Mock Version: 5.0 Mock Version: 5.0 Mock Version: 5.0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.spec'], chrootPath='/var/lib/mock/f40-build-789429-135700/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=604800uid=982gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.zfegigb1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.zfegigb1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', '6f6bb6e9504e49509c3935aef3133f13', '-D', '/var/lib/mock/f40-build-789429-135700/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.zfegigb1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.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 warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1705881600 Wrote: /builddir/build/SRPMS/R-affyio-1.66.0-6.fc40.src.rpm RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.spec'], chrootPath='/var/lib/mock/f40-build-789429-135700/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=604800uid=982gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.zfegigb1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.zfegigb1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', 'ce8bc314cc094e0da7ffc3490a81f025', '-D', '/var/lib/mock/f40-build-789429-135700/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.zfegigb1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.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 warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1705881600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.yAEFGH + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf affyio + /usr/bin/mkdir -p affyio + cd affyio + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/affyio_1.66.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + rm -rf /builddir/build/BUILD/affyio-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/affyio-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + sed -i '/Imports: zlibbioc/d' affyio/DESCRIPTION + sed -i '/import(zlibbioc)/d' affyio/NAMESPACE + echo 'Patch #0 (affyio-fix-DESCRIPTION-Depends.patch):' Patch #0 (affyio-fix-DESCRIPTION-Depends.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .fixdep --fuzz=0 patching file affyio/DESCRIPTION + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.q3NHVe + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 affyio + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.MqEGlJ + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64 ++ dirname /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64 + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 affyio + rm -rf /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64 + mkdir -p /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64/usr/lib64/R/library + R CMD INSTALL affyio -l /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64/usr/lib64/R/library * installing *source* package ‘affyio’ ... ** using staged installation 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 how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/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 for main in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: Enabling threading for affyio configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0)’ gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c fread_functions.c -o fread_functions.o gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c init_package.c -o init_package.o gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_abatch.c -o read_abatch.o read_abatch.c: In function ‘gzbinary_get_detailed_header_info’: read_abatch.c:3410:3: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 3410 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); | ^ read_abatch.c:3410:65: note: length computed here 3410 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_abatch.c: In function ‘binary_get_detailed_header_info’: read_abatch.c:2661:3: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2661 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); | ^ read_abatch.c:2661:65: note: length computed here 2661 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function ‘ReadBPMAPFileIntoRList’: read_bpmap.c:698:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 698 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:980, from /usr/include/R/R.h:44, from read_bpmap.c:23: In function ‘sprintf’, inlined from ‘readBPMAPSeqIdPositionInfo’ at read_bpmap.c:698:4, inlined from ‘ReadBPMAPFileIntoRList’ at read_bpmap.c:873:3: /usr/include/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function ‘ReadBPMAPFileIntoRList’: read_bpmap.c:655:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 655 | sprintf(buf, "%d", j+1); | ^ In function ‘sprintf’, inlined from ‘readBPMAPSeqIdPositionInfo’ at read_bpmap.c:655:4, inlined from ‘ReadBPMAPFileIntoRList’ at read_bpmap.c:873:3: /usr/include/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function ‘ReadBPMAPFileIntoRList’: read_bpmap.c:603:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 603 | sprintf(buf, "%d", j+1); | ^ In function ‘sprintf’, inlined from ‘readBPMAPSeqIdPositionInfo’ at read_bpmap.c:603:2, inlined from ‘ReadBPMAPFileIntoRList’ at read_bpmap.c:873:3: /usr/include/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_cdf_xda.c -o read_cdf_xda.o gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_cdffile2.c -o read_cdffile2.o gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_celfile_generic.c -o read_celfile_generic.o read_celfile_generic.c: In function ‘generic_get_detailed_header_info’: read_celfile_generic.c:272:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 272 | strncpy(header_info->AlgorithmParameters,"Percentile:",11); | ^ read_celfile_generic.c:294:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 294 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11); | ^ read_celfile_generic.c:315:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] 315 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12); | ^ read_celfile_generic.c:336:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 336 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11); | ^ read_celfile_generic.c:357:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 357 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11); | ^ read_celfile_generic.c:378:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] 378 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14); | ^ read_celfile_generic.c:399:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] 399 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17); | ^ read_celfile_generic.c:420:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] 420 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18); | ^ read_celfile_generic.c:441:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] 441 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26); | ^ read_celfile_generic.c:464:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] 464 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18); | ^ read_celfile_generic.c:488:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] 488 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20); | ^ read_celfile_generic.c:510:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] 510 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20); | ^ read_celfile_generic.c:532:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] 532 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12); | ^ read_celfile_generic.c:553:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] 553 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16); | ^ read_celfile_generic.c:575:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 575 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11); | ^ read_celfile_generic.c:597:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] 597 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8); | ^ read_celfile_generic.c: In function ‘gzgeneric_get_detailed_header_info’: read_celfile_generic.c:1270:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1270 | strncpy(header_info->AlgorithmParameters,"Percentile:",11); | ^ read_celfile_generic.c:1292:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1292 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11); | ^ read_celfile_generic.c:1313:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] 1313 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12); | ^ read_celfile_generic.c:1334:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1334 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11); | ^ read_celfile_generic.c:1355:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1355 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11); | ^ read_celfile_generic.c:1376:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] 1376 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14); | ^ read_celfile_generic.c:1397:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] 1397 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17); | ^ read_celfile_generic.c:1418:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] 1418 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18); | ^ read_celfile_generic.c:1439:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] 1439 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26); | ^ read_celfile_generic.c:1462:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] 1462 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18); | ^ read_celfile_generic.c:1486:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] 1486 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20); | ^ read_celfile_generic.c:1508:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] 1508 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20); | ^ read_celfile_generic.c:1530:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] 1530 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12); | ^ read_celfile_generic.c:1551:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] 1551 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16); | ^ read_celfile_generic.c:1573:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1573 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11); | ^ read_celfile_generic.c:1595:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] 1595 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8); | ^ gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_clf.c -o read_clf.o gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_generic.c -o read_generic.o gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o gcc -I"/usr/include/R" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_pgf.c -o read_pgf.o read_pgf.c:363:12: warning: ‘token_ends_with’ defined but not used [-Wunused-function] 363 | static int token_ends_with(char *token, char *ends_in){ | ^~~~~~~~~~~~~~~ gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64/usr/lib64/R/library/00LOCK-affyio/00new/affyio/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘affyio’ finding HTML links ... done affyio-internal html check.cdf.type html get.celfile.dates html read.cdffile.list html read.celfile html read.celfile.header html read.celfile.probeintensity.matrices html read_abatch html ** 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 (affyio) + test -d affyio/src + cd affyio/src + rm -f fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o affyio.so + rm -rf /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64/usr/lib64/R/library/R.css + /usr/bin/find-debuginfo -j64 --strict-build-id -m -i --build-id-seed 1.66.0-6.fc40 --unique-debug-suffix -1.66.0-6.fc40.riscv64 --unique-debug-src-base R-affyio-1.66.0-6.fc40.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/affyio find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/R-affyio-1.66.0-6.fc40.riscv64 1084 blocks find-debuginfo: done + /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 + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j64 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.vGEFKC + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 affyio + /usr/bin/R CMD check affyio * using log directory ‘/builddir/build/BUILD/affyio/affyio.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: riscv64-redhat-linux-gnu (64-bit) * R was compiled by gcc (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0) GNU Fortran (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0) * running under: Fedora Linux 40 (Rawhide Prerelease) * using session charset: UTF-8 * checking for file ‘affyio/DESCRIPTION’ ... OK * this is package ‘affyio’ version ‘1.66.0’ * 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/3.18/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.18/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 ... OK * checking whether package ‘affyio’ can be installed ... WARNING Found the following significant warnings: read_abatch.c:3410:3: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] read_abatch.c:2661:3: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] read_bpmap.c:698:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] read_bpmap.c:655:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] read_bpmap.c:603:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] read_celfile_generic.c:272:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:294:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:315:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:336:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:357:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:378:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:399:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:420:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:441:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:464:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:488:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:510:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:532:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:553:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:575:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:597:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1270:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1292:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1313:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1334:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1355:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1376:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1397:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1418:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1439:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1462:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1486:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1508:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1530:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1551:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1573:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] read_celfile_generic.c:1595:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] See ‘/builddir/build/BUILD/affyio/affyio.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0)’ * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred. * 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown package ‘makecdfenv’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 ... WARNING File ‘affyio/libs/affyio.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Objects: ‘read_bpmap.o’, ‘read_cdf_xda.o’, ‘read_cdffile2.o’, ‘read_generic.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 nor [v]sprintf. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking examples ... NONE * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: File `inconsolata.sty' not found. Type X to quit or to proceed, or enter new name. (Default extension: sty) ! Emergency stop. l.303 ^^M ! ==> Fatal error occurred, no output PDF file produced! * checking PDF version of manual without index ... OK * DONE Status: 3 WARNINGs, 3 NOTEs See ‘/builddir/build/BUILD/affyio/affyio.Rcheck/00check.log’ for details. + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-affyio-1.66.0-6.fc40.riscv64 Provides: R(affyio) = 1.66.0 R-affyio = 1.66.0-6.fc40 R-affyio(riscv-64) = 1.66.0-6.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(ABI) = 4.3 R(methods) R-core >= 2.6.0 ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libc.so.6(GLIBC_2.34)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: R-affyio-debugsource-1.66.0-6.fc40.riscv64 Provides: R-affyio-debugsource = 1.66.0-6.fc40 R-affyio-debugsource(riscv-64) = 1.66.0-6.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-affyio-debuginfo-1.66.0-6.fc40.riscv64 Provides: R-affyio-debuginfo = 1.66.0-6.fc40 R-affyio-debuginfo(riscv-64) = 1.66.0-6.fc40 debuginfo(build-id) = f5f6d6255aef30c0635bd609c672fcb986fe4895 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-affyio-debugsource(riscv-64) = 1.66.0-6.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-affyio-1.66.0-6.fc40.riscv64 Wrote: /builddir/build/RPMS/R-affyio-1.66.0-6.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/R-affyio-debuginfo-1.66.0-6.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/R-affyio-debugsource-1.66.0-6.fc40.riscv64.rpm RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Child return code was: 0