Mock Version: 1.4.21 Mock Version: 1.4.21 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-GenomicRanges.spec'], chrootPath='/var/lib/mock/f33-build-178552-44995/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=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-GenomicRanges.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=1580169600 Wrote: /builddir/build/SRPMS/R-GenomicRanges-1.38.0-2.fc33.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-GenomicRanges.spec'], chrootPath='/var/lib/mock/f33-build-178552-44995/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=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-GenomicRanges.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=1580169600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.Ii9rwI + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf GenomicRanges + /usr/bin/mkdir -p GenomicRanges + cd GenomicRanges + /usr/bin/gzip -dc /builddir/build/SOURCES/GenomicRanges_1.38.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.7eeadK + umask 022 + cd /builddir/build/BUILD + cd GenomicRanges + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.CajdCI + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64 ++ dirname /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64 + cd GenomicRanges + rm -rf /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64 + mkdir -p /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64/usr/lib64/R/library + /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64/usr/lib64/R/library GenomicRanges * installing *source* package 'GenomicRanges' ... ** using staged installation ** libs gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I/usr/local/include -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 IRanges_stubs.c -o IRanges_stubs.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I/usr/local/include -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 R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I/usr/local/include -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 S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I/usr/local/include -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 transcript_utils.c -o transcript_utils.o transcript_utils.c: In function 'tlocs2rlocs': transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized] 143 | return on_minus_strand ? end - tloc : start + tloc; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c:120:17: note: 'start' was declared here 120 | int nexons, j, start, end, width; | ^~~~~ transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized] 143 | return on_minus_strand ? end - tloc : start + tloc; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c:120:24: note: 'end' was declared here 120 | int nexons, j, start, end, width; | ^~~ 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 GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64/usr/lib64/R/library/00LOCK-GenomicRanges/00new/GenomicRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package 'BiocGenerics' was built under R version 3.6.2 2: package 'GenomeInfoDb' was built under R version 3.6.2 ** help *** installing help indices converting help for package 'GenomicRanges' finding HTML links ... done DelegatingGenomicRanges-class html GNCList-class html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GNCList-class.Rd:46: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GNCList-class.Rd:47: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GNCList-class.Rd:48: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GNCList-class.Rd:49: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GNCList-class.Rd:55: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic GPos-class html finding level-2 HTML links ... done Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:73: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:74: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:74: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:77: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:92: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:94: file link 'UnstitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:95: file link 'StitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:112: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:132: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:133: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:134: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:136: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:148: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:150: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:151: file link 'isCircular' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:152: file link 'genome' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:202: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:225: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GPos-class.Rd:232: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic GRanges-class html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:100: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:102: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:104: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:106: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:124: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:128: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:132: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:142: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:183: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:189: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:230: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:289: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:313: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:356: file link 'ManyToOneGrouping' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:363: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:369: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:371: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:408: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:436: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:476: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:485: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:493: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:495: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:530: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:530: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRanges-class.Rd:531: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic GRangesFactor-class html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:28: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:31: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:32: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:41: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:66: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:69: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:78: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:88: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:93: file link 'unfactor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:98: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:107: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:114: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:118: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:127: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesFactor-class.Rd:130: file link 'anyDuplicated' in package 'BiocGenerics' does not exist and so has been treated as a topic GRangesList-class html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesList-class.Rd:194: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesList-class.Rd:347: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesList-class.Rd:350: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GRangesList-class.Rd:353: file link 'DataFrameList' in package 'IRanges' does not exist and so has been treated as a topic GenomicRanges-comparison html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GenomicRanges-comparison.Rd:115: file link 'reduce' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GenomicRanges-comparison.Rd:115: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic GenomicRangesList-class html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GenomicRangesList-class.Rd:91: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GenomicRangesList-class.Rd:91: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GenomicRangesList-class.Rd:92: missing file link 'RangesList' Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/GenomicRangesList-class.Rd:92: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic absoluteRanges html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/absoluteRanges.Rd:39: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/absoluteRanges.Rd:41: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/absoluteRanges.Rd:50: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/absoluteRanges.Rd:65: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/absoluteRanges.Rd:86: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic constraint html coverage-methods html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:13: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:16: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:17: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:17: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:46: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:58: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:62: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:73: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:81: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/coverage-methods.Rd:86: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic findOverlaps-methods html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/findOverlaps-methods.Rd:25: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/findOverlaps-methods.Rd:26: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/findOverlaps-methods.Rd:27: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/findOverlaps-methods.Rd:59: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/findOverlaps-methods.Rd:103: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/findOverlaps-methods.Rd:117: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic genomic-range-squeezers html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:16: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:17: file link 'rglist' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:19: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:19: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:21: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:21: file link 'rglist' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:32: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:37: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:40: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomic-range-squeezers.Rd:46: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic genomicvars html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomicvars.Rd:20: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomicvars.Rd:49: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomicvars.Rd:60: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomicvars.Rd:80: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomicvars.Rd:91: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/genomicvars.Rd:105: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic inter-range-methods html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/inter-range-methods.Rd:95: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/inter-range-methods.Rd:103: file link 'gaps' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/inter-range-methods.Rd:112: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/inter-range-methods.Rd:136: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/inter-range-methods.Rd:144: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic intra-range-methods html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/intra-range-methods.Rd:83: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/intra-range-methods.Rd:87: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/intra-range-methods.Rd:91: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/intra-range-methods.Rd:160: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic makeGRangesFromDataFrame html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/makeGRangesFromDataFrame.Rd:16: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/makeGRangesFromDataFrame.Rd:37: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/makeGRangesFromDataFrame.Rd:54: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/makeGRangesFromDataFrame.Rd:122: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/makeGRangesFromDataFrame.Rd:136: file link 'Seqinfo' in package 'GenomeInfoDb' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/makeGRangesFromDataFrame.Rd:148: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic makeGRangesListFromDataFrame html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/makeGRangesListFromDataFrame.Rd:15: file link 'split' in package 'S4Vectors' does not exist and so has been treated as a topic nearest-methods html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/nearest-methods.Rd:69: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/nearest-methods.Rd:142: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/nearest-methods.Rd:145: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/nearest-methods.Rd:158: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/nearest-methods.Rd:159: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic phicoef html setops-methods html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/setops-methods.Rd:45: file link 'punion' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/setops-methods.Rd:45: file link 'pintersect' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/setops-methods.Rd:46: file link 'psetdiff' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/setops-methods.Rd:46: file link 'pgap' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/setops-methods.Rd:47: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/setops-methods.Rd:155: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/setops-methods.Rd:156: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/setops-methods.Rd:167: file link 'mendoapply' in package 'S4Vectors' does not exist and so has been treated as a topic strand-utils html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/strand-utils.Rd:52: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/strand-utils.Rd:64: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/strand-utils.Rd:65: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/strand-utils.Rd:73: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/strand-utils.Rd:96: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic tile-methods html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/tile-methods.Rd:12: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/tile-methods.Rd:12: file link 'slidingWindows' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/tile-methods.Rd:30: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/tile-methods.Rd:35: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/tile-methods.Rd:65: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic tileGenome html Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/tileGenome.Rd:68: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/GenomicRanges/GenomicRanges/man/tileGenome.Rd:70: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package 'BiocGenerics' was built under R version 3.6.2 Warning: package 'GenomeInfoDb' was built under R version 3.6.2 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: package 'BiocGenerics' was built under R version 3.6.2 Warning: package 'GenomeInfoDb' was built under R version 3.6.2 ** testing if installed package keeps a record of temporary installation path * DONE (GenomicRanges) + test -d GenomicRanges/src + cd GenomicRanges/src + rm -f IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o GenomicRanges.so + rm -f /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64/usr/lib64/R/library/R.css + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.38.0-2.fc33 --unique-debug-suffix -1.38.0-2.fc33.riscv64 --unique-debug-src-base R-GenomicRanges-1.38.0-2.fc33.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/GenomicRanges explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64/usr/lib64/R/library/GenomicRanges/libs/GenomicRanges.so extracting debug info from /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64/usr/lib64/R/library/GenomicRanges/libs/GenomicRanges.so original debug info size: 184kB, size after compression: 184kB /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 13 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-python-bytecompile /usr/bin/python 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.DmywiH + umask 022 + cd /builddir/build/BUILD + cd GenomicRanges + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-GenomicRanges-1.38.0-2.fc33.riscv64 Provides: R(GenomicRanges) = 1.38.0 R-GenomicRanges = 1.38.0-2.fc33 R-GenomicRanges(riscv-64) = 1.38.0-2.fc33 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(BiocGenerics) >= 0.25.3 R(GenomeInfoDb) >= 1.15.2 R(IRanges) >= 2.19.9 R(S4Vectors) >= 0.23.19 R(XVector) >= 0.19.8 R(methods) R(stats) R(stats4) R(utils) R-core >= 2.10 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) rtld(GNU_HASH) Suggests: R(AnnotationDbi) R(AnnotationHub) R(BSgenome) R(BSgenome.Hsapiens.UCSC.hg19) R(BSgenome.Mmusculus.UCSC.mm10) R(BSgenome.Scerevisiae.UCSC.sacCer2) R(Biobase) R(BiocStyle) R(Biostrings) >= 2.25.3 R(DESeq2) R(DEXSeq) R(GenomicAlignments) R(GenomicFeatures) R(Gviz) R(KEGG.db) R(KEGGgraph) R(Matrix) R(RNAseqData.HNRNPC.bam.chr14) R(RUnit) R(Rsamtools) >= 1.13.53 R(SummarizedExperiment) >= 0.1.5 R(TxDb.Athaliana.BioMart.plantsmart22) R(TxDb.Dmelanogaster.UCSC.dm3.ensGene) R(TxDb.Hsapiens.UCSC.hg19.knownGene) R(TxDb.Mmusculus.UCSC.mm10.knownGene) R(VariantAnnotation) R(annotate) R(digest) R(edgeR) R(hgu95av2.db) R(hgu95av2probe) R(knitr) R(pasillaBamSubset) R(rtracklayer) Processing files: R-GenomicRanges-debugsource-1.38.0-2.fc33.riscv64 Provides: R-GenomicRanges-debugsource = 1.38.0-2.fc33 R-GenomicRanges-debugsource(riscv-64) = 1.38.0-2.fc33 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-GenomicRanges-debuginfo-1.38.0-2.fc33.riscv64 Provides: R-GenomicRanges-debuginfo = 1.38.0-2.fc33 R-GenomicRanges-debuginfo(riscv-64) = 1.38.0-2.fc33 debuginfo(build-id) = 9c3785bb7603bc4ed20850654f176506e66f8c87 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-GenomicRanges-debugsource(riscv-64) = 1.38.0-2.fc33 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64 Wrote: /builddir/build/RPMS/R-GenomicRanges-debugsource-1.38.0-2.fc33.riscv64.rpm Wrote: /builddir/build/RPMS/R-GenomicRanges-debuginfo-1.38.0-2.fc33.riscv64.rpm Wrote: /builddir/build/RPMS/R-GenomicRanges-1.38.0-2.fc33.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.SdoTyI + umask 022 + cd /builddir/build/BUILD + cd GenomicRanges + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-GenomicRanges-1.38.0-2.fc33.riscv64 + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0