Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-Rsolid.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1671758472.901626/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.27fzjpww:/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.27fzjpww:/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', 'e6dfa27ef1d14cdcaf133bf278745a72', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1671758472.901626/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.27fzjpww:/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/R-Rsolid.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=1662163200 Wrote: /builddir/build/SRPMS/R-Rsolid-0.9.31-40.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/R-Rsolid.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1671758472.901626/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.27fzjpww:/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.27fzjpww:/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', '33ad1482e50949a6be62f3514124889e', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1671758472.901626/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.27fzjpww:/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/R-Rsolid.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=1662163200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.pd4iwg + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf Rsolid + /usr/bin/mkdir -p Rsolid + cd Rsolid + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Rsolid_0.9-31.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (R-Rsolid-R3.patch):' Patch #0 (R-Rsolid-R3.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .fixed --fuzz=0 patching file Rsolid/NAMESPACE patching file Rsolid/src/util.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.pLQbDt + 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,--as-needed -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 Rsolid + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.3aynVF + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.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,--as-needed -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 Rsolid + mkdir -p /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64/usr/lib64/R/library + R CMD INSTALL Rsolid --configure-args=--with-hdf5=/usr -l /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64/usr/lib64/R/library * installing *source* package 'Rsolid' ... ** using staged installation checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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 ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for egrep... grep -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 hdf5.h usability... yes checking hdf5.h presence... yes checking for hdf5.h... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c Rdriver.c -o Rdriver.o Rdriver.c: In function 'rdriver': Rdriver.c:271:8: warning: unused variable 'p_yxloc' [-Wunused-variable] 271 | SEXP p_yxloc; | ^~~~~~~ Rdriver.c:270:8: warning: unused variable 'p_intensities' [-Wunused-variable] 270 | SEXP p_intensities; | ^~~~~~~~~~~~~ Rdriver.c:269:8: warning: unused variable 'ligation_names' [-Wunused-variable] 269 | SEXP ligation_names; | ^~~~~~~~~~~~~~ Rdriver.c:268:8: warning: unused variable 'primer_names' [-Wunused-variable] 268 | SEXP primer_names; | ^~~~~~~~~~~~ Rdriver.c:266:15: warning: unused variable 'i' [-Wunused-variable] 266 | int status, i; | ^ Rdriver.c:264:13: warning: unused variable 'panel_info' [-Wunused-variable] 264 | panelInfo panel_info; | ^~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c reader.c -o reader.o reader.c: In function 'ligationIter_data': reader.c:315:7: warning: unused variable 'offset' [-Wunused-variable] 315 | int offset; | ^~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c reader_util.c -o reader_util.o gcc -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util.c -o util.o util.c: In function 'callBases': util.c:163:41: warning: unused variable 'dscore' [-Wunused-variable] 163 | double *input=REAL(mat), dtmp, dtmp2, dscore; | ^~~~~~ gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o Rsolid.so Rdriver.o reader.o reader_util.o util.o -L/usr/lib -lhdf5 -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64/usr/lib64/R/library/00LOCK-Rsolid/00new/Rsolid/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Rsolid' finding HTML links ... done Rsolid html finding level-2 HTML links ... done Rd warning: Rsolid.Rd:44: missing link 'snow' Rd warning: Rsolid.Rd:45: missing link 'Rmpi' ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsolid) + test -d Rsolid/src + cd Rsolid/src + rm -f Rdriver.o reader.o reader_util.o util.o Rsolid.so + rm -rf /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64/usr/lib64/R/library/R.css + rm -rf Rsolid/src/hdf5-1.8.3 + rm -rf Rsolid/config.status + rm -rf Rsolid/configure + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 0.9.31-40.fc38 --unique-debug-suffix -0.9.31-40.fc38.x86_64 --unique-debug-src-base R-Rsolid-0.9.31-40.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/Rsolid extracting debug info from /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64/usr/lib64/R/library/Rsolid/libs/Rsolid.so original debug info size: 72kB, size after compression: 68kB /usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 72 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 + /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.6Qmjc3 + 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,--as-needed -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 Rsolid + /usr/bin/R CMD check Rsolid * using log directory '/builddir/build/BUILD/Rsolid/Rsolid.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: ASCII * checking for file 'Rsolid/DESCRIPTION' ... OK * this is package 'Rsolid' version '0.9-31' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... WARNING The following files should most likely be executable (for the owner): cleanup Please fix their permissions * checking whether package 'Rsolid' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... WARNING quantile: function(x, ...) quantile.norm: function(y, target, cycles) See section 'Generic functions and methods' in the 'Writing R Extensions' manual. Found the following apparent S3 methods exported but not registered: quantile.norm See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... WARNING Foreign function calls without 'PACKAGE' argument: .Call("callBases", ...) .Call("callBases", ...) .Call("rowMaxPos", ...) .Call("rdriver", ...) See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE NB: .First.lib is obsolete and will not be used in R >= 3.0.0 readspch: warning in matrix(0, nr = nbeads, nc = total.nligation.cycles): partial argument match of 'nr' to 'nrow' readspch: warning in matrix(0, nr = nbeads, nc = total.nligation.cycles): partial argument match of 'nc' to 'ncol' readspch: warning in matrix(NA, nr = max.ligation.cycles, nc = max.primer.cycles): partial argument match of 'nr' to 'nrow' readspch: warning in matrix(NA, nr = max.ligation.cycles, nc = max.primer.cycles): partial argument match of 'nc' to 'ncol' Rsolid: no visible global function definition for 'write.table' Undefined global functions or variables: write.table Consider adding importFrom("utils", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: Rsolid.Rd:61-63: Dropping empty section \seealso * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'Rsolid.Rd': 'snow' 'Rmpi' See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: 'makeTarget' 'quantile.norm' 'readspch' Undocumented data sets: 'prop.Hs' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both 'src/Makevars.in' and 'src/Makevars'. Installation with --no-configure' is unlikely to work. If you intended 'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win' otherwise remove it. If 'configure' created 'src/Makevars', you need a 'cleanup' script. * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE File 'Rsolid/libs/Rsolid.so': Found '__printf_chk', possibly from 'printf' (C) Objects: 'reader.o', 'reader_util.o' Found 'putchar', possibly from 'putchar' (C) Object: 'reader_util.o' Found 'puts', possibly from 'printf' (C), 'puts' (C) Objects: 'reader.o', 'reader_util.o' Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking examples ... OK * checking PDF version of manual ... OK * DONE Status: 5 WARNINGs, 4 NOTEs See '/builddir/build/BUILD/Rsolid/Rsolid.Rcheck/00check.log' for details. + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-Rsolid-0.9.31-40.fc38.x86_64 Provides: R(Rsolid) = 0.9.31 R-Rsolid = 0.9.31-40.fc38 R-Rsolid(x86-64) = 0.9.31-40.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(ABI) = 4.2 R-core libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libhdf5.so.200()(64bit) rtld(GNU_HASH) Processing files: R-Rsolid-devel-0.9.31-40.fc38.x86_64 Provides: R-Rsolid-devel = 0.9.31-40.fc38 R-Rsolid-devel(x86-64) = 0.9.31-40.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsolid-debugsource-0.9.31-40.fc38.x86_64 Provides: R-Rsolid-debugsource = 0.9.31-40.fc38 R-Rsolid-debugsource(x86-64) = 0.9.31-40.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsolid-debuginfo-0.9.31-40.fc38.x86_64 Provides: R-Rsolid-debuginfo = 0.9.31-40.fc38 R-Rsolid-debuginfo(x86-64) = 0.9.31-40.fc38 debuginfo(build-id) = 451fbaf53779ab149af2b293c89d4898a8282975 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-Rsolid-debugsource(x86-64) = 0.9.31-40.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64 Wrote: /builddir/build/RPMS/R-Rsolid-debuginfo-0.9.31-40.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/R-Rsolid-devel-0.9.31-40.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/R-Rsolid-0.9.31-40.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/R-Rsolid-debugsource-0.9.31-40.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.0sP6ah + umask 022 + cd /builddir/build/BUILD + cd Rsolid + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-Rsolid-0.9.31-40.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.SFHqB5 + umask 022 + cd /builddir/build/BUILD + rm -rf Rsolid Rsolid.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0