Mock Version: 1.2.12 ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/libhmsbeagle.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-2704/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=uid=1001) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/libhmsbeagle.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False warning: Could not canonicalize hostname: copr-builder-114699648.novalocal Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/libhmsbeagle-2.1.2-1.el7.centos.src.rpm Child return code was: 0 LEAVE do --> ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/libhmsbeagle.spec '], chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-2704/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=uid=1001) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/libhmsbeagle.spec '] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.QC2KtK + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf beagle-lib-beagle_release_2_1_2 + /usr/bin/gzip -dc /builddir/build/SOURCES/beagle_release_2_1_2.tar.gz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd beagle-lib-beagle_release_2_1_2 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + ./autogen.sh libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `.config'. libtoolize: copying file `.config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'. libtoolize: copying file `m4/libtool.m4' libtoolize: copying file `m4/ltoptions.m4' libtoolize: copying file `m4/ltsugar.m4' libtoolize: copying file `m4/ltversion.m4' libtoolize: copying file `m4/lt~obsolete.m4' configure.ac:66: installing '.config/config.guess' configure.ac:66: installing '.config/config.sub' configure.ac:58: installing '.config/install-sh' configure.ac:58: installing '.config/missing' Makefile.am: installing './INSTALL' examples/complextest/Makefile.am: installing '.config/depcomp' parallel-tests: installing '.config/test-driver' + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.4uHzhI + umask 022 + cd /builddir/build/BUILD + cd beagle-lib-beagle_release_2_1_2 + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro ' + export LDFLAGS + '[' 1 == 1 ']' + '[' x86_64 == ppc64le ']' ++ find . -name config.guess -o -name config.sub + for i in '$(find . -name config.guess -o -name config.sub)' ++ basename ./.config/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./.config/config.sub ++ basename ./.config/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./.config/config.sub '/usr/lib/rpm/redhat/config.sub' -> './.config/config.sub' + for i in '$(find . -name config.guess -o -name config.sub)' ++ basename ./.config/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./.config/config.guess ++ basename ./.config/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./.config/config.guess '/usr/lib/rpm/redhat/config.guess' -> './.config/config.guess' + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --enable-openmp checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for x86_64-redhat-linux-gnu-gcc... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for x86_64-redhat-linux-gnu-g++... no checking for x86_64-redhat-linux-gnu-c++... no checking for x86_64-redhat-linux-gnu-gpp... no checking for x86_64-redhat-linux-gnu-aCC... no checking for x86_64-redhat-linux-gnu-CC... no checking for x86_64-redhat-linux-gnu-cxx... no checking for x86_64-redhat-linux-gnu-cc++... no checking for x86_64-redhat-linux-gnu-cl.exe... no checking for x86_64-redhat-linux-gnu-FCC... no checking for x86_64-redhat-linux-gnu-KCC... no checking for x86_64-redhat-linux-gnu-RCC... no checking for x86_64-redhat-linux-gnu-xlC_r... no checking for x86_64-redhat-linux-gnu-xlC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking whether ln -s works... yes checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-redhat-linux-gnu file names to x86_64-redhat-linux-gnu format... func_convert_file_noop checking how to convert x86_64-redhat-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for x86_64-redhat-linux-gnu-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for x86_64-redhat-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-redhat-linux-gnu-ar... no checking for ar... ar checking for archiver @FILE support... @ checking for x86_64-redhat-linux-gnu-strip... no checking for strip... strip checking for x86_64-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for x86_64-redhat-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for library containing lt_dlinit... no checking for library containing dlopen... -ldl checking if gcc accepts -dumpversion option... yes checking gcc version... 4.8.3 checking for OpenMP flag of C compiler... -fopenmp checking for /usr/include/CL... no checking for /usr/local/cuda/... no checking for /usr/local/cuda/include... no checking for /usr/local/cuda/lib... no checking for x86 cpuid output... unknown checking for x86 cpuid 0x00000001 output... 206c1:1000800:82ba2223:f8bfbff checking whether mmx is supported... yes checking whether sse is supported... yes checking whether sse2 is supported... yes checking whether sse3 is supported... yes checking whether ssse3 is supported... yes checking whether sse4.1 is supported... yes checking whether sse4.2 is supported... yes checking whether avx is supported... no checking whether C compiler accepts -mmmx... yes checking whether C compiler accepts -msse... yes checking whether C compiler accepts -msse2... yes checking whether C compiler accepts -msse3... yes checking whether C compiler accepts -mssse3... yes checking whether C compiler accepts -msse4.1... yes checking whether C compiler accepts -msse4.2... yes checking cpuid.h usability... yes checking cpuid.h presence... yes checking for cpuid.h... yes checking for javac... javac checking for javac... /usr/bin/javac checking symlink for /usr/bin/javac... /etc/alternatives/javac checking symlink for /etc/alternatives/javac... /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/bin/javac checking for x86_64-redhat-linux-gnu-doxygen... no checking for doxygen... /usr/bin/doxygen checking for x86_64-redhat-linux-gnu-perl... no checking for perl... /usr/bin/perl checking for x86_64-redhat-linux-gnu-dot... no checking for dot... /usr/bin/dot checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating hmsbeagle-1.pc config.status: creating libhmsbeagle/Makefile config.status: creating libhmsbeagle/GPU/Makefile config.status: creating libhmsbeagle/GPU/kernels/Makefile config.status: creating libhmsbeagle/CPU/Makefile config.status: creating libhmsbeagle/plugin/Makefile config.status: creating libhmsbeagle/JNI/Makefile config.status: creating examples/Makefile config.status: creating examples/tinytest/Makefile config.status: creating examples/complextest/Makefile config.status: creating examples/oddstatetest/Makefile config.status: creating examples/fourtaxon/Makefile config.status: creating examples/genomictest/Makefile config.status: creating examples/matrixtest/Makefile config.status: creating libhmsbeagle/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: OpenCL not found or disabled. OpenCL implementation will not be built. If OpenCL support is desired, check the path to OpenCL and specify --with-opencl=/path/to/opencl configure: WARNING: NVIDIA CUDA nvcc compiler not found or CUDA support disabled. CUDA implementation will not be built. If CUDA support is desired, check the path to CUDA and specify --with-cuda=/path/to/cuda + make -j2 all doxygen-doc rm -rf doc SRCDIR='.' PROJECT='libhmsbeagle' DOCDIR='doc' VERSION='2.1.2' PERL_PATH='/usr/bin/perl' HAVE_DOT='YES' DOT_PATH='/usr/bin' GENERATE_MAN='YES' GENERATE_RTF='NO' GENERATE_XML='NO' GENERATE_HTMLHELP='NO' GENERATE_CHI='NO' GENERATE_HTML='YES' GENERATE_LATEX='NO' /usr/bin/doxygen ./beagle.dox Making all in libhmsbeagle Warning: Tag `SYMBOL_CACHE_SIZE' at line 320 of file ./beagle.dox has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Warning: Tag `SHOW_DIRECTORIES' at line 529 of file ./beagle.dox has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" make[1]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' Warning: Tag `HTML_ALIGN_MEMBERS' at line 921 of file ./beagle.dox has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Warning: Tag `USE_INLINE_TREES' at line 1108 of file ./beagle.dox has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" make all-recursive make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' Making all in GPU make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' Making all in kernels make[4]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make all-am make[5]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make[5]: Nothing to be done for `all-am'. make[5]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make[4]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make[4]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' make[4]: Nothing to be done for `all-am'. make[4]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' Making all in CPU make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU' /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c -o libhmsbeagle_cpu_la-BeagleCPUPlugin.lo `test -f 'BeagleCPUPlugin.cpp' || echo './'`BeagleCPUPlugin.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c BeagleCPUPlugin.cpp -fPIC -DPIC -o .libs/libhmsbeagle_cpu_la-BeagleCPUPlugin.o In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.h:439:0, from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:35, from BeagleCPUPlugin.cpp:9: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:1921:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:1950:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:1987:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:2036:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:2088:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:2145:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:2196:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:179:0, from BeagleCPUPlugin.cpp:9: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:83:1: warning: multi-line comment [-Wcomment] //#define DO_INTEGRATION(num) \ ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:160:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:191:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:225:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:258:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:292:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:327:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:381:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:481:0: warning: ignoring #pragma unroll [-Wunknown-pragmas] #pragma unroll ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:496:0: warning: ignoring #pragma unroll [-Wunknown-pragmas] #pragma unroll ^ In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUPlugin.h:16:0, from BeagleCPUPlugin.cpp:8: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin/Plugin.h: In destructor 'beagle::plugin::PluginManager::PluginInfo::~PluginInfo()': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin/Plugin.h:67:32: warning: deleting object of polymorphic class type 'beagle::plugin::Plugin' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] ~PluginInfo() { delete m_plugin; delete m_library; } ^ Notice: Output directory `doc' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for files to exclude Searching for files to process... Searching for files in directory /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle Reading and parsing tag files Parsing files Preprocessing /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/beagle.h... Parsing file /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/beagle.h... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Creating members for template instances... Computing class relations... Add enum values to enums... Searching for member function documentation... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Computing dependencies between directories... Generating citations page... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file libhmsbeagle/beagle.h... Generating file documentation... Generating docs for file libhmsbeagle/beagle.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound BeagleInstanceDetails... Generating docs for compound BeagleOperation... Generating docs for compound BeagleResource... Generating docs for compound BeagleResourceList... Generating namespace index... Generating graph info page... Generating directory documentation... Generating dependency graph for directory libhmsbeagle Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... Running dot... Generating dot graphs using 3 parallel threads... Running dot for graph 1/4 Running dot for graph 2/4 Running dot for graph 3/4 Running dot for graph 4/4 Patching output file 1/3 Patching output file 2/3 Patching output file 3/3 lookup cache used 96/65536 hits=137 misses=97 finished... /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -msse2 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c -o libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo `test -f 'BeagleCPUSSEPlugin.cpp' || echo './'`BeagleCPUSSEPlugin.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -msse2 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c BeagleCPUSSEPlugin.cpp -fPIC -DPIC -o .libs/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.o In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.h:439:0, from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:35, from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:33, from BeagleCPUSSEPlugin.cpp:9: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:1921:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:1950:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:1987:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:2036:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:2088:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:2145:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:2196:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:179:0, from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:33, from BeagleCPUSSEPlugin.cpp:9: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:83:1: warning: multi-line comment [-Wcomment] //#define DO_INTEGRATION(num) \ ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:160:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:191:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:225:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:258:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:292:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:327:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:381:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:481:0: warning: ignoring #pragma unroll [-Wunknown-pragmas] #pragma unroll ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:496:0: warning: ignoring #pragma unroll [-Wunknown-pragmas] #pragma unroll ^ In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:243:0, from BeagleCPUSSEPlugin.cpp:10: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUSSEImpl.hpp:216:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUSSEImpl.hpp:299:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for num_threads(kCategoryCount) ^ In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUSSEPlugin.h:16:0, from BeagleCPUSSEPlugin.cpp:8: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin/Plugin.h: In destructor 'beagle::plugin::PluginManager::PluginInfo::~PluginInfo()': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin/Plugin.h:67:32: warning: deleting object of polymorphic class type 'beagle::plugin::Plugin' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] ~PluginInfo() { delete m_plugin; delete m_library; } ^ In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:241:0, from BeagleCPUSSEPlugin.cpp:9: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp: In instantiation of 'int beagle::cpu::BeagleCPU4StateSSEImpl::calcEdgeLogLikelihoods(int, int, int, int, int, int, double*) [with int T_PAD = 2; int P_PAD = 0]': BeagleCPUSSEPlugin.cpp:174:1: required from here /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:586:17: warning: operation on 'vcl_p' may be undefined [-Wsequence-point] *vcl_p++ = VEC_MADD(vu_m[stateChild][0].vx, wtdPartials, *vcl_p); ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:589:17: warning: operation on 'vcl_p' may be undefined [-Wsequence-point] *vcl_p++ = VEC_MADD(vu_m[stateChild][1].vx, wtdPartials, *vcl_p); ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:626:17: warning: operation on 'vcl_p' may be undefined [-Wsequence-point] *vcl_p++ = VEC_MADD(vclp_01, *vcl_r++, *vcl_p); ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:627:17: warning: operation on 'vcl_p' may be undefined [-Wsequence-point] *vcl_p++ = VEC_MADD(vclp_23, *vcl_r++, *vcl_p); ^ In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.h:439:0, from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:35, from BeagleCPUPlugin.cpp:9: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp: In member function 'int beagle::cpu::BeagleCPUImpl::getPartials(int, int, double*) [with REALTYPE = double; int T_PAD = 1; int P_PAD = 0]': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:506:7: warning: 'offsetOutPartials' may be used uninitialized in this function [-Wmaybe-uninitialized] offsetOutPartials += kPatternCount * kStateCount; ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp: In member function 'int beagle::cpu::BeagleCPUImpl::getPartials(int, int, double*) [with REALTYPE = float; int T_PAD = 1; int P_PAD = 0]': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:506:7: warning: 'offsetOutPartials' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.h:439:0, from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:35, from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:33, from BeagleCPUSSEPlugin.cpp:9: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp: In member function 'int beagle::cpu::BeagleCPUImpl::getPartials(int, int, double*) [with REALTYPE = double; int T_PAD = 2; int P_PAD = 0]': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:506:7: warning: 'offsetOutPartials' may be used uninitialized in this function [-Wmaybe-uninitialized] offsetOutPartials += kPatternCount * kStateCount; ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp: In member function 'int beagle::cpu::BeagleCPUImpl::getPartials(int, int, double*) [with REALTYPE = double; int T_PAD = 1; int P_PAD = 1]': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:506:7: warning: 'offsetOutPartials' may be used uninitialized in this function [-Wmaybe-uninitialized] /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c -o libhmsbeagle_cpu_openmp_la-BeagleCPUOpenMPPlugin.lo `test -f 'BeagleCPUOpenMPPlugin.cpp' || echo './'`BeagleCPUOpenMPPlugin.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c BeagleCPUOpenMPPlugin.cpp -fPIC -DPIC -o .libs/libhmsbeagle_cpu_openmp_la-BeagleCPUOpenMPPlugin.o In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:179:0, from BeagleCPUOpenMPPlugin.cpp:9: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:83:1: warning: multi-line comment [-Wcomment] //#define DO_INTEGRATION(num) \ ^ /bin/sh ../../libtool --tag=CXX --mode=link g++ -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -module -version-number 21 -Wl,-z,relro -o libhmsbeagle-cpu.la -rpath /usr/lib64 libhmsbeagle_cpu_la-BeagleCPUPlugin.lo -ldl /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:481:0: warning: ignoring #pragma unroll [-Wunknown-pragmas] #pragma unroll ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp:496:0: warning: ignoring #pragma unroll [-Wunknown-pragmas] #pragma unroll ^ libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtbeginS.o .libs/libhmsbeagle_cpu_la-BeagleCPUPlugin.o -ldl -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crtn.o -march=native -O2 -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libhmsbeagle-cpu.so.21 -o .libs/libhmsbeagle-cpu.so.21.0.0 In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.h:16:0, from BeagleCPUOpenMPPlugin.cpp:8: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin/Plugin.h: In destructor 'beagle::plugin::PluginManager::PluginInfo::~PluginInfo()': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin/Plugin.h:67:32: warning: deleting object of polymorphic class type 'beagle::plugin::Plugin' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] ~PluginInfo() { delete m_plugin; delete m_library; } ^ libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu.so.21" && ln -s "libhmsbeagle-cpu.so.21.0.0" "libhmsbeagle-cpu.so.21") libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu.so" && ln -s "libhmsbeagle-cpu.so.21.0.0" "libhmsbeagle-cpu.so") libtool: link: ( cd ".libs" && rm -f "libhmsbeagle-cpu.la" && ln -s "../libhmsbeagle-cpu.la" "libhmsbeagle-cpu.la" ) /bin/sh ../../libtool --tag=CXX --mode=link g++ -march=native -msse2 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -module -version-number 21 -Wl,-z,relro -o libhmsbeagle-cpu-sse.la -rpath /usr/lib64 libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo -ldl libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtbeginS.o .libs/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.o -ldl -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crtn.o -march=native -msse2 -O2 -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libhmsbeagle-cpu-sse.so.21 -o .libs/libhmsbeagle-cpu-sse.so.21.0.0 libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu-sse.so.21" && ln -s "libhmsbeagle-cpu-sse.so.21.0.0" "libhmsbeagle-cpu-sse.so.21") libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu-sse.so" && ln -s "libhmsbeagle-cpu-sse.so.21.0.0" "libhmsbeagle-cpu-sse.so") libtool: link: ( cd ".libs" && rm -f "libhmsbeagle-cpu-sse.la" && ln -s "../libhmsbeagle-cpu-sse.la" "libhmsbeagle-cpu-sse.la" ) In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:241:0, from BeagleCPUOpenMPPlugin.cpp:12: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp: In instantiation of 'int beagle::cpu::BeagleCPU4StateSSEImpl::calcEdgeLogLikelihoods(int, int, int, int, int, int, double*) [with int T_PAD = 2; int P_PAD = 0]': BeagleCPUOpenMPPlugin.cpp:62:1: required from here /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:586:17: warning: operation on 'vcl_p' may be undefined [-Wsequence-point] *vcl_p++ = VEC_MADD(vu_m[stateChild][0].vx, wtdPartials, *vcl_p); ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:589:17: warning: operation on 'vcl_p' may be undefined [-Wsequence-point] *vcl_p++ = VEC_MADD(vu_m[stateChild][1].vx, wtdPartials, *vcl_p); ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:626:17: warning: operation on 'vcl_p' may be undefined [-Wsequence-point] *vcl_p++ = VEC_MADD(vclp_01, *vcl_r++, *vcl_p); ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:627:17: warning: operation on 'vcl_p' may be undefined [-Wsequence-point] *vcl_p++ = VEC_MADD(vclp_23, *vcl_r++, *vcl_p); ^ In file included from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.h:439:0, from /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:35, from BeagleCPUOpenMPPlugin.cpp:9: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp: In member function 'int beagle::cpu::BeagleCPUImpl::getPartials(int, int, double*) [with REALTYPE = double; int T_PAD = 2; int P_PAD = 0]': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:506:7: warning: 'offsetOutPartials' may be used uninitialized in this function [-Wmaybe-uninitialized] offsetOutPartials += kPatternCount * kStateCount; ^ /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp: In member function 'int beagle::cpu::BeagleCPUImpl::getPartials(int, int, double*) [with REALTYPE = double; int T_PAD = 1; int P_PAD = 1]': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:506:7: warning: 'offsetOutPartials' may be used uninitialized in this function [-Wmaybe-uninitialized] /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp: In member function 'int beagle::cpu::BeagleCPUImpl::getPartials(int, int, double*) [with REALTYPE = double; int T_PAD = 1; int P_PAD = 0]': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:506:7: warning: 'offsetOutPartials' may be used uninitialized in this function [-Wmaybe-uninitialized] /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp: In member function 'int beagle::cpu::BeagleCPUImpl::getPartials(int, int, double*) [with REALTYPE = float; int T_PAD = 1; int P_PAD = 0]': /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU/BeagleCPUImpl.hpp:506:7: warning: 'offsetOutPartials' may be used uninitialized in this function [-Wmaybe-uninitialized] /bin/sh ../../libtool --tag=CXX --mode=link g++ -march=native -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -module -version-number 21 -Wl,-z,relro -o libhmsbeagle-cpu-openmp.la -rpath /usr/lib64 libhmsbeagle_cpu_openmp_la-BeagleCPUOpenMPPlugin.lo -fopenmp -ldl libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtbeginS.o .libs/libhmsbeagle_cpu_openmp_la-BeagleCPUOpenMPPlugin.o -ldl -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crtn.o -march=native -fopenmp -O2 -m64 -mtune=generic -Wl,-z -Wl,relro -fopenmp -fopenmp -Wl,-soname -Wl,libhmsbeagle-cpu-openmp.so.21 -o .libs/libhmsbeagle-cpu-openmp.so.21.0.0 libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu-openmp.so.21" && ln -s "libhmsbeagle-cpu-openmp.so.21.0.0" "libhmsbeagle-cpu-openmp.so.21") libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu-openmp.so" && ln -s "libhmsbeagle-cpu-openmp.so.21.0.0" "libhmsbeagle-cpu-openmp.so") libtool: link: ( cd ".libs" && rm -f "libhmsbeagle-cpu-openmp.la" && ln -s "../libhmsbeagle-cpu-openmp.la" "libhmsbeagle-cpu-openmp.la" ) make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU' Making all in plugin make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin' /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c -o libplugin_la-Plugin.lo `test -f 'Plugin.cpp' || echo './'`Plugin.cpp /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c -o libplugin_la-UnixSharedLibrary.lo `test -f 'UnixSharedLibrary.cpp' || echo './'`UnixSharedLibrary.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c UnixSharedLibrary.cpp -fPIC -DPIC -o .libs/libplugin_la-UnixSharedLibrary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c Plugin.cpp -fPIC -DPIC -o .libs/libplugin_la-Plugin.o In file included from Plugin.cpp:9:0: ../../libhmsbeagle/plugin/Plugin.h: In destructor 'beagle::plugin::PluginManager::PluginInfo::~PluginInfo()': ../../libhmsbeagle/plugin/Plugin.h:67:32: warning: deleting object of polymorphic class type 'beagle::plugin::Plugin' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] ~PluginInfo() { delete m_plugin; delete m_library; } ^ /bin/sh ../../libtool --tag=CXX --mode=link g++ -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -Wl,-z,relro -o libplugin.la libplugin_la-Plugin.lo libplugin_la-UnixSharedLibrary.lo -ldl libtool: link: ar cru .libs/libplugin.a .libs/libplugin_la-Plugin.o .libs/libplugin_la-UnixSharedLibrary.o libtool: link: ranlib .libs/libplugin.a libtool: link: ( cd ".libs" && rm -f "libplugin.la" && ln -s "../libplugin.la" "libplugin.la" ) make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c -o libhmsbeagle_la-beagle.lo `test -f 'beagle.cpp' || echo './'`beagle.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c beagle.cpp -fPIC -DPIC -o .libs/libhmsbeagle_la-beagle.o In file included from beagle.cpp:50:0: ../libhmsbeagle/plugin/Plugin.h: In destructor 'beagle::plugin::PluginManager::PluginInfo::~PluginInfo()': ../libhmsbeagle/plugin/Plugin.h:67:32: warning: deleting object of polymorphic class type 'beagle::plugin::Plugin' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor] ~PluginInfo() { delete m_plugin; delete m_library; } ^ beagle.cpp: In function 'beagle::BeagleImpl* beagle::getBeagleInstance(int)': beagle.cpp:71:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (instanceIndex > instances->size()) ^ /bin/sh ../libtool --tag=CXX --mode=link g++ -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -version-info 2:1:1 -Wl,-z,relro -o libhmsbeagle.la -rpath /usr/lib64 libhmsbeagle_la-beagle.lo plugin/libplugin.la -ldl libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtbeginS.o .libs/libhmsbeagle_la-beagle.o -Wl,--whole-archive plugin/.libs/libplugin.a -Wl,--no-whole-archive -ldl -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crtn.o -march=native -O2 -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libhmsbeagle.so.1 -o .libs/libhmsbeagle.so.1.1.1 libtool: link: (cd ".libs" && rm -f "libhmsbeagle.so.1" && ln -s "libhmsbeagle.so.1.1.1" "libhmsbeagle.so.1") libtool: link: (cd ".libs" && rm -f "libhmsbeagle.so" && ln -s "libhmsbeagle.so.1.1.1" "libhmsbeagle.so") libtool: link: ( cd ".libs" && rm -f "libhmsbeagle.la" && ln -s "../libhmsbeagle.la" "libhmsbeagle.la" ) make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' make[1]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' Making all in libhmsbeagle/JNI make[1]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/JNI' /bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c -o libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo `test -f 'beagle_BeagleJNIWrapper.cpp' || echo './'`beagle_BeagleJNIWrapper.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91-2.6.2.1.el7_1.x86_64/include/linux -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c beagle_BeagleJNIWrapper.cpp -fPIC -DPIC -o .libs/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o /bin/sh ../../libtool --tag=CXX --mode=link g++ -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -module -avoid-version -Wl,-z,relro -o libhmsbeagle-jni.la -rpath /usr/lib64 libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo -L../../libhmsbeagle -lhmsbeagle -ldl libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtbeginS.o .libs/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o -Wl,-rpath -Wl,/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/.libs -L../../libhmsbeagle /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/.libs/libhmsbeagle.so -ldl -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crtn.o -march=native -O2 -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libhmsbeagle-jni.so -o .libs/libhmsbeagle-jni.so libtool: link: ( cd ".libs" && rm -f "libhmsbeagle-jni.la" && ln -s "../libhmsbeagle-jni.la" "libhmsbeagle-jni.la" ) make[1]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/JNI' Making all in examples make[1]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' Making all in genomictest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/genomictest' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/genomictest' Making all in tinytest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/tinytest' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/tinytest' Making all in oddstatetest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/oddstatetest' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/oddstatetest' Making all in complextest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/complextest' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/complextest' Making all in fourtaxon make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/fourtaxon' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/fourtaxon' Making all in matrixtest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/matrixtest' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/matrixtest' make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' make[1]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' make[1]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2' + ant Buildfile: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/build.xml init: [mkdir] Created dir: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/build [mkdir] Created dir: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/lib compile: [javac] /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/build.xml:37: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 13 source files to /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/build [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.6 [javac] 1 warning dist: [jar] Building jar: /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/lib/beagle.jar BUILD SUCCESSFUL Total time: 1 second + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.AySABA + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64 ++ dirname /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64 + cd beagle-lib-beagle_release_2_1_2 + rm -rf /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64 + make install DESTDIR=/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64 Making install in libhmsbeagle make[1]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' Making install in GPU make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' Making install in kernels make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make install-am make[4]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make[5]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make[4]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU/kernels' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' make[4]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/GPU' Making install in CPU make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64' /bin/sh ../../libtool --mode=install /usr/bin/install -c libhmsbeagle-cpu.la libhmsbeagle-cpu-sse.la libhmsbeagle-cpu-openmp.la '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64' libtool: install: /usr/bin/install -c .libs/libhmsbeagle-cpu.so.21.0.0 /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-cpu.so.21.0.0 libtool: install: (cd /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64 && { ln -s -f libhmsbeagle-cpu.so.21.0.0 libhmsbeagle-cpu.so.21 || { rm -f libhmsbeagle-cpu.so.21 && ln -s libhmsbeagle-cpu.so.21.0.0 libhmsbeagle-cpu.so.21; }; }) libtool: install: (cd /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64 && { ln -s -f libhmsbeagle-cpu.so.21.0.0 libhmsbeagle-cpu.so || { rm -f libhmsbeagle-cpu.so && ln -s libhmsbeagle-cpu.so.21.0.0 libhmsbeagle-cpu.so; }; }) libtool: install: /usr/bin/install -c .libs/libhmsbeagle-cpu.lai /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-cpu.la libtool: install: /usr/bin/install -c .libs/libhmsbeagle-cpu-sse.so.21.0.0 /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-cpu-sse.so.21.0.0 libtool: install: (cd /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64 && { ln -s -f libhmsbeagle-cpu-sse.so.21.0.0 libhmsbeagle-cpu-sse.so.21 || { rm -f libhmsbeagle-cpu-sse.so.21 && ln -s libhmsbeagle-cpu-sse.so.21.0.0 libhmsbeagle-cpu-sse.so.21; }; }) libtool: install: (cd /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64 && { ln -s -f libhmsbeagle-cpu-sse.so.21.0.0 libhmsbeagle-cpu-sse.so || { rm -f libhmsbeagle-cpu-sse.so && ln -s libhmsbeagle-cpu-sse.so.21.0.0 libhmsbeagle-cpu-sse.so; }; }) libtool: install: /usr/bin/install -c .libs/libhmsbeagle-cpu-sse.lai /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-cpu-sse.la libtool: install: /usr/bin/install -c .libs/libhmsbeagle-cpu-openmp.so.21.0.0 /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-cpu-openmp.so.21.0.0 libtool: install: (cd /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64 && { ln -s -f libhmsbeagle-cpu-openmp.so.21.0.0 libhmsbeagle-cpu-openmp.so.21 || { rm -f libhmsbeagle-cpu-openmp.so.21 && ln -s libhmsbeagle-cpu-openmp.so.21.0.0 libhmsbeagle-cpu-openmp.so.21; }; }) libtool: install: (cd /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64 && { ln -s -f libhmsbeagle-cpu-openmp.so.21.0.0 libhmsbeagle-cpu-openmp.so || { rm -f libhmsbeagle-cpu-openmp.so && ln -s libhmsbeagle-cpu-openmp.so.21.0.0 libhmsbeagle-cpu-openmp.so; }; }) libtool: install: /usr/bin/install -c .libs/libhmsbeagle-cpu-openmp.lai /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-cpu-openmp.la libtool: install: warning: remember to run `libtool --finish /usr/lib64' make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/CPU' Making install in plugin make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/plugin' make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64' /bin/sh ../libtool --mode=install /usr/bin/install -c libhmsbeagle.la '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64' libtool: install: /usr/bin/install -c .libs/libhmsbeagle.so.1.1.1 /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle.so.1.1.1 libtool: install: (cd /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64 && { ln -s -f libhmsbeagle.so.1.1.1 libhmsbeagle.so.1 || { rm -f libhmsbeagle.so.1 && ln -s libhmsbeagle.so.1.1.1 libhmsbeagle.so.1; }; }) libtool: install: (cd /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64 && { ln -s -f libhmsbeagle.so.1.1.1 libhmsbeagle.so || { rm -f libhmsbeagle.so && ln -s libhmsbeagle.so.1.1.1 libhmsbeagle.so; }; }) libtool: install: /usr/bin/install -c .libs/libhmsbeagle.lai /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle.la libtool: install: warning: remember to run `libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/include/libhmsbeagle-1/libhmsbeagle' /usr/bin/install -c -m 644 beagle.h platform.h '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/include/libhmsbeagle-1/libhmsbeagle' make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' make[1]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle' Making install in libhmsbeagle/JNI make[1]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/JNI' make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/JNI' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64' /bin/sh ../../libtool --mode=install /usr/bin/install -c libhmsbeagle-jni.la '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64' libtool: install: warning: relinking `libhmsbeagle-jni.la' libtool: install: (cd /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/JNI; /bin/sh /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libtool --tag CXX --mode=relink g++ -march=native -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -module -avoid-version -Wl,-z,relro -o libhmsbeagle-jni.la -rpath /usr/lib64 libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo -L../../libhmsbeagle -lhmsbeagle -ldl -inst-prefix-dir /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtbeginS.o .libs/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o -L../../libhmsbeagle -L/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64 -L/usr/lib64 -lhmsbeagle -ldl -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/4.8.3/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.8.3/../../../../lib64/crtn.o -march=native -O2 -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libhmsbeagle-jni.so -o .libs/libhmsbeagle-jni.so libtool: install: /usr/bin/install -c .libs/libhmsbeagle-jni.soT /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-jni.so libtool: install: /usr/bin/install -c .libs/libhmsbeagle-jni.lai /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-jni.la libtool: install: warning: remember to run `libtool --finish /usr/lib64' make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/JNI' make[1]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/libhmsbeagle/JNI' Making install in examples make[1]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' Making install in genomictest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/genomictest' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/genomictest' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/genomictest' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/genomictest' Making install in tinytest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/tinytest' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/tinytest' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/tinytest' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/tinytest' Making install in oddstatetest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/oddstatetest' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/oddstatetest' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/oddstatetest' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/oddstatetest' Making install in complextest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/complextest' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/complextest' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/complextest' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/complextest' Making install in fourtaxon make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/fourtaxon' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/fourtaxon' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/fourtaxon' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/fourtaxon' Making install in matrixtest make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/matrixtest' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/matrixtest' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/matrixtest' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples/matrixtest' make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' make[3]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' make[1]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2/examples' make[1]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2' make[2]: Entering directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2' make[2]: Nothing to be done for `install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/pkgconfig' /usr/bin/install -c -m 644 hmsbeagle-1.pc '/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/pkgconfig' make[2]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2' make[1]: Leaving directory `/builddir/build/BUILD/beagle-lib-beagle_release_2_1_2' + find /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64 -name '*.la' -exec rm -f '{}' ';' + find -name .deps + xargs rm -r + mkdir -p /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/man/man3 + install -m 644 doc/man/man3/BeagleInstanceDetails.3 doc/man/man3/BeagleOperation.3 doc/man/man3/BeagleResource.3 doc/man/man3/BeagleResourceList.3 doc/man/man3/_builddir_build_BUILD_beagle-lib-beagle_release_2_1_2_libhmsbeagle_.3 doc/man/man3/beagle.h.3 /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/man/man3 + install -D lib/beagle.jar /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib/java/beagle.jar + ln -s libhmsbeagle-2 /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/include/libhmsbeagle + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/beagle-lib-beagle_release_2_1_2 extracting debug info from /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-jni.so extracting debug info from /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle.so.1.1.1 extracting debug info from /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-cpu-openmp.so.21.0.0 extracting debug info from /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-cpu-sse.so.21.0.0 extracting debug info from /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/lib64/libhmsbeagle-cpu.so.21.0.0 /usr/lib/rpm/sepdebugcrcfix: Updated 5 CRC32s, 0 CRC32s did match. symlinked /usr/lib/debug/usr/lib64/libhmsbeagle.so.1.1.1.debug to /usr/lib/debug/usr/lib64/libhmsbeagle.so.debug symlinked /usr/lib/debug/usr/lib64/libhmsbeagle.so.1.1.1.debug to /usr/lib/debug/usr/lib64/libhmsbeagle.so.1.debug symlinked /usr/lib/debug/usr/lib64/libhmsbeagle-cpu-openmp.so.21.0.0.debug to /usr/lib/debug/usr/lib64/libhmsbeagle-cpu-openmp.so.debug symlinked /usr/lib/debug/usr/lib64/libhmsbeagle-cpu-openmp.so.21.0.0.debug to /usr/lib/debug/usr/lib64/libhmsbeagle-cpu-openmp.so.21.debug symlinked /usr/lib/debug/usr/lib64/libhmsbeagle-cpu-sse.so.21.0.0.debug to /usr/lib/debug/usr/lib64/libhmsbeagle-cpu-sse.so.debug symlinked /usr/lib/debug/usr/lib64/libhmsbeagle-cpu-sse.so.21.0.0.debug to /usr/lib/debug/usr/lib64/libhmsbeagle-cpu-sse.so.21.debug symlinked /usr/lib/debug/usr/lib64/libhmsbeagle-cpu.so.21.0.0.debug to /usr/lib/debug/usr/lib64/libhmsbeagle-cpu.so.debug symlinked /usr/lib/debug/usr/lib64/libhmsbeagle-cpu.so.21.0.0.debug to /usr/lib/debug/usr/lib64/libhmsbeagle-cpu.so.21.debug 745 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-compress + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.MTJbXw + umask 022 + cd /builddir/build/BUILD + cd beagle-lib-beagle_release_2_1_2 + pushd tests ~/build/BUILD/beagle-lib-beagle_release_2_1_2/tests ~/build/BUILD/beagle-lib-beagle_release_2_1_2 + ./run_tests.sh # states taxa sites rates reps ctips rseed root derivs rescale rfreq lscalers ecount ecomplex ievect smatrix lnl_exp d1_exp d2_exp test_all_impls "4" "14" "1240" "4" "2" "7" "1" "yes" "no" "manual" "2" "no" "1" "no" "no" "no" "-3528.89396" "0" "0" testing resource=0 precision=SINGLE ./parse_test.sh: line 102: svnversion: command not found ./parse_test.sh: line 23: bc: command not found ./parse_test.sh: line 24: bc: command not found ./parse_test.sh: line 75: bc: command not found ./parse_test.sh: line 80: bc: command not found ./parse_test.sh: line 85: bc: command not found testing resource=0 precision=DOUBLE ./parse_test.sh: line 102: svnversion: command not found ./parse_test.sh: line 23: bc: command not found ./parse_test.sh: line 24: bc: command not found ./parse_test.sh: line 75: bc: command not found ./parse_test.sh: line 80: bc: command not found ./parse_test.sh: line 85: bc: command not found test_all_impls "4" "14" "1240" "4" "2" "7" "1" "yes" "no" "manual" "1" "yes" "1" "no" "no" "no" "-3528.89396" "0" "0" testing resource=0 precision=SINGLE ./parse_test.sh: line 102: svnversion: command not found ./parse_test.sh: line 23: bc: command not found ./parse_test.sh: line 24: bc: command not found 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"2" "2" "3" "1" "no" "yes" "none" "2" "no" "1" "no" "no" "no" "-3661.78867" "-25.00759" "7.92562" testing resource=0 precision=SINGLE ./parse_test.sh: line 102: svnversion: command not found ./parse_test.sh: line 23: bc: command not found ./parse_test.sh: line 24: bc: command not found ./parse_test.sh: line 34: bc: command not found ./parse_test.sh: line 35: bc: command not found ./parse_test.sh: line 36: bc: command not found ./parse_test.sh: line 37: bc: command not found ./parse_test.sh: line 75: bc: command not found ./parse_test.sh: line 80: bc: command not found ./parse_test.sh: line 85: bc: command not found testing resource=0 precision=DOUBLE ./parse_test.sh: line 102: svnversion: command not found ./parse_test.sh: line 23: bc: command not found ./parse_test.sh: line 24: bc: command not found ./parse_test.sh: line 34: bc: command not found ./parse_test.sh: line 35: bc: command not found ./parse_test.sh: line 36: bc: command not found ./parse_test.sh: line 37: bc: command not 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./parse_test.sh: line 23: bc: command not found ./parse_test.sh: line 24: bc: command not found ./parse_test.sh: line 34: bc: command not found ./parse_test.sh: line 35: bc: command not found ./parse_test.sh: line 36: bc: command not found ./parse_test.sh: line 37: bc: command not found ./parse_test.sh: line 75: bc: command not found ./parse_test.sh: line 80: bc: command not found ./parse_test.sh: line 85: bc: command not found testing resource=0 precision=DOUBLE ./parse_test.sh: line 102: svnversion: command not found ./parse_test.sh: line 23: bc: command not found ./parse_test.sh: line 24: bc: command not found ./parse_test.sh: line 34: bc: command not found ./parse_test.sh: line 35: bc: command not found ./parse_test.sh: line 36: bc: command not found ./parse_test.sh: line 37: bc: command not found ./parse_test.sh: line 75: bc: command not found ./parse_test.sh: line 80: bc: command not found ./parse_test.sh: line 85: bc: command not found set +v + popd ~/build/BUILD/beagle-lib-beagle_release_2_1_2 + exit 0 Processing files: libhmsbeagle-2.1.2-1.el7.centos.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Cks3Nz + umask 022 + cd /builddir/build/BUILD + cd beagle-lib-beagle_release_2_1_2 + DOCDIR=/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/doc/libhmsbeagle-2.1.2 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/doc/libhmsbeagle-2.1.2 + cp -pr AUTHORS /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/doc/libhmsbeagle-2.1.2 + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.as2WFC + umask 022 + cd /builddir/build/BUILD + cd beagle-lib-beagle_release_2_1_2 + LICENSEDIR=/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/licenses/libhmsbeagle-2.1.2 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/licenses/libhmsbeagle-2.1.2 + cp -pr COPYING COPYING.LESSER /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/licenses/libhmsbeagle-2.1.2 + exit 0 Provides: libhmsbeagle = 2.1.2-1.el7.centos libhmsbeagle(x86-64) = 2.1.2-1.el7.centos libhmsbeagle-cpu-openmp.so.21()(64bit) libhmsbeagle-cpu-sse.so.21()(64bit) libhmsbeagle-cpu.so.21()(64bit) libhmsbeagle.so.1()(64bit) Requires(interp): /sbin/ldconfig /sbin/ldconfig Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /sbin/ldconfig Requires(postun): /sbin/ldconfig Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.2.5)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) rtld(GNU_HASH) Processing files: libhmsbeagle-devel-2.1.2-1.el7.centos.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.u0gzLF + umask 022 + cd /builddir/build/BUILD + cd beagle-lib-beagle_release_2_1_2 + DOCDIR=/builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/doc/libhmsbeagle-devel-2.1.2 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/doc/libhmsbeagle-devel-2.1.2 + cp -pr doc/html /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/doc/libhmsbeagle-devel-2.1.2 + cp -pr examples /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64/usr/share/doc/libhmsbeagle-devel-2.1.2 + exit 0 Provides: libhmsbeagle-devel = 2.1.2-1.el7.centos libhmsbeagle-devel(x86-64) = 2.1.2-1.el7.centos libhmsbeagle-jni.so()(64bit) pkgconfig(hmsbeagle-1) = 2.1.2 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /bin/sh /usr/bin/pkg-config libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libdl.so.2()(64bit) libgcc_s.so.1()(64bit) libhmsbeagle-cpu-openmp.so.21()(64bit) libhmsbeagle-cpu-sse.so.21()(64bit) libhmsbeagle-cpu.so.21()(64bit) libhmsbeagle.so.1()(64bit) libltdl.so.7()(64bit) libm.so.6()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) rtld(GNU_HASH) Processing files: libhmsbeagle-java-2.1.2-1.el7.centos.x86_64 Provides: libhmsbeagle-java = 2.1.2-1.el7.centos libhmsbeagle-java(x86-64) = 2.1.2-1.el7.centos Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: libhmsbeagle-debuginfo-2.1.2-1.el7.centos.x86_64 Provides: libhmsbeagle-debuginfo = 2.1.2-1.el7.centos libhmsbeagle-debuginfo(x86-64) = 2.1.2-1.el7.centos Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64 Wrote: /builddir/build/RPMS/libhmsbeagle-2.1.2-1.el7.centos.x86_64.rpm Wrote: /builddir/build/RPMS/libhmsbeagle-devel-2.1.2-1.el7.centos.x86_64.rpm Wrote: /builddir/build/RPMS/libhmsbeagle-java-2.1.2-1.el7.centos.x86_64.rpm Wrote: /builddir/build/RPMS/libhmsbeagle-debuginfo-2.1.2-1.el7.centos.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.q1ryzp + umask 022 + cd /builddir/build/BUILD + cd beagle-lib-beagle_release_2_1_2 + rm -rf /builddir/build/BUILDROOT/libhmsbeagle-2.1.2-1.el7.centos.x86_64 + exit 0 Child return code was: 0 LEAVE do -->