [100%] Linking CXX executable percolator cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/percolator.dir/main.cpp.o -o percolator libperclibrary.a blas/libblas.a fido/libfido.a picked_protein/libpicked_protein.a -lxerces-c -lstdc++ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' In function 'readRawSequence', inlined from 'parseProteinFastaFile' at /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:366:23: /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 505 | raw_sequence[i_seq] = '\0'; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'parseProteinFastaFile': /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object 'buffer' of size 40000 355 | static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in. | ^ make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [100%] Built target percolator make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles 0 + popd ~/build/BUILD/percolator-rel-3-05 + mkdir -p fido + pushd fido ~/build/BUILD/percolator-rel-3-05/fido ~/build/BUILD/percolator-rel-3-05 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=x86_64 ../src/fido -- The C compiler identification is GNU 13.0.0 -- The CXX compiler identification is GNU 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_RELEASE CMAKE_EXE_LINKER_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH CMAKE_SKIP_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR TARGET_ARCH TokyoCabinet_INCLUDE_DIR TokyoCabinet_LIBRARY -- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/fido + /usr/bin/make -O -j2 V=1 VERBOSE=1 /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/fido -B/builddir/build/BUILD/percolator-rel-3-05/fido --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/fido//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' cd /builddir/build/BUILD/percolator-rel-3-05/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/fido /builddir/build/BUILD/percolator-rel-3-05/fido /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles/fido.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' /usr/bin/make -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' [ 25%] Building CXX object CMakeFiles/fido.dir/BasicGroupBigraph.o /usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicGroupBigraph.o -MF CMakeFiles/fido.dir/BasicGroupBigraph.o.d -o CMakeFiles/fido.dir/BasicGroupBigraph.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8: ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': ../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ ../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': ../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ ../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ ../src/Scores.h: At global scope: ../src/Scores.h:76:32: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 76 | struct lexicOrderProb : public binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:11: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:99:37: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | struct OrderScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:108:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 108 | struct OrderScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:119:32: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 119 | struct OrderScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:127:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 127 | struct UniqueScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:133:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 133 | struct UniqueScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:139:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 139 | struct UniqueScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' [ 25%] Building CXX object CMakeFiles/fido.dir/BasicBigraph.o /usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicBigraph.o -MF CMakeFiles/fido.dir/BasicBigraph.o.d -o CMakeFiles/fido.dir/BasicBigraph.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp:4: ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': ../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ ../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': ../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ ../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ ../src/Scores.h: At global scope: ../src/Scores.h:76:32: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 76 | struct lexicOrderProb : public binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:4: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:99:37: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | struct OrderScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:108:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 108 | struct OrderScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:119:32: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 119 | struct OrderScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:127:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 127 | struct UniqueScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:133:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 133 | struct UniqueScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:139:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 139 | struct UniqueScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/StringTable.h:9, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:6: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:8: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' [ 50%] Building CXX object CMakeFiles/fido.dir/Numerical.o /usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Numerical.o -MF CMakeFiles/fido.dir/Numerical.o.d -o CMakeFiles/fido.dir/Numerical.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Numerical.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' [ 62%] Building CXX object CMakeFiles/fido.dir/Random.o /usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Random.o -MF CMakeFiles/fido.dir/Random.o.d -o CMakeFiles/fido.dir/Random.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Random.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' [ 75%] Building CXX object CMakeFiles/fido.dir/Set.o /usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Set.o -MF CMakeFiles/fido.dir/Set.o.d -o CMakeFiles/fido.dir/Set.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' [ 87%] Building CXX object CMakeFiles/fido.dir/Vector.o /usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Vector.o -MF CMakeFiles/fido.dir/Vector.o.d -o CMakeFiles/fido.dir/Vector.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' [ 37%] Building CXX object CMakeFiles/fido.dir/GroupPowerBigraph.o /usr/bin/g++ -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/GroupPowerBigraph.o -MF CMakeFiles/fido.dir/GroupPowerBigraph.o.d -o CMakeFiles/fido.dir/GroupPowerBigraph.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.h:7, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array Array::operator[](const Array&) const [with T = int]' was hidden [-Woverloaded-virtual=] 119 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8: /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=] 32 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note: by 'Set::operator[]' 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8: ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()': ../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ ../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:58:3: warning: when initialized here [-Wreorder] 58 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)': ../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder] 55 | int label; | ^~~~~ ../src/Scores.h:54:19: warning: 'PSMDescription* ScoreHolder::pPSM' [-Wreorder] 54 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:59:3: warning: when initialized here [-Wreorder] 59 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ ../src/Scores.h: At global scope: ../src/Scores.h:76:32: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 76 | struct lexicOrderProb : public binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:11: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:99:37: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | struct OrderScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:108:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 108 | struct OrderScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:119:32: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 119 | struct OrderScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:127:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 127 | struct UniqueScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:133:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 133 | struct UniqueScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:139:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 139 | struct UniqueScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' [100%] Linking CXX static library libfido.a /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1 /usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.o CMakeFiles/fido.dir/BasicGroupBigraph.o CMakeFiles/fido.dir/GroupPowerBigraph.o CMakeFiles/fido.dir/Numerical.o CMakeFiles/fido.dir/Random.o CMakeFiles/fido.dir/Set.o CMakeFiles/fido.dir/Vector.o /usr/bin/ranlib libfido.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido' [100%] Built target fido make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles 0 + popd ~/build/BUILD/percolator-rel-3-05 + mkdir -p converters + pushd converters ~/build/BUILD/percolator-rel-3-05/converters ~/build/BUILD/percolator-rel-3-05 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DPERCOLATOR-CONVERTERS_BINARY_DIR:STATIC=converters -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so -DSERIALIZE=TokyoCabinet -DTARGET_ARCH=x86_64 ../src/converters -- The C compiler identification is GNU 13.0.0 -- The CXX compiler identification is GNU 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- -- ------------------------------------------------------------------------------- -- Building PERCOLATOR-CONVERTERS: -- change a configuration variable with: cmake -D= -- Indicate the type of XML serialization scheme : -DSERIALIZE="Boost" or -DSERIALIZE="TokyoCabinet" or -DSERIALIZE="LevelDB". By setting up the variable SERIALIZE to either Boost or TokyoCabinet or LevelDB you will choose the serialization scheme that will be used to build Converters. Boost serialization option will be used as default if no option is given. -- CMAKE_INSTALL_PREFIX = /usr -- CMAKE_BUILD_TYPE = Release -- XML_SUPPORT = ON -- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-05/src/converters/../.. -- CMAKE_PREFIX_PATH = ../ -- TARGET_ARCH = x86_64 -- TOOL CHAIN FILE = -- SERIALIZE = TokyoCabinet -- PROFILING = -- Using Tokyo Cabinet Serialization scheme -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages.. -- Found Xerces-C: /usr/lib64/libxerces-c.so -- : /usr/include -- Version: 3.2.3 -- Package CodeSynthesis XSD found: /usr/include -- Found TokyoCabinet: /usr/lib64/libtokyocabinet.so -- Package Tokyo Cabinet found : /usr/include -- Found BZip2: /usr/lib64/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so - found -- Bzip2 found -- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.46.0") found components: filesystem system -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Generating classes from xsd-schema using CodeSynthesis -- Generating /builddir/build/BUILD/percolator-rel-3-05/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-rel-3-05/converters/gaml_tandem1.0.hxx -- SQL Lite 3 found: /usr/include -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.13") -- ZLIB found: /usr/include, /usr/lib64/libz.so -- Using FragSpectrumScanDatabaseTokyodb.cpp -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/converters + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../src/xml/percolator_in.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../src/xml/percolator_out.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns ../src/xml/mzIdentML1.1.0.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/gaml_tandem1.0.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/tandem2011.12.01.1.xsd + /usr/bin/make -O -j2 V=1 VERBOSE=1 /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/converters -B/builddir/build/BUILD/percolator-rel-3-05/converters --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/converters//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend /usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build /usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'. make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 5%] Built target generate_perc_xsdfiles make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 7%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o -MF CMakeFiles/RAMP.dir/ramp_base64.cpp.o.d -o CMakeFiles/RAMP.dir/ramp_base64.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp_base64.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 9%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o -MF CMakeFiles/RAMP.dir/ramp.cpp.o.d -o CMakeFiles/RAMP.dir/ramp.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1698:13: warning: variable 'err' set but not used [-Wunused-but-set-variable] 1698 | int err; | ^~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:34: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:188:16: note: in expansion of macro 'ramp_fgets' 188 | (void) ramp_fgets(buf, sizeof(buf) - 1, result); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:343:3: note: in expansion of macro 'ramp_fread' 343 | ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:509:18: note: in expansion of macro 'ramp_fgets' 509 | (void) ramp_fgets(buf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:541:18: note: in expansion of macro 'ramp_fgets' 541 | (void) ramp_fgets(buf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:575:16: note: in expansion of macro 'ramp_fgets' 575 | (void) ramp_fgets(buf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:967:18: note: in expansion of macro 'ramp_fgets' 967 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:984:18: note: in expansion of macro 'ramp_fgets' 984 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1056:10: note: in expansion of macro 'ramp_fgets' 1056 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1058:12: note: in expansion of macro 'ramp_fgets' 1058 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1479:11: note: in expansion of macro 'ramp_fread' 1479 | ramp_fread(pData + partial, (int)(peaksLen - partial), pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1571:14: note: in expansion of macro 'ramp_fgets' 1571 | (void) ramp_fgets(buf, sizeof(buf) - 1, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1573:16: note: in expansion of macro 'ramp_fgets' 1573 | (void) ramp_fgets(buf, sizeof(buf) - 1, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1626:18: note: in expansion of macro 'ramp_fgets' 1626 | (void) ramp_fgets(buf, sizeof(buf) - 1 , pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1658:9: note: in expansion of macro 'ramp_fread' 1658 | ramp_fread(pData + partial, peaksLen - partial, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1792:10: note: in expansion of macro 'ramp_fgets' 1792 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1795:12: note: in expansion of macro 'ramp_fgets' 1795 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1816:12: note: in expansion of macro 'ramp_fgets' 1816 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1926:10: note: in expansion of macro 'ramp_fgets' 1926 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1933:13: note: in expansion of macro 'ramp_fgets' 1933 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1989:14: note: in expansion of macro 'ramp_fgets' 1989 | (void) ramp_fgets(stringBuf, SIZE_BUF, pFI); | ^~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:123: In function '*strchr', inlined from 'readPeaks(RAMPFILE*, long)' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35: /usr/include/string.h:241:27: warning: 'strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In function 'readPeaks(RAMPFILE*, long)': cc1plus: note: source object is likely at address zero In function '*strchr', inlined from 'readPeaks(RAMPFILE*, long)' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35: /usr/include/string.h:241:27: warning: 'strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In function 'readPeaks(RAMPFILE*, long)': cc1plus: note: source object is likely at address zero /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'rampSelfTest(char*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:2050:12: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 2050 | strncpy(buf, filename, sizeof(buf)); | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 2054 | strncpy(buf, filename, sizeof(buf)); | ^ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 10%] Linking CXX static library libRAMP.a cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP && /usr/bin/cmake -P CMakeFiles/RAMP.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP && /usr/bin/cmake -E cmake_link_script CMakeFiles/RAMP.dir/link.txt --verbose=1 /usr/bin/ar qc libRAMP.a CMakeFiles/RAMP.dir/ramp_base64.cpp.o CMakeFiles/RAMP.dir/ramp.cpp.o /usr/bin/ranlib libRAMP.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 10%] Built target RAMP make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/converters.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f 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-fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o -MF CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/converters/percolator_out.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 12%] Building CXX object CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit 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-I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o -MF CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o.d -o CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/converters/mzIdentML1.1.0.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 16%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 20%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 21%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 23%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/MassHandler.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/MassHandler.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/MassHandler.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MassHandler.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 25%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/serializer.cxx.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/serializer.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/serializer.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/src/serializer.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 27%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In constructor 'parser_impl::parser_impl()': /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder] 106 | std::auto_ptr gp_; // (new XMLGrammarPoolImpl (mm)); | ^~~ /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:102:22: warning: 'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder] 102 | DOMImplementation& dom_impl_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:144:1: warning: when initialized here [-Wreorder] 144 | parser_impl::parser_impl() : clean_(true), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In member function 'xsd::cxx::xml::dom::auto_ptr parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable] 178 | size_t n(s.size()); | ^ /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable] 170 | int i(1); | ^ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 29%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 30%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 32%] Linking CXX static library libperclibrary_part.a /usr/bin/cmake -P CMakeFiles/perclibrary_part.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary_part.dir/link.txt --verbose=1 /usr/bin/ar qc libperclibrary_part.a CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/MassHandler.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/serializer.cxx.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o" 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-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -MF CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o.d -o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/converters/gaml_tandem1.0.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 38%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -MF CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o.d -o CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In function 'LazyMatrix* flip_lazy_matrix(LazyMatrix&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:21:30: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 21 | for ( uint j = 0 ; j < lm.rows() ; j++ ) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:22:38: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 22 | for ( uint i = 0 ; i < lm.cols() ; i++ ) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor 'LazyMatrix::LazyMatrix(const self&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value] 56 | *data_copies++; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::copy_m_flip(const self&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:67:28: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'const int' [-Wsign-compare] 67 | for ( uint i = 0 ; i < x.nrows ; i++ ) { | ~~^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(bool)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:101:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector*>::size_type' {aka 'long unsigned int'} [-Wsign-compare] 101 | for ( int i = 0 ; i < m.size() ; i++ ) { | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(value_type, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:115:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector*>::size_type' {aka 'long unsigned int'} [-Wsign-compare] 115 | for ( int i = 0 ; i < m.size() ; i++ ) { | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::_get_row_retain(std::vector&, int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:179:43: warning: variable 'b' set but not used [-Wunused-but-set-variable] 179 | std::vector::iterator b = this->m[i]->begin(); | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::add_val(float)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:313:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 313 | for ( uint i = 0 ; i < nrows ; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::mult_val(float)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:322:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 322 | for ( uint i = 0 ; i < nrows ; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::div_val(float)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:331:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 331 | for ( uint i = 0 ; i < nrows ; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_min_val(float)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:339:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 339 | for ( uint i = 0 ; i < nrows ; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_max_val(float)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:351:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 351 | for ( uint i = 0 ; i < nrows ; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::column_shift(int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:369:23: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 369 | for ( uint i = 0 ;i < rows() ; i++ ) { | ~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:370:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 370 | for ( uint j = 0 ; j < cols() ; j++ ) { | ~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:373:21: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 373 | if ( dest_idx >= cols() ) break; | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::linear_shift(int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:389:25: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 389 | for ( uint i = 0; i < shift ; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:393:29: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 393 | for ( uint i = shift; i < nrows; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:412:39: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare] 412 | for ( uint i = nrows - offset ; i < nrows; i++ ) { | ~~^~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 41%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -MF CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSConvertFile.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 43%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o -MF CMakeFiles/MSToolkit.dir/MSObject.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSObject.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp: In copy constructor 'MSObject::MSObject(const MSObject&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp:21:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 21 | for(i=0;isize();i++){ | ~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp: In member function 'MSObject& MSObject::operator=(const MSObject&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp:36:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 36 | for(i=0;isize();i++){ | ~^~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 45%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o -MF CMakeFiles/MSToolkit.dir/MSReader.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::writeSqlite(const char*, MSObject&, char*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:634:34: warning: the address of 'MSHeader::header' will never be NULL [-Waddress] 634 | if(m.getHeader().header[i] != 0) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.h:4, from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.h:4, from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSToolkitTypes.h:54:14: note: 'MSHeader::header' declared here 54 | char header[16][128]; | ^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::appendFile(Spectrum&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:916:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 916 | for(int i=0; i=3) fread(&ms.numEZStates,4,1,fileIn); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1902:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1902 | fread(&ms.numDataPoints,4,1,fileIn); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'MSFileFormat MSReader::checkFileFormat(const char*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1952:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1952 | fread(&i,4,1,f); | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1953:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | fread(&iVersion,4,1,f); | ~~~~~^~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/parallel/compiletime_settings.h:33, from /usr/include/c++/13/parallel/parallel.h:37, from /usr/include/c++/13/parallel/base.h:40, from /usr/include/c++/13/parallel/algobase.h:40, from /usr/include/c++/13/bits/stl_algobase.h:2229, from /usr/include/c++/13/vector:62, from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.h:5: In function 'sprintf', inlined from 'MSReader::appendFile(Spectrum&)' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:869:11: /usr/include/bits/stdio2.h:30:34: warning: 'lastScanID' may be used uninitialized [-Wmaybe-uninitialized] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'MSReader::appendFile(Spectrum&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:853:7: note: 'lastScanID' was declared here 853 | int lastScanID; | ^~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 47%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -MF CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSSingleScan.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 49%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp: In function 'int main(int, char**)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp:51:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 51 | for ( int i = 0 ; i < rts.size() ; i++ ) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp:26:22: warning: variable 'ff' set but not used [-Wunused-but-set-variable] 26 | MSFileFormat ff; | ^~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 50%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTDemo.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 40%] Building CXX object CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -MF CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o.d -o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/converters/tandem2011.12.01.1.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 52%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -MF CMakeFiles/MSToolkit.dir/MSWarper.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp:17: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair msmat::get_transition_by_idx() const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type] 517 | } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type] 519 | } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable] 600 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable] 703 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp: In function 'int main(int, char**)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp:87:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 87 | for ( int f_idx = 0; f_idx < ms1_file_names.size() ; f_idx++ ) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function] 812 | static int test_msmat_time_interp( msmat * msmat_f ); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function] 813 | static int test_msmat_sg_test( msmat * msmat_fh); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function] 814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function] 815 | static msmat * test_msmat(int argc, char ** argv); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function] 818 | static void output_bp_chrom( msmat & m , char * fname); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function] 819 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA ); | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector&, const std::vector&, std::vector >&, bool)' declared 'static' but never defined [-Wunused-function] 820 | static msmat * msmat_from_thevoid ( const std::vector & mzs, const std::vector & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true ); | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable] 69 | const static char * valid_fields[] = { | ^~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 56%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -MF CMakeFiles/MSToolkit.dir/Spectrum.cpp.o.d -o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'Spectrum& Spectrum::operator=(const Spectrum&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:81:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 81 | for(i=0;isize();i++){ | ~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:85:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 85 | for(i=0;isize();i++){ | ~^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:89:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 89 | for(i=0;isize();i++){ | ~^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'bool Spectrum::getRawFilter(char*, int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:282:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 282 | if(sz::size_type' {aka 'long unsigned int'} [-Wsign-compare] 389 | for(int i=0; isize(); i++) | ~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::setPeaks(std::vector)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:428:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 428 | for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 453 | for(int i=0; isize(); i++) | ~^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 54%] Building CXX object CMakeFiles/converters.dir/Reader.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/Reader.cpp.o -MF CMakeFiles/converters.dir/Reader.cpp.o.d -o CMakeFiles/converters.dir/Reader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp: In member function 'Reader::translateFileToXML(std::__cxx11::basic_string, std::allocator > const&, bool, unsigned int, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp:327:32: warning: 'tcd' may be used uninitialized [-Wmaybe-uninitialized] 327 | tmpDirs[lineNumber_par]=tcd; /builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp:302:22: note: 'tcd' was declared here 302 | char * tcd; | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 60%] Building CXX object CMakeFiles/converters.dir/SqtReader.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/SqtReader.cpp.o -MF CMakeFiles/converters.dir/SqtReader.cpp.o.d -o CMakeFiles/converters.dir/SqtReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/SqtReader.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 58%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o -MF CMakeFiles/MSToolkit.dir/crawutils.cpp.o.d -o CMakeFiles/MSToolkit.dir/crawutils.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rankties(std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable 'start_idx' [-Wunused-variable] 261 | int start_idx = -1; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable 'stop_idx' [-Wunused-variable] 262 | int stop_idx = -1; | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rank_by_pos_ties(const std::vector >&, std::vector&, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:354:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 354 | if ( ( i != (sorted_by_i.size() ) ) && ( sorted_by_i[i].first == last_val) ) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable 'last_rank' [-Wunused-variable] 346 | int last_rank = -1; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:944:32: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 944 | if (cumulative_area.size() == idx) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector&, const std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:990:32: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 990 | if (cumulative_area.size() == idx) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::tryptic_digester_proto(std::string, std::vector >&, int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:1121:10: warning: unused variable 'last_tryp' [-Wunused-variable] 1121 | bool last_tryp = false; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'std::vector, std::set > > crawutils::permute_two_groups(IdxGroupType, IdxGroupType)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:1214:8: warning: unused variable 'g2_len' [-Wunused-variable] 1214 | int g2_len = g2.size(); | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 61%] Building CXX object CMakeFiles/converters.dir/MzidentmlReader.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/MzidentmlReader.cpp.o -MF CMakeFiles/converters.dir/MzidentmlReader.cpp.o.d -o CMakeFiles/converters.dir/MzidentmlReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp: In member function 'virtual void MzidentmlReader::getMaxMinCharge(const std::string&, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp:86:30: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 86 | } catch (ifstream::failure e) { | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp:94:24: warning: catching polymorphic type 'class MyException' by value [-Wcatch-value=] 94 | } catch (MyException e) { | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp:97:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 97 | } catch (std::exception e) { | ^ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 63%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:17: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair msmat::get_transition_by_idx() const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type] 517 | } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type] 519 | } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable] 600 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable] 703 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector transition_manager::get_trans_by_precursor(float)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:37:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 37 | for ( int i = 0 ; i < precursors.size() ; i++ ) | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector transition_manager::get_trans_by_precursor_idx(int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:48:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 48 | for ( int i = 0 ; i < ti.size() ; i++ ) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In constructor 'transition_manager::transition_manager(std::vector)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:57:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 57 | for ( int i = 0 ; i < transitions.size() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::init_transitions_from_labels()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 86 | for ( int i = 0 ; i < labels.size() ; i++ ) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_input(std::ifstream&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:119:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 119 | for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:120:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 120 | for ( int c_idx = 0 ; c_idx < this->get_num_rts() ; c_idx++ ) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:117:10: warning: unused variable 'num_chroms' [-Wunused-variable] 117 | int num_chroms = this->get_num_mzs(); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:118:10: warning: unused variable 'num_rts' [-Wunused-variable] 118 | int num_rts = this->get_num_rts(); | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_dist_set(int, std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:228:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 228 | for ( int i = 0 ; i < this->get_num_rts() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom_set(int, std::vector >&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:247:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 247 | for ( int i = 1 ; i < retain_range.size() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:255:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | for ( int i = 0 ; i < delete_range.size() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:237:9: warning: unused variable 'set_idx' [-Wunused-variable] 237 | int set_idx = 0; | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom(int, int, int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:266:39: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 266 | for ( int i = stop_scan_idx + 1 ; i < get_num_rts() ; i++ ) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::check_size_from_position() const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:283:30: warning: comparison of integer expressions of different signedness: 'off64_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 283 | if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::rt_to_rtidx(float) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:417:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 417 | if ( iter_delt == rts.size() - 1 ) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::calc_bp_chrom()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:680:28: warning: variable 'scan_length' set but not used [-Wunused-but-set-variabmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' le] 680 | int scan_idx, num_scans, scan_length; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::time_interpolate(double, msmat&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1068:14: warning: variable 'dim' set but not used [-Wunused-but-set-variable] 1068 | matrix_dim dim = get_data_dim(); | ^~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_median() const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1278:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1278 | for ( int i = 0 ; i < this->get_num_rows() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1279:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1279 | for ( int j = 0 ; j < this->get_num_cols() ; j++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_avg(int) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1294:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1294 | if ( i < 0 || i >= get_num_rts() ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_twomat_num(const msmat&, double, double, int) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1325:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1325 | for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) { | ~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1327:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1327 | if ( other_idx < 0 || other_idx >= other.get_num_rts() ) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_mat_denom(double, int) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1350:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1350 | if ( i < 0 || i >= get_num_rts() ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::correlation_w_shift(const msmat&, int) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1368:17: warning: unused variable 'self' [-Wunused-variable] 1368 | const msmat & self = *this; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1422:9: warning: unused variable 'foo' [-Wunused-variable] 1422 | int foo = 5; | ^~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_chrom(int, std::vector&) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1498:11: warning: unused variable 'volatile_this' [-Wunused-variable] 1498 | msmat * volatile_this; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::scan_scramble()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1555:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1555 | for ( int i = 0 ; i < get_num_rts() ; i++ ) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1561:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1561 | for ( int i = 0 ; i < scram_cmds.size() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In function 'msmat* test_msmat(int, char**)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1605:19: warning: variable 'ti_file' set but not used [-Wunused-but-set-variable] 1605 | FILE * o_file, *ti_file, *sg_file; | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1605:29: warning: variable 'sg_file' set but not used [-Wunused-but-set-variable] 1605 | FILE * o_file, *ti_file, *sg_file; | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In function 'msmat* msmat_from_thevoid(const std::vector&, const std::vector&, std::vector >&, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1746:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1746 | for ( int i = 0 ; i < chroms.size() ; i++ ){ | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1762:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1762 | for ( int i = 0 ; i < chroms.size() ; i++ ){ | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_avg(int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1828:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1828 | new_cnt < mzs.size() ; | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_avg(int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1858:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1858 | new_cnt < rts.size() ; | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_sample(int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1880:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1880 | new_cnt < mzs.size() ; | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_sample(int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1898:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1898 | new_cnt < rts.size() ; | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'bool msmat::equals_data(const msmat&, double) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1921:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1921 | for ( int i = 0 ; i < get_num_rows() ; i++ ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::sum_abs_diffs(const msmat&) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1944:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1944 | for ( int i = 0 ; i < get_num_rows() ; i++ ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1941:10: warning: unused variable 'nrows' [-Wunused-variable] 1941 | size_t nrows = get_num_rows(); | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_output(std::ostream&, int, int, int, int, bool, char)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2004:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2004 | for ( int i = 0 ; i < rts_slice.size() - 1 ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2010:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2010 | for ( int i = 0 ; i < mzs_slice.size() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2019:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2019 | for ( int j = 0 ; j < out_chrom.size() - 1 ; j++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1990:13: warning: unused variable 'num_mzs' [-Wunused-variable] 1990 | const int num_mzs = get_num_mzs(); | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_scan_interp(float, std::vector&) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2071:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2071 | for ( int i = 0 ; i < s1.size() ;i++ ) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_chroms::get_scan_interp(float, std::vector&) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2095:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2095 | for ( int i = 0 ; i < s1.size() ;i++ ) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void ttest_score_matrix::unmask_search(msmat::mz_type, msmat::rt_type, msmat::rt_type)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2109:7: warning: unused variable 'start_rt_idx' [-Wunused-variable] 2109 | int start_rt_idx = this->rt_to_rtidx(start_rt); | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2110:7: warning: unused variable 'stop_rt_idx' [-Wunused-variable] 2110 | int stop_rt_idx = this->rt_to_rtidx(stop_rt); | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function] 812 | static int test_msmat_time_interp( msmat * msmat_f ); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function] 813 | static int test_msmat_sg_test( msmat * msmat_fh); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function] 814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1740:9: warning: 'msmat* msmat_from_thevoid(const std::vector&, const std::vector&, std::vector >&, bool)' defined but not used [-Wunused-function] 1740 | msmat * msmat_from_thevoid | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1713:6: warning: 'void output_bp_chrom(msmat&, char*)' defined but not used [-Wunused-function] 1713 | void output_bp_chrom( msmat & m, char * fname ) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1582:9: warning: 'msmat* test_msmat(int, char**)' defined but not used [-Wunused-function] 1582 | msmat * test_msmat ( int argc , char ** argv ) { | ^~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable] 69 | const static char * valid_fields[] = { | ^~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 65%] Building CXX object CMakeFiles/converters.dir/SequestReader.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/SequestReader.cpp.o -MF CMakeFiles/converters.dir/SequestReader.cpp.o.d -o CMakeFiles/converters.dir/SequestReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp: In member function 'virtual void SequestReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr, const std::string&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp:169:12: warning: unused variable 'PI' [-Wunused-variable] 169 | double PI = boost::lexical_cast(item.calculatedPI().get()); | ^~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp:174:14: warning: unused variable 'peptide_length' [-Wunused-variable] 174 | unsigned peptide_length = peptideLength(peptideSeqWithFlanks); | ^~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 67%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_base.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.cpp:16: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable] 69 | const static char * valid_fields[] = { | ^~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 70%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:20: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair msmat::get_transition_by_idx() const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type] 517 | } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type] 519 | } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable] 600 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable] 703 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'int msmat_header_parser::read_header(msmat*, FILE*, bool, int*)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:92:14: warning: unused variable 'should_be_semi' [-Wunused-variable] 92 | char should_be_semi = (char)fgetc(header_fh); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'void msmat_header_parser::load_strmap_from_str(std::map, float>&, const char*, int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:22: warning: unused variable 'key_fields_len' [-Wunused-variable] 343 | int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:38: warning: unused variable 'key_last_loc' [-Wunused-variable] 343 | int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:52: warning: unused variable 'key_data_len' [-Wunused-variable] 343 | int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:344:8: warning: unused variable 'key_len_data' [-Wunused-variable] 344 | char key_len_data[128], val_len_data[128]; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:344:27: warning: unused variable 'val_len_data' [-Wunused-variable] 344 | char key_len_data[128], val_len_data[128]; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:367:7: warning: unused variable 'key_data_idx' [-Wunused-variable] 367 | int key_data_idx; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'void msmat_header_parser::write_header_field_string_list(FILE*, const char*, const std::vector >&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:431:9: warning: unused variable 'num_elements' [-Wunused-variable] 431 | int num_elements = s.size(); | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function] 812 | static int test_msmat_time_interp( msmat * msmat_f ); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function] 813 | static int test_msmat_sg_test( msmat * msmat_fh); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function] 814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function] 815 | static msmat * test_msmat(int argc, char ** argv); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function] 818 | static void output_bp_chrom( msmat & m , char * fname); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function] 819 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA ); | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector&, const std::vector&, std::vector >&, bool)' declared 'static' but never defined [-Wunused-function] 820 | static msmat * msmat_from_thevoid ( const std::vector & mzs, const std::vector & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true ); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'msmat_header_parser::load_map_from_str(std::map, std::allocator > >&, char const*, int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:314:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 314 | delete k; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:306:48: note: returned from 'operator new[](unsigned long)' 306 | flt_map_type * k = new flt_map_type[num_items]; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:315:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 315 | delete v; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:307:48: note: returned from 'operator new[](unsigned long)' 307 | flt_map_type * v = new flt_map_type[num_items]; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'msmat_header_parser::load_strmap_from_str(std::map, std::allocator >, float, std::less, std::almake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' locator > >, std::allocator, std::allocator > const, float> > >&, char const*, int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:394:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 394 | delete values; | ^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:389:37: note: returned from 'operator new[](unsigned long)' 389 | float * values = new float[val_len]; | ^ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 72%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_test.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp:4: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair msmat::get_transition_by_idx() const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type] 517 | } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair) const': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type] 519 | } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable] 600 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable] 703 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp: In function 'int main(int, char**)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable 'm' [-Wunused-variable] 13 | msmat * m; | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function] 812 | static int test_msmat_time_interp( msmat * msmat_f ); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function] 813 | static int test_msmat_sg_test( msmat * msmat_fh); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function] 814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function] 815 | static msmat * test_msmat(int argc, char ** argv); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function] 818 | static void output_bp_chrom( msmat & m , char * fname); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function] 819 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA ); | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector&, const std::vector&, std::vector >&, bool)' declared 'static' but never defined [-Wunused-function] 820 | static msmat * msmat_from_thevoid ( const std::vector & mzs, const std::vector & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true ); | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48: /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable] 69 | const static char * valid_fields[] = { | ^~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 74%] Linking CXX static library libMSToolkit.a cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/MSToolkit.dir/link.txt --verbose=1 /usr/bin/ar qc libMSToolkit.a CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o CMakeFiles/MSToolkit.dir/MSObject.cpp.o CMakeFiles/MSToolkit.dir/MSReader.cpp.o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o CMakeFiles/MSToolkit.dir/crawutils.cpp.o CMakeFiles/MSToolkit.dir/msmat.cpp.o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o /usr/bin/ranlib libMSToolkit.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 74%] Built target MSToolkit make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 69%] Building CXX object CMakeFiles/converters.dir/MsgfplusReader.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/MsgfplusReader.cpp.o -MF CMakeFiles/converters.dir/MsgfplusReader.cpp.o.d -o CMakeFiles/converters.dir/MsgfplusReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp: In member function 'virtual void MsgfplusReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr, const std::string&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:333:27: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 333 | else StdevErrorTop7 = boost::lexical_cast(up.value().get().c_str()); break; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:333:104: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 333 | else StdevErrorTop7 = boost::lexical_cast(up.value().get().c_str()); break; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:272:14: warning: unused variable 'peptide_length' [-Wunused-variable] 272 | unsigned peptide_length = peptideLength(peptideSeqWithFlanks); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:291:12: warning: variable 'SpecEValue' set but not used [-Wunused-but-set-variable] 291 | double SpecEValue = 0.0; | ^~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 78%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp: In member function 'std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp:80:19: warning: comparison of integer expressions of different signedness: 'const int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 80 | if (it->first <= peptideSeq.length()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 76%] Building CXX object CMakeFiles/converters.dir/TandemReader.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/TandemReader.cpp.o -MF CMakeFiles/converters.dir/TandemReader.cpp.o.d -o CMakeFiles/converters.dir/TandemReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp: In member function 'virtual void TandemReader::getMaxMinCharge(const std::string&, bool)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:274:24: warning: catching polymorphic type 'class MyException' by value [-Wcatch-value=] 274 | } catch (MyException e) { | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:277:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 277 | } catch (std::exception e) { | ^ /builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp: In member function 'void TandemReader::createPSM(const tandem_ns::peptide::domain_type&, double, unsigned int, double, double, bool, boost::shared_ptr, const peptideProteinMapType&, const std::string&, int)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:497:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 497 | f_seq.push_back( charge == c ? 1.0 : 0.0); | ~~~~~~~^~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 81%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp /builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function 'virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)': /builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable 'valueSize' [-Wunused-variable] 165 | size_t valueSize(buf.size ()); | ^~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 80%] Building CXX object CMakeFiles/converters.dir/Interface.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/Interface.cpp.o -MF CMakeFiles/converters.dir/Interface.cpp.o.d -o CMakeFiles/converters.dir/Interface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp:18: /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h: In constructor 'Interface::Interface()': /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h:50:14: warning: 'Interface::xmlOutput' will be initialized after [-Wreorder] 50 | bool xmlOutput; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h:47:21: warning: 'std::string Interface::outputFN' [-Wreorder] 47 | std::string outputFN; | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp:21:1: warning: when initialized here [-Wreorder] 21 | Interface::Interface() : xmlOutput(false), outputFN("") { } | ^~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 83%] Linking CXX static library libconverters.a /usr/bin/cmake -P CMakeFiles/converters.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/converters.dir/link.txt --verbose=1 /usr/bin/ar qc libconverters.a CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o CMakeFiles/converters.dir/Reader.cpp.o CMakeFiles/converters.dir/SqtReader.cpp.o CMakeFiles/converters.dir/MzidentmlReader.cpp.o CMakeFiles/converters.dir/SequestReader.cpp.o CMakeFiles/converters.dir/MsgfplusReader.cpp.o CMakeFiles/converters.dir/TandemReader.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o CMakeFiles/converters.dir/Interface.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o /usr/bin/ranlib libconverters.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 89%] Built target converters make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend /usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build /usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 92%] Building CXX object CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -MF CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o.d -o CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Sqt2Pin.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 90%] Building CXX object CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -MF CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o.d -o CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Msgfplus2Pin.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 94%] Linking CXX executable sqt2pin /usr/bin/cmake -E cmake_link_script CMakeFiles/sqt2pin.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -o sqt2pin -L/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' In function 'strchr', inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35: /usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ^ In function 'readPeaks': lto1: note: source object is likely at address zero In function 'strchr', inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35: /usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ^ In function 'readPeaks': lto1: note: source object is likely at address zero make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 96%] Built target sqt2pin make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 98%] Building CXX object CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -MF CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o.d -o CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Tandem2Pin.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 96%] Linking CXX executable msgf2pin /usr/bin/cmake -E cmake_link_script CMakeFiles/msgf2pin.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -o msgf2pin -L/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl In function 'strchr', inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35: /usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ^ In function 'readPeaks': lto1: note: source object is likely at address zero In function 'strchr', inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35: /usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ^ In function 'readPeaks': lto1: note: source object is likely at address zero make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [100%] Built target msgf2pin make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [100%] Linking CXX executable tandem2pin /usr/bin/cmake -E cmake_link_script CMakeFiles/tandem2pin.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -o tandem2pin -L/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' In function 'strchr', inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35: /usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ^ In function 'readPeaks': lto1: note: source object is likely at address zero In function 'strchr', inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35: /usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ^ In function 'readPeaks': lto1: note: source object is likely at address zero make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [100%] Built target tandem2pin make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles 0 + popd ~/build/BUILD/percolator-rel-3-05 + mkdir -p elude + pushd elude ~/build/BUILD/percolator-rel-3-05/elude ~/build/BUILD/percolator-rel-3-05 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_PREFIX_PATH:STRING=/usr -DBoost_USE_STATIC_LIBS:BOOL=OFF -DCMAKE_USE_RELATIVE_PATHS:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DTARGET_ARCH=x86_64 ../src/elude_tool -- The C compiler identification is GNU 13.0.0 -- The CXX compiler identification is GNU 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- -- ------------------------------------------------------------------------------- -- Building ELUDE: -- change a configuration variable with: cmake -D= -- CMAKE_INSTALL_PREFIX = /usr -- CMAKE_BUILD_TYPE = Release -- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../.. -- CMAKE_PREFIX_PATH = /usr -- GOOGLE_TEST = -- GOOGLE_TEST_PATH = -- TARGET_ARCH = x86_64 -- PROFILING = -- ------------------------------------------------------------------------------- -- -- Architecture: -- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found version "1.78.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH CMAKE_USE_RELATIVE_PATHS INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/elude + /usr/bin/make -O -j2 V=1 VERBOSE=1 /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-05/elude --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/elude//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 8%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o -MF CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o.d -o CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp: In static member function 'static double RetentionFeatures::IndexN(const std::string&, const std::map, double>&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp:304:21: warning: unused variable 'len' [-Wunused-variable] 304 | int end_position, len = peptide.size(); | ^~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 13%] Building CXX object CMakeFiles/eludelibrary.dir/EludeMain.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/EludeMain.cpp.o -MF CMakeFiles/eludelibrary.dir/EludeMain.cpp.o.d -o CMakeFiles/eludelibrary.dir/EludeMain.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeMain.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 17%] Building CXX object CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o -MF CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o.d -o CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:27: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value] 57 | inline bool IsModelNull() const { svr_ == NULL ? true : false; } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value] /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type] 57 | inline bool IsModelNull() const { svr_ == NULL ? true : false; } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'virtual int LibSVRModel::LoadModel(FILE*)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:284:1: warning: control reaches end of non-void function [-Wreturn-type] 284 | } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateLinearModel(std::vector > const&, int const&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized] 204 | svr_parameters_.C = best_c; | ~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:10: note: 'best_c' was declared here 182 | double best_c, best_e; | ^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized] 205 | svr_parameters_.p = best_e; | ~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:18: note: 'best_e' was declared here 182 | double best_c, best_e; | ^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateRBFModel(std::vector > const&, int const&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized] 240 | svr_parameters_.C = best_c; | ~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:10: note: 'best_c' was declared here 213 | double best_c, best_e, best_g; | ^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized] 241 | svr_parameters_.p = best_e; | ~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:18: note: 'best_e' was declared here 213 | double best_c, best_e, best_g; | ^~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized [-Wmaybe-uninitialized] 242 | svr_parameters_.gamma = best_g; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:26: note: 'best_g' was declared here 213 | double best_c, best_e, best_g; | ^~~~~~ In member function 'LibSVRModel::CalibrateRBFModel(std::vector > const&, int const&)', inlined from 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized] 240 | svr_parameters_.C = best_c; | ~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:10: note: 'best_c' was declared here 213 | double best_c, best_e, best_g; | ^~~~~~ In member function 'LibSVRModel::CalibrateRBFModel(std::vector > const&, int const&)', inlined from 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized] 241 | svr_parameters_.p = best_e; | ~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:18: note: 'best_e' was declared here 213 | double best_c, best_e, best_g; | ^~~~~~ In member function 'LibSVRModel::CalibrateRBFModel(std::vector > const&, int const&)', inlined from 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized [-Wmaybe-uninitialized] 242 | svr_parameters_.gamma = best_g; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:26: note: 'best_g' was declared here 213 | double best_c, best_e, best_g; | ^~~~~~ In member function 'LibSVRModel::CalibrateLinearModel(std::vector > const&, int const&)', inlined from 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:253:32: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized] 204 | svr_parameters_.C = best_c; | ~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:10: note: 'best_c' was declared here 182 | double best_c, best_e; | ^~~~~~ In member function 'LibSVRModel::CalibrateLinearModel(std::vector > const&, int const&)', inlined from 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:253:32: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized] 205 | svr_parameters_.p = best_e; | ~~~~~make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' ~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector > const&, int const&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:18: note: 'best_e' was declared here 182 | double best_c, best_e; | ^~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 21%] Building CXX object CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o -MF CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o.d -o CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp: In function 'svm_model* libsvm_wrapper::LoadModel(FILE*)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp:172:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 172 | int ret; | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 8%] Building CXX object CMakeFiles/eludelibrary.dir/DataManager.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/DataManager.cpp.o -MF CMakeFiles/eludelibrary.dir/DataManager.cpp.o.d -o CMakeFiles/eludelibrary.dir/DataManager.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp: In static member function 'static std::vector > > DataManager::RemoveInSourceFragments(const Enzyme*, const double&, const std::map, double>&, bool, std::vector&, std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp:334:50: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 334 | if (!remove_from_test && (initial_train_size != train_psms.size())) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp: In static member function 'static std::vector DataManager::RemoveNonEnzymatic(const Enzyme*, std::vector&, const std::string&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp:354:7: warning: unused variable 'initial_size' [-Wunused-variable] 354 | int initial_size = psms.size(); | ^~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 26%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o -MF CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o.d -o CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:17:1: warning: "/*" within comment [-Wcomment] 17 | /* | In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:27: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value] 57 | inline bool IsModelNull() const { svr_ == NULL ? true : false; } | ^ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value] /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type] 57 | inline bool IsModelNull() const { svr_ == NULL ? true : false; } | ^ In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:24: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h: In constructor 'RetentionModel::RetentionModel(Normalizer*)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h:99:16: warning: 'RetentionModel::the_normalizer_' will be initialized after [-Wreorder] 99 | Normalizer *the_normalizer_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h:95:14: warning: 'SVRModel* RetentionModel::svr_model_' [-Wreorder] 95 | SVRModel *svr_model_; | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:30:1: warning: when initialized here [-Wreorder] 30 | RetentionModel::RetentionModel(Normalizer *norm) : the_normalizer_(norm), | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In destructor 'RetentionModel::~RetentionModel()': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:36:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 36 | delete svr_model_; | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'void RetentionModel::PrintSub()': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 62 | for(int i = 0; i < vsub_.size(); ++i) | ~~^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::TrainRetentionModel(const std::set >&, const std::map, double>&, bool, std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:187:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 187 | delete svr_model_; | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::SaveModelToFile(const std::string&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:291:20: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 291 | if (vsub_.size() != number_features) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::LoadModelFromFile(const std::string&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:356:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 356 | delete svr_model_; | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:363:24: warning: variable 'ret' set but not used [-Wunused-but-set-variable] 363 | int number_features, ret; | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 34%] Building CXX object CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o -MF CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o.d -o CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::setData(std::vector&, std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:48:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 48 | for (int i = 0; i < x.size(); ++i) { | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::fillResiduals(std::pair)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:84:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 84 | for (int i = 0; i < data.size(); ++i) { | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::runLTS()': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:168:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 168 | for (int i = 1; i < Q.size(); ++i) | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:177:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 177 | for (int j = 0; j < best10Subsets.size(); ++j) { | ~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printVector(std::vector)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:209:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 209 | for (int i = 0; i < v.size(); ++i) { | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printDataPoints()': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:220:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 220 | for (int i = h; i < data.size(); ++i) { | ~~^~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 39%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 43%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 47%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 30%] Building CXX object CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o -MF CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o.d -o CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:30: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder] 167 | bool remove_non_enzymatic_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:143:9: warning: 'bool EludeCaller::context_format_' [-Wreorder] 143 | bool context_format_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder] 44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder] 189 | RetentionModel *rt_model_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:173:9: warning: 'bool EludeCaller::ignore_ptms_' [-Wreorder] 173 | bool ignore_ptms_; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder] 44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder] 196 | bool supress_print_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:175:9: warning: 'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder] 175 | bool only_hydrophobicity_index_; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder] 44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 519 | while (found != string::npos) { | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable] 639 | int ret = 1; | ^~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable] 940 | double corr = 0.0, d = 0.0, avg_rank, rank_p; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const std::string&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 1026 | if ((pos1 = path.find_last_of("/")) == string::npos) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 1027 | if ((pos1 = path.find_last_of("\\"))== string::npos) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 1032 | if ((pos2 = file_name.find_last_of(".")) != string::npos) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 52%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/StdvNormalizer.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security 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-flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 65%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 56%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 69%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp In file included from /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:21: /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()': /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder] 92 | double pI_, massDiff_, predictedTime_, retentionTime_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning: 'double PSMDescriptionDOC::predictedTime_' [-Wreorder] 92 | double pI_, massDiff_, predictedTime_, retentionTime_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:26:1: warning: when initialized here [-Wreorder] 26 | PSMDescriptionDOC::PSMDescriptionDOC() : | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)': /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder] 92 | double pI_, massDiff_, predictedTime_, retentionTime_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning: 'double PSMDescriptionDOC::predictedTime_' [-Wreorder] 92 | double pI_, massDiff_, predictedTime_, retentionTime_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:30:1: warning: when initialized here [-Wreorder] 30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) : | ^~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 73%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o -c 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-Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 86%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PseudoRandom.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude 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'/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 91%] Linking CXX static library libeludelibrary.a /usr/bin/cmake -P CMakeFiles/eludelibrary.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/eludelibrary.dir/link.txt --verbose=1 /usr/bin/ar qc libeludelibrary.a CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o CMakeFiles/eludelibrary.dir/DataManager.cpp.o CMakeFiles/eludelibrary.dir/EludeMain.cpp.o CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/StdvNormalizer.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp.o" "CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PseudoRandom.cpp.o" /usr/bin/ranlib libeludelibrary.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 91%] Built target eludelibrary make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/elude.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 95%] Building CXX object CMakeFiles/elude.dir/EludeCaller.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/elude.dir/EludeCaller.cpp.o -MF CMakeFiles/elude.dir/EludeCaller.cpp.o.d -o CMakeFiles/elude.dir/EludeCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:30: /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder] 167 | bool remove_non_enzymatic_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:143:9: warning: 'bool EludeCaller::context_format_' [-Wreorder] 143 | bool context_format_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder] 44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder] 189 | RetentionModel *rt_model_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:173:9: warning: 'bool EludeCaller::ignore_ptms_' [-Wreorder] 173 | bool ignore_ptms_; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder] 44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder] 196 | bool supress_print_; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:175:9: warning: 'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder] 175 | bool only_hydrophobicity_index_; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning: when initialized here [-Wreorder] 44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 519 | while (found != string::npos) { | ~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable] 639 | int ret = 1; | ^~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable] 940 | double corr = 0.0, d = 0.0, avg_rank, rank_p; | ^~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const std::string&)': /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 1026 | if ((pos1 = path.find_last_of("/")) == string::npos) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 1027 | if ((pos1 = path.find_last_of("\\"))== string::npos) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const long unsigned int'} [-Wsign-compare] 1032 | if ((pos2 = file_name.find_last_of(".")) != string::npos) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [100%] Linking CXX executable elude /usr/bin/cmake -E cmake_link_script CMakeFiles/elude.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/elude.dir/EludeCaller.cpp.o -o elude -L/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src libeludelibrary.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [100%] Built target elude make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles 0 + popd ~/build/BUILD/percolator-rel-3-05 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.RVCWmB + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd percolator-rel-3-05 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 'INSTALL=/usr/bin/install -p' -C percolator make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05 -B/builddir/build/BUILD/percolator-rel-3-05/percolator --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/percolator//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Nothing to be done for 'src/CMakeFiles/perclibrary.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 60%] Built target perclibrary /usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Nothing to be done for 'src/picked_protein/CMakeFiles/picked_protein.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 76%] Built target picked_protein /usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/blas /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Nothing to be done for 'src/blas/CMakeFiles/blas.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 84%] Built target blas /usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Nothing to be done for 'src/fido/CMakeFiles/fido.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 94%] Built target fido /usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Nothing to be done for 'src/CMakeFiles/percolator.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [ 97%] Built target percolator /usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[2]: Nothing to be done for 'src/qvality/CMakeFiles/qvality.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' [100%] Built target qvality make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/percolator -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/qvality make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator' + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 'INSTALL=/usr/bin/install -p' -C converters make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/converters -B/builddir/build/BUILD/percolator-rel-3-05/converters --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/converters//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 23%] Built target perclibrary_part /usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 27%] Built target generate_perc_xsdfiles /usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/converters.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 56%] Built target converters /usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 61%] Built target RAMP /usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 89%] Built target MSToolkit /usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 92%] Built target msgf2pin /usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [ 96%] Built target sqt2pin /usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' [100%] Built target tandem2pin make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/msgf2pin -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/sqt2pin -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/tandem2pin -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters' + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 'INSTALL=/usr/bin/install -p' -C elude make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-05/elude --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/elude//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Nothing to be done for 'CMakeFiles/eludelibrary.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [ 91%] Built target eludelibrary /usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/elude.dir/DependInfo.cmake --color= make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[2]: Nothing to be done for 'CMakeFiles/elude.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' [100%] Built target elude make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/elude -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/yeast_60.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/yeast_40.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/yeast_20.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/tfa.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_90.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_60.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_240.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_180.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_120.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_90.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_60.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_240.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_180.model -- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_120.model make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude' + mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator ++ find . -type f '(' -name '*.a' ')' + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./elude/libeludelibrary.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./percolator/src/blas/libblas.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/lib64/percolator + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.05-10.fc38 --unique-debug-suffix -3.05-10.fc38.x86_64 --unique-debug-src-base percolator-3.05-10.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-05 extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/msgf2pin extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/elude extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/percolator extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/qvality extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/sqt2pin extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/tandem2pin original debug info size: 83456kB, size after compression: 67668kB /usr/bin/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match. 6052 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs *** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/serializer.hxx is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/serializer.cxx is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/parser.hxx is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/parser.cxx is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/percolator/src/Globals.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/elude/Globals.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/converters/Globals.h is executable but has no shebang, removing executable bit + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.M8JPOI + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd percolator-rel-3-05 + mkdir -p test + cd test + ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt Pin-converter version 3.05.0, Build Date Jul 22 2022 00:00:00 Copyright (c) 2013 Lukas Käll. All rights reserved. Written by Lukas Käll (lukas.kall@scilifelab.se) in the School of Biotechnology at KTH - Royal Institute of Technology, Stockholm. Issued command: ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt on 65f335fb382d42a187c03d2c60a5598e Reading ../yeast-01.sqt Reading ../yeast-01.shuffled.sqt + ../percolator/src/percolator -X pout.xml pin.tab Percolator version 3.05.0, Build Date Jul 22 2022 00:00:00 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: ../percolator/src/percolator -X pout.xml pin.tab Started Tue Dec 27 05:31:34 2022 on 65f335fb382d42a187c03d2c60a5598e Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile pin.tab Features: lnrSp deltLCn deltCn Xcorr Sp IonFrac Mass PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumSP dM absdM Found 139410 PSMs Separate target and decoy search inputs detected, using mix-max method. Train/test set contains 69705 positives and 69705 negatives, size ratio=1 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Found 7004 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.410924 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 10193 PSMs with q<0.01 Iteration 2: Estimated 11236 PSMs with q<0.01 Iteration 3: Estimated 11461 PSMs with q<0.01 Iteration 4: Estimated 11509 PSMs with q<0.01 Iteration 5: Estimated 11560 PSMs with q<0.01 Iteration 6: Estimated 11576 PSMs with q<0.01 Iteration 7: Estimated 11602 PSMs with q<0.01 Iteration 8: Estimated 11617 PSMs with q<0.01 Iteration 9: Estimated 11617 PSMs with q<0.01 Iteration 10: Estimated 11616 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.4835 -0.3200 -0.4134 lnrSp 0.1414 0.1989 0.1695 deltLCn 0.6622 0.6394 0.7524 deltCn 0.6588 0.6486 0.6804 Xcorr -0.0413 0.0625 -0.0978 Sp 0.0244 0.1588 0.2191 IonFrac 0.8867 0.6292 0.4141 Mass -0.7489 -0.3031 -0.0249 PepLen 0.1083 0.1800 0.1009 Charge1 0.0250 0.0242 0.0043 Charge2 -0.0471 -0.0610 -0.0250 Charge3 1.3220 1.2346 1.2522 enzN 1.3377 1.1510 1.1172 enzC -1.9073 -1.7718 -1.6438 enzInt -0.0159 -0.0088 0.1201 lnNumSP 0.0188 0.0011 0.0218 dM 0.0044 0.0139 0.0016 absdM -6.5792 -6.3779 -5.8394 m0 Found 11446 test set PSMs with q<0.01. Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. Selecting pi_0=0.86749 Calculating q values. New pi_0 estimate on final list yields 7371 target peptides with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 26.73 cpu seconds or 15 seconds wall clock time. + RPM_EC=0 ++ jobs -p + exit 0 Processing files: percolator-3.05-10.fc38.x86_64 Provides: percolator = 3.05-10.fc38 percolator(x86-64) = 3.05-10.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.6)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_2.8)(64bit) libc.so.6(GLIBC_2.9)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libsqlite3.so.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.10)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.5)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libtirpc.so.3()(64bit) libtirpc.so.3(TIRPC_0.3.0)(64bit) libtokyocabinet.so.9()(64bit) libxerces-c-3.2.so()(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH) Obsoletes: fido-pi = 0:0 Processing files: percolator-data-3.05-10.fc38.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.H6sePX + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-05 + DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-data + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-data + cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-data + cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-data + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.oSomQj + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-05 + LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-data + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-data + cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-data + cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-data + RPM_EC=0 ++ jobs -p + exit 0 Provides: percolator-data = 3.05-10.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: percolator-static-3.05-10.fc38.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ACUniJ + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-05 + DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-static + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-static + cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-static + cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/doc/percolator-static + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.SBhmwQ + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-05 + LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static + cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static + cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static + RPM_EC=0 ++ jobs -p + exit 0 Provides: percolator-static = 3.05-10.fc38 percolator-static(x86-64) = 3.05-10.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: percolator-debugsource-3.05-10.fc38.x86_64 Provides: percolator-debugsource = 3.05-10.fc38 percolator-debugsource(x86-64) = 3.05-10.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: percolator-debuginfo-3.05-10.fc38.x86_64 Provides: debuginfo(build-id) = 14e1b941adb333f8f5bf9b9b775b47b7cda0ddb8 debuginfo(build-id) = 25dec41cf530400321dd3057cf1ca46069b8dfc9 debuginfo(build-id) = 3f25b1baaaec7545f433b743e8c6bdaf512abe97 debuginfo(build-id) = 53ad868eea8beb788eb88ad64b30fb879350599f debuginfo(build-id) = c43d08589bba9cd3f4c8feef3788468d12d16cdd debuginfo(build-id) = d79508577b118708a375ee1929c7a2e061fe27ac percolator-debuginfo = 3.05-10.fc38 percolator-debuginfo(x86-64) = 3.05-10.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: percolator-debugsource(x86-64) = 3.05-10.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 Wrote: /builddir/build/RPMS/percolator-static-3.05-10.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/percolator-data-3.05-10.fc38.noarch.rpm Wrote: /builddir/build/RPMS/percolator-3.05-10.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/percolator-debugsource-3.05-10.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/percolator-debuginfo-3.05-10.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.6cCahI + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-05 + /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.u23wIz + umask 022 + cd /builddir/build/BUILD + rm -rf percolator-rel-3-05 percolator-rel-3-05.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0