Mock Version: 1.4.14 Mock Version: 1.4.14 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.spec'], chrootPath='/var/lib/mock/f31-build-97140-32906/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': 'en_US.UTF-8'}shell=Falselogger=timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --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': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1565568000 Wrote: /builddir/build/SRPMS/R-affyio-1.50.0-5.fc31.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-affyio.spec'], chrootPath='/var/lib/mock/f31-build-97140-32906/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': 'en_US.UTF-8'}shell=Falselogger=timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --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': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1565568000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.bnB6yJ + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf affyio + /usr/bin/mkdir -p affyio + cd affyio + /usr/bin/gzip -dc /builddir/build/SOURCES/affyio_1.50.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + /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):' + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .fixdep --fuzz=0 + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Patch #0 (affyio-fix-DESCRIPTION-Depends.patch): patching file affyio/DESCRIPTION Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.8IqvQI + umask 022 + cd /builddir/build/BUILD + cd affyio + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.V7QffN + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64 + cd affyio + rm -rf /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64 + mkdir -p /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64/usr/lib64/R/library + R CMD INSTALL affyio -l /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64/usr/lib64/R/library BUILDSTDERR: * installing *source* package 'affyio' ... BUILDSTDERR: ** using staged installation BUILDSTDERR: ** libs BUILDSTDERR: In file included from /usr/include/string.h:494, BUILDSTDERR: from /usr/include/R/R_ext/RS.h:34, BUILDSTDERR: from /usr/include/R/R.h:91, BUILDSTDERR: from read_abatch.c:159: BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzbinary_get_detailed_header_info' at read_abatch.c:3410:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: read_abatch.c: In function 'gzbinary_get_detailed_header_info': BUILDSTDERR: read_abatch.c:3410:65: note: length computed here BUILDSTDERR: 3410 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/string.h:494, BUILDSTDERR: from /usr/include/R/R_ext/RS.h:34, BUILDSTDERR: from /usr/include/R/R.h:91, BUILDSTDERR: from read_abatch.c:159: BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'binary_get_detailed_header_info' at read_abatch.c:2661:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: read_abatch.c: In function 'binary_get_detailed_header_info': BUILDSTDERR: read_abatch.c:2661:65: note: length computed here BUILDSTDERR: 2661 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_abatch.c -o read_abatch.o BUILDSTDERR: 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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-securread_bpmap.c: In function 'ReadBPMAPFileIntoRList': BUILDSTDERR: read_bpmap.c:698:20: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] BUILDSTDERR: 698 | sprintf(buf, "%d", j+1); BUILDSTDERR: | ^ BUILDSTDERR: In file included from /usr/include/stdio.h:867, BUILDSTDERR: from /usr/include/R/R.h:56, BUILDSTDERR: from read_bpmap.c:23: BUILDSTDERR: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 BUILDSTDERR: 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: 37 | __bos (__s), __fmt, __va_arg_pack ()); BUILDSTDERR: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: read_bpmap.c:655:20: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] BUILDSTDERR: 655 | sprintf(buf, "%d", j+1); BUILDSTDERR: | ^ BUILDSTDERR: In file included from /usr/include/stdio.h:867, BUILDSTDERR: from /usr/include/R/R.h:56, BUILDSTDERR: from read_bpmap.c:23: BUILDSTDERR: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 BUILDSTDERR: 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: 37 | __bos (__s), __fmt, __va_arg_pack ()); BUILDSTDERR: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: read_bpmap.c:603:18: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] BUILDSTDERR: 603 | sprintf(buf, "%d", j+1); BUILDSTDERR: | ^ BUILDSTDERR: In file included from /usr/include/stdio.h:867, BUILDSTDERR: from /usr/include/R/R.h:56, BUILDSTDERR: from read_bpmap.c:23: BUILDSTDERR: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 BUILDSTDERR: 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: 37 | __bos (__s), __fmt, __va_arg_pack ()); BUILDSTDERR: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In file included from /usr/include/string.h:494, BUILDSTDERR: from /usr/include/R/R_ext/RS.h:34, BUILDSTDERR: from /usr/include/R/R.h:91, BUILDSTDERR: from read_celfile_generic.c:30: BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:272:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:294:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:315:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:336:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:357:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:378:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:399:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:420:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:441:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:464:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:488:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:510:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:532:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:553:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:575:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'generic_get_detailed_header_info' at read_celfile_generic.c:597:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1270:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1292:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1313:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1334:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1355:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1376:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1397:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1418:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1439:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1462:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1486:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1508:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1530:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1551:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1573:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In function 'strncpy', BUILDSTDERR: inlined from 'gzgeneric_get_detailed_header_info' at read_celfile_generic.c:1595:3: BUILDSTDERR: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] BUILDSTDERR: 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ity -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_bpmap.c -o read_bpmap.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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_celfile_generic.c -o read_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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_clf.c -o read_clf.o BUILDSTDERR: 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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-ccread_generic.c: In function 'Read_Generic_R_List': BUILDSTDERR: read_generic.c:2030:2: warning: 'return_value' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 2030 | SET_VECTOR_ELT(VECTOR_ELT(temp_sxp2,2),i,generic_data_set_rows_R_List(&my_data_set, i)); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: read_pgf.c:363:12: warning: 'token_ends_with' defined but not used [-Wunused-function] BUILDSTDERR: 363 | static int token_ends_with(char *token, char *ends_in){ BUILDSTDERR: | ^~~~~~~~~~~~~~~ BUILDSTDERR: installing to /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64/usr/lib64/R/library/00LOCK-affyio/00new/affyio/libs BUILDSTDERR: ** R BUILDSTDERR: ** byte-compile and prepare package for lazy loading BUILDSTDERR: ** help BUILDSTDERR: *** installing help indices BUILDSTDERR: finding HTML links ... done BUILDSTDERR: ** building package indices BUILDSTDERR: ** testing if installed package can be loaded from temporary location BUILDSTDERR: ** checking absolute paths in shared objects and dynamic libraries BUILDSTDERR: ** testing if installed package can be loaded from final location BUILDSTDERR: ** testing if installed package keeps a record of temporary installation path BUILDSTDERR: * 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-1.50.0-5.fc31.riscv64/usr/lib64/R/library/R.css + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.50.0-5.fc31 --unique-debug-suffix -1.50.0-5.fc31.riscv64 --unique-debug-src-base R-affyio-1.50.0-5.fc31.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/affyio BUILDSTDERR: 1066 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-python-bytecompile /usr/bin/python 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs 1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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 -g -O2 -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c read_pgf.c -o read_pgf.o gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 converting help for package 'affyio' 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 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64/usr/lib64/R/library/affyio/libs/affyio.so extracting debug info from /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64/usr/lib64/R/library/affyio/libs/affyio.so original debug info size: 768kB, size after compression: 732kB /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.HGvJLI + umask 022 + cd /builddir/build/BUILD + cd affyio + /usr/bin/R CMD check affyio BUILDSTDERR: Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: BUILDSTDERR: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.9/bioc/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/annotation/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/experiment/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PACKAGES' * using log directory '/builddir/build/BUILD/affyio/affyio.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: riscv64-redhat-linux-gnu (64-bit) * using session charset: ASCII * checking for file 'affyio/DESCRIPTION' ... OK * this is package 'affyio' version '1.50.0' * checking package namespace information ... OK * checking package dependencies ... 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: /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] read_bpmap.c:698:20: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] read_bpmap.c:655:20: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] read_bpmap.c:603:18: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] /usr/include/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] /usr/include/bits/string_fortified.h:106:10: 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. * 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 BUILDSTDERR: * checking for BUILDSTDERR: See BUILDSTDERR: '/builddir/build/BUILD/affyio/affyio.Rcheck/00check.log' BUILDSTDERR: for details. + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 eign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING 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 compiled code ... OK * checking examples ... NONE * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs Processing files: R-affyio-1.50.0-5.fc31.riscv64 Provides: R(affyio) = 1.50.0 R-affyio = 1.50.0-5.fc31 R-affyio(riscv-64) = 1.50.0-5.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: 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) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: R-affyio-debugsource-1.50.0-5.fc31.riscv64 Provides: R-affyio-debugsource = 1.50.0-5.fc31 R-affyio-debugsource(riscv-64) = 1.50.0-5.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-affyio-debuginfo-1.50.0-5.fc31.riscv64 Provides: R-affyio-debuginfo = 1.50.0-5.fc31 R-affyio-debuginfo(riscv-64) = 1.50.0-5.fc31 debuginfo(build-id) = ace4f5008512cb738e9bbd98cf21148fd447dae4 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) = 1.50.0-5.fc31 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64 Wrote: /builddir/build/RPMS/R-affyio-1.50.0-5.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-affyio-debuginfo-1.50.0-5.fc31.riscv64.rpm Wrote: /builddir/build/RPMS/R-affyio-debugsource-1.50.0-5.fc31.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.98CiMI + umask 022 + cd /builddir/build/BUILD + cd affyio + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-affyio-1.50.0-5.fc31.riscv64 + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Child return code was: 0