Mock Version: 1.4.9 Mock Version: 1.4.9 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-Rsamtools.spec'], chrootPath='/var/lib/mock/f29-build-10245-4629/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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/R-Rsamtools.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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False Building target platforms: riscv64 Building for target riscv64 Wrote: /builddir/build/SRPMS/R-Rsamtools-1.32.0-1.fc29.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-Rsamtools.spec'], chrootPath='/var/lib/mock/f29-build-10245-4629/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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/R-Rsamtools.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', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False Building target platforms: riscv64 Building for target riscv64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.X1DJaT + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf Rsamtools + /usr/bin/mkdir -p Rsamtools + cd Rsamtools + /usr/bin/gzip -dc /builddir/build/SOURCES/Rsamtools_1.32.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (R-Rsamtools-zlibbioc.patch):' Patch #0 (R-Rsamtools-zlibbioc.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .zlibbioc --fuzz=0 patching file Rsamtools/DESCRIPTION patching file Rsamtools/NAMESPACE + echo 'Patch #1 (R-Rsamtools-system-samtools.patch):' Patch #1 (R-Rsamtools-system-samtools.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .system-samtools --fuzz=0 patching file Rsamtools/src/Makevars.common patching file Rsamtools/src/Makevars patching file Rsamtools/src/samtools/bcftools/bcf.h + rm -rf Rsamtools/src/samtools/bam.h Rsamtools/src/samtools/bam_endian.h Rsamtools/src/samtools/bgzf.h Rsamtools/src/samtools/faidx.h Rsamtools/src/samtools/kaln.h Rsamtools/src/samtools/khash.h Rsamtools/src/samtools/knetfile.h Rsamtools/src/samtools/kprobaln.h Rsamtools/src/samtools/kseq.h Rsamtools/src/samtools/ksort.h Rsamtools/src/samtools/kstring.h Rsamtools/src/samtools/razf.h Rsamtools/src/samtools/sam.h Rsamtools/src/samtools/sam_header.h Rsamtools/src/samtools/bam.c Rsamtools/src/samtools/bam_aux.c Rsamtools/src/samtools/bam_import.c Rsamtools/src/samtools/bam_index.c Rsamtools/src/samtools/bam_lpileup.c Rsamtools/src/samtools/bam_md.c Rsamtools/src/samtools/bam_pileup.c Rsamtools/src/samtools/bam_reheader.c Rsamtools/src/samtools/bam_sort.c Rsamtools/src/samtools/bgzf.c Rsamtools/src/samtools/faidx.c Rsamtools/src/samtools/knetfile.c Rsamtools/src/samtools/kprobaln.c Rsamtools/src/samtools/kstring.c Rsamtools/src/samtools/razf.c Rsamtools/src/samtools/sam.c Rsamtools/src/samtools/sam_header.c + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.cidmnr + umask 022 + cd /builddir/build/BUILD + cd Rsamtools + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.5cjCsc + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64 + cd Rsamtools + mkdir -p /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library + R CMD INSTALL -l /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library Rsamtools BUILDSTDERR: * installing *source* package 'Rsamtools' ... BUILDSTDERR: ** libs gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 g++ -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/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 PileupBuffer.cpp -o PileupBuffer.o g++ -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/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 PosCacheColl.cpp -o PosCacheColl.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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_Rsamtools.c -o R_init_Rsamtools.o g++ -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/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 ResultManager.cpp -o ResultManager.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 XVector_stubs.c -o XVector_stubs.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 as_bam.c -o as_bam.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 bam_data.c -o bam_data.o g++ -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/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 bam_mate_iter.cpp -o bam_mate_iter.o BUILDSTDERR: In file included from BamRangeIterator.h:7, BUILDSTDERR: from bam_mate_iter.cpp:2: BUILDSTDERR: BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)': BUILDSTDERR: BamIterator.h:80:10: warning: 'BamIterator::iter_done' will be initialized after [-Wreorder] BUILDSTDERR: bool iter_done; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: BamIterator.h:29:13: warning: 'bam1_t* BamIterator::bam' [-Wreorder] BUILDSTDERR: bam1_t *bam; BUILDSTDERR: ^~~ BUILDSTDERR: BamIterator.h:83:5: warning: when initialized here [-Wreorder] BUILDSTDERR: BamIterator(bamFile bfile, const bam_index_t *bindex) : BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: BamIterator.h:29:13: warning: 'BamIterator::bam' will be initialized after [-Wreorder] BUILDSTDERR: bam1_t *bam; BUILDSTDERR: ^~~ BUILDSTDERR: BamIterator.h:15:14: warning: '_BAM_DATA* BamIterator::bam_data' [-Wreorder] BUILDSTDERR: BAM_DATA bam_data; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: BamIterator.h:83:5: warning: when initialized here [-Wreorder] BUILDSTDERR: BamIterator(bamFile bfile, const bam_index_t *bindex) : BUILDSTDERR: ^~~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 bambuffer.c -o bambuffer.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 bamfile.c -o bamfile.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 bcffile.c -o bcffile.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 encode.c -o encode.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 fafile.c -o fafile.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 idxstats.c -o idxstats.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 io_sam.c -o io_sam.o g++ -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/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 pbuffer_wrapper.cpp -o pbuffer_wrapper.o g++ -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/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 pileup.cpp -o pileup.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 pileupbam.c -o pileupbam.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 samtools_patch.c -o samtools_patch.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 scan_bam_data.c -o scan_bam_data.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 tabixfile.c -o tabixfile.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 tagfilter.c -o tagfilter.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 utilities.c -o utilities.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 zip_compression.c -o zip_compression.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o BUILDSTDERR: In file included from /usr/include/bits/libc-header-start.h:33, BUILDSTDERR: from /usr/include/limits.h:26, BUILDSTDERR: from /usr/lib/gcc/riscv64-redhat-linux/8/include/limits.h:194, BUILDSTDERR: from /usr/lib/gcc/riscv64-redhat-linux/8/include/syslimits.h:7, BUILDSTDERR: from /usr/lib/gcc/riscv64-redhat-linux/8/include/limits.h:34, BUILDSTDERR: from /usr/include/zconf.h:418, BUILDSTDERR: from /usr/include/zlib.h:34, BUILDSTDERR: from samtools/bcftools/vcf.c:3: BUILDSTDERR: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] BUILDSTDERR: # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" BUILDSTDERR: ^~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o BUILDSTDERR: In file included from /usr/include/alloca.h:21, BUILDSTDERR: from samtools/bcftools/bcfutils.c:3: BUILDSTDERR: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] BUILDSTDERR: # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" BUILDSTDERR: ^~~~~~~ BUILDSTDERR: samtools/bcftools/bcfutils.c: In function 'bcf_fix_gt': BUILDSTDERR: samtools/bcftools/bcfutils.c:259:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: else BUILDSTDERR: ^~~~ BUILDSTDERR: samtools/bcftools/bcfutils.c:261:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' BUILDSTDERR: b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':'; BUILDSTDERR: ^ gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/index.c -o samtools/bcftools/index.o BUILDSTDERR: In file included from /usr/include/assert.h:35, BUILDSTDERR: from samtools/bcftools/index.c:2: BUILDSTDERR: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] BUILDSTDERR: # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" BUILDSTDERR: ^~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/fet.c -o samtools/bcftools/fet.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 tabix/index.c -o tabix/index.o gcc -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/S4Vectors/include" -I"/usr/lib64/R/library/IRanges/include" -I"/usr/lib64/R/library/XVector/include" -I"/usr/lib64/R/library/Biostrings/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix -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 tabix/bedidx.c -o tabix/bedidx.o ar -crus libtabix.a tabix/index.o tabix/bedidx.o samtools_patch.o mkdir -p "/builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/include/samtools/bcftools" mkdir -p "/builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/include/tabix" # cp samtools/*.h "/builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/include/samtools/" cp samtools/bcftools/*h "/builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/include/samtools/bcftools/" cp tabix/*h "/builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/include/tabix/" # cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \ # "/builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/include/tabix/" mkdir -p "/builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/usrlib" cp libbcf.a libtabix.a "/builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/usrlib" g++ -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp -lbam /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/usrlib/libbcf.a /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/usrlib/libtabix.a -lz -lbam -L/usr/lib64/R/lib -lR BUILDSTDERR: installing to /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/libs BUILDSTDERR: ** R BUILDSTDERR: ** inst BUILDSTDERR: ** byte-compile and prepare package for lazy loading BUILDSTDERR: ** help BUILDSTDERR: *** installing help indices converting help for package 'Rsamtools' BUILDSTDERR: finding HTML links ... done ApplyPileupsParam-class html BUILDSTDERR: BamFile-class html BUILDSTDERR: finding level-2 HTML links ... done BamViews-class html BcfFile-class html FaFile-class html PileupFiles-class html Rsamtools-package html RsamtoolsFile-class html RsamtoolsFileList-class html ScanBamParam-class html ScanBcfParam-class html TabixFile-class html applyPileups html defunct html deprecated html headerTabix html indexTabix html pileup html quickBamFlagSummary html readPileup html Rd warning: /builddir/build/BUILD/Rsamtools/Rsamtools/man/readPileup.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic scanBam html scanBcf html scanFa html scanTabix html seqnamesTabix html testPairedEndBam html zip html BUILDSTDERR: ** building package indices BUILDSTDERR: ** installing vignettes BUILDSTDERR: ** testing if installed package can be loaded BUILDSTDERR: * DONE (Rsamtools) + test -d Rsamtools/src + cd Rsamtools/src + rm -f Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o Rsamtools.so + rm -f /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/R.css + pushd /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/include ~/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/include ~/build/BUILD/Rsamtools + cd samtools + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/bam.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/bam2bcf.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/bam_endian.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/bam_tview.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/bgzf.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/errmod.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/faidx.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/kaln.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/khash.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/klist.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/knetfile.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/kprobaln.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/kseq.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/ksort.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/kstring.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/razf.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/sam.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/sam_header.h . + for i in /usr/include/samtools/*.h + ln -s /usr/include/samtools/sample.h . + cd .. + cd tabix + ln -s /usr/include/samtools/bgzf.h . + ln -s /usr/include/samtools/kstring.h . + ln -s /usr/include/samtools/knetfile.h . + cd .. + popd ~/build/BUILD/Rsamtools + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.32.0-1.fc29 --unique-debug-suffix -1.32.0-1.fc29.riscv64 --unique-debug-src-base R-Rsamtools-1.32.0-1.fc29.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/Rsamtools extracting debug info from /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64/usr/lib64/R/library/Rsamtools/libs/Rsamtools.so /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. BUILDSTDERR: 611 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig BUILDSTDERR: /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.DK1eiM Processing files: R-Rsamtools-1.32.0-1.fc29.riscv64 Provides: R-Rsamtools = 1.32.0-1.fc29 R-Rsamtools(riscv-64) = 1.32.0-1.fc29 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /bin/sh ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libbam.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.4)(64bit) libgomp.so.1()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.27)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) rtld(GNU_HASH) Processing files: R-Rsamtools-devel-1.32.0-1.fc29.riscv64 Provides: R-Rsamtools-devel = 1.32.0-1.fc29 R-Rsamtools-devel(riscv-64) = 1.32.0-1.fc29 R-Rsamtools-static = 1.32.0-1.fc29 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsamtools-debugsource-1.32.0-1.fc29.riscv64 Provides: R-Rsamtools-debugsource = 1.32.0-1.fc29 R-Rsamtools-debugsource(riscv-64) = 1.32.0-1.fc29 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsamtools-debuginfo-1.32.0-1.fc29.riscv64 Provides: R-Rsamtools-debuginfo = 1.32.0-1.fc29 R-Rsamtools-debuginfo(riscv-64) = 1.32.0-1.fc29 debuginfo(build-id) = c91102e360add85350155d1054f72ffd7b2e4a6c Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-Rsamtools-debugsource(riscv-64) = 1.32.0-1.fc29 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64 Wrote: /builddir/build/RPMS/R-Rsamtools-1.32.0-1.fc29.riscv64.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-devel-1.32.0-1.fc29.riscv64.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-debugsource-1.32.0-1.fc29.riscv64.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-debuginfo-1.32.0-1.fc29.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.bFla55 + umask 022 + cd /builddir/build/BUILD + cd Rsamtools + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-Rsamtools-1.32.0-1.fc29.riscv64 + exit 0 Child return code was: 0