Mock Version: 1.2.14 ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv6hl --nodeps /builddir/build/SPECS/R-Rsamtools.spec'], gid=135user='mockbuild'env={'TERM': 'vt100', 'HOSTNAME': 'mock', 'CCACHE_DIR': '/tmp/ccache', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'SHELL': '/bin/bash', 'CCACHE_UMASK': '002', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'LANG': 'en_US.UTF-8'}logger=timeout=0shell=Falseuid=1000chrootPath='/var/lib/mock/fedora-23-armhfp-pidora-round2-root-22350/root'printOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv6hl --nodeps /builddir/build/SPECS/R-Rsamtools.spec'] with env {'TERM': 'vt100', 'HOSTNAME': 'mock', 'CCACHE_DIR': '/tmp/ccache', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'SHELL': '/bin/bash', 'CCACHE_UMASK': '002', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: armv6hl Building for target armv6hl Wrote: /builddir/build/SRPMS/R-Rsamtools-1.20.2-2bs02npfc23.src.rpm Child return code was: 0 LEAVE do --> ENTER do(['bash', '--login', '-c', "/usr/bin/rpmbuild -bb --target armv6hl --nodeps --define '__spec_check_template exit 0; ' /builddir/build/SPECS/R-Rsamtools.spec "], gid=135user='mockbuild'env={'TERM': 'vt100', 'HOSTNAME': 'mock', 'CCACHE_DIR': '/tmp/ccache', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'SHELL': '/bin/bash', 'CCACHE_UMASK': '002', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'LANG': 'en_US.UTF-8'}logger=timeout=0private_network=Trueshell=Falseuid=1000chrootPath='/var/lib/mock/fedora-23-armhfp-pidora-round2-root-22350/root'printOutput=False) Executing command: ['bash', '--login', '-c', "/usr/bin/rpmbuild -bb --target armv6hl --nodeps --define '__spec_check_template exit 0; ' /builddir/build/SPECS/R-Rsamtools.spec "] with env {'TERM': 'vt100', 'HOSTNAME': 'mock', 'CCACHE_DIR': '/tmp/ccache', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'SHELL': '/bin/bash', 'CCACHE_UMASK': '002', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: armv6hl Building for target armv6hl Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.sUL2o4 + 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_1.20.2.tar.gz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (R-Rsamtools-zlibbioc.patch): + echo 'Patch #0 (R-Rsamtools-zlibbioc.patch):' + /usr/bin/cat /builddir/build/SOURCES/R-Rsamtools-zlibbioc.patch + /usr/bin/patch -p1 -b --suffix .zlibbioc --fuzz=0 patching file Rsamtools/DESCRIPTION patching file Rsamtools/NAMESPACE Patch #1 (R-Rsamtools-system-samtools.patch): + echo 'Patch #1 (R-Rsamtools-system-samtools.patch):' + /usr/bin/cat /builddir/build/SOURCES/R-Rsamtools-system-samtools.patch + /usr/bin/patch -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.6Zkjcb + umask 022 + cd /builddir/build/BUILD Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.0nRTpl + cd Rsamtools + exit 0 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm ++ dirname /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm + cd Rsamtools + mkdir -p /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library + R CMD INSTALL -l /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library Rsamtools * installing *source* package 'Rsamtools' ... ** libs gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c IRanges_stubs.c -o IRanges_stubs.o g++ -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c PileupBuffer.cpp -o PileupBuffer.o g++ -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c PosCacheColl.cpp -o PosCacheColl.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c R_init_Rsamtools.c -o R_init_Rsamtools.o g++ -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c ResultManager.cpp -o ResultManager.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c XVector_stubs.c -o XVector_stubs.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c as_bam.c -o as_bam.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c bam_data.c -o bam_data.o g++ -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c bam_mate_iter.cpp -o bam_mate_iter.o In file included from BamRangeIterator.h:7:0, from bam_mate_iter.cpp:2: BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)': BamIterator.h:81:10: warning: 'BamIterator::iter_done' will be initialized after [-Wreorder] bool iter_done; ^ In file included from BamRangeIterator.h:7:0, from bam_mate_iter.cpp:2: BamIterator.h:29:13: warning: 'bam1_t* BamIterator::bam' [-Wreorder] bam1_t *bam; ^ In file included from BamRangeIterator.h:7:0, from bam_mate_iter.cpp:2: BamIterator.h:84:5: warning: when initialized here [-Wreorder] BamIterator(bamFile bfile, const bam_index_t *bindex) : ^ In file included from BamRangeIterator.h:7:0, from bam_mate_iter.cpp:2: BamIterator.h:29:13: warning: 'BamIterator::bam' will be initialized after [-Wreorder] bam1_t *bam; ^ BamIterator.h:15:14: warning: '_BAM_DATA* BamIterator::bam_data' [-Wreorder] BAM_DATA bam_data; ^ In file included from BamRangeIterator.h:7:0, from bam_mate_iter.cpp:2: BamIterator.h:84:5: warning: when initialized here [-Wreorder] BamIterator(bamFile bfile, const bam_index_t *bindex) : ^ gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c bambuffer.c -o bambuffer.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c bamfile.c -o bamfile.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c bcffile.c -o bcffile.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c encode.c -o encode.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c fafile.c -o fafile.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c io_sam.c -o io_sam.o g++ -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o g++ -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/include" -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c pileup.cpp -o pileup.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c pileupbam.c -o pileupbam.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c samtools_patch.c -o samtools_patch.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c scan_bam_data.c -o scan_bam_data.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c tabixfile.c -o tabixfile.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c tagfilter.c -o tagfilter.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c utilities.c -o utilities.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c zip_compression.c -o zip_compression.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o In file included from /usr/include/limits.h:25:0, from /usr/lib/gcc/armv6hl-redhat-linux-gnueabi/5.2.1/include/limits.h:168, from /usr/lib/gcc/armv6hl-redhat-linux-gnueabi/5.2.1/include/syslimits.h:7, from /usr/lib/gcc/armv6hl-redhat-linux-gnueabi/5.2.1/include/limits.h:34, from /usr/include/zconf.h:395, from /usr/include/zlib.h:34, from samtools/bcftools/vcf.c:3: /usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o In file included from /usr/include/alloca.h:21:0, from samtools/bcftools/bcfutils.c:3: /usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c samtools/bcftools/index.c -o samtools/bcftools/index.o In file included from /usr/include/assert.h:35:0, from samtools/bcftools/index.c:2: /usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^ gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -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 ar: `u' modifier ignored since `D' is the default (see `U') gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c tabix/index.c -o tabix/index.o gcc -I/usr/include/R -DNDEBUG -I/usr/local/include -I"/usr/lib/R/library/S4Vectors/include" -I"/usr/lib/R/library/IRanges/include" -I"/usr/lib/R/library/XVector/include" -I"/usr/lib/R/library/Biostrings/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 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -march=armv6 -mfloat-abi=hard -mfpu=vfp -c tabix/bedidx.c -o tabix/bedidx.o ar -crus libtabix.a tabix/index.o tabix/bedidx.o samtools_patch.o ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p "/builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/include/samtools/bcftools" mkdir -p "/builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/include/tabix" # cp samtools/*.h "/builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/include/samtools/" cp samtools/bcftools/*h "/builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/include/samtools/bcftools/" cp tabix/*h "/builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/include/tabix/" # cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \ # "/builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/include/tabix/" mkdir -p "/builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/usrlib" cp libbcf.a libtabix.a "/builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/usrlib" g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -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 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-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/usrlib/libbcf.a /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/usrlib/libtabix.a -lz -lbam -L/usr/lib/R/lib -lR installing to /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package 'Rsamtools' finding HTML links ... done ApplyPileupsParam-class html BamFile-class html 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: missing file link 'GRanges' scanBam html scanBcf html scanFa html scanTabix html seqnamesTabix html testPairedEndBam html zip html ** building package indices ** installing vignettes ** testing if installed package can be loaded * 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 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-1.20.2-2bs02npfc23.arm/usr/lib/R/library/R.css ~/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/include ~/build/BUILD/Rsamtools + pushd /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/include + 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 .. ~/build/BUILD/Rsamtools + popd + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/Rsamtools extracting debug info from /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm/usr/lib/R/library/Rsamtools/libs/Rsamtools.so dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 590 blocks + /usr/lib/rpm/check-buildroot + /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-java-repack-jars Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.VaAfh7 Processing files: R-Rsamtools-1.20.2-2bs02npfc23.armv6hl Provides: R-Rsamtools = 1.20.2-2bs02npfc23 R-Rsamtools(armv6hl-32) = 1.20.2-2bs02npfc23 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /bin/sh ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libR.so libbam.so.1 libc.so.6 libc.so.6(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libgomp.so.1 libm.so.6 libm.so.6(GLIBC_2.4) libpthread.so.0 libpthread.so.0(GLIBC_2.4) libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.21) libz.so.1 libz.so.1(ZLIB_1.2.3.3) rtld(GNU_HASH) Processing files: R-Rsamtools-devel-1.20.2-2bs02npfc23.armv6hl Provides: R-Rsamtools-devel = 1.20.2-2bs02npfc23 R-Rsamtools-devel(armv6hl-32) = 1.20.2-2bs02npfc23 R-Rsamtools-static = 1.20.2-2bs02npfc23 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsamtools-debuginfo-1.20.2-2bs02npfc23.armv6hl Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm Wrote: /builddir/build/RPMS/R-Rsamtools-1.20.2-2bs02npfc23.armv6hl.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-devel-1.20.2-2bs02npfc23.armv6hl.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-debuginfo-1.20.2-2bs02npfc23.armv6hl.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.AMSXYa + umask 022 + cd /builddir/build/BUILD + cd Rsamtools + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-Rsamtools-1.20.2-2bs02npfc23.arm + exit 0 Child return code was: 0 LEAVE do -->