starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/bin:/gnu/store/v6f44zccwh9z5zk3pjlywjybbi8n2hjh-tar-1.32/bin:/gnu/store/ncydgq2znms5n1d2k5yqshhf58nsixwv-gzip-1.10/bin:/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w48v-bzip2-1.0.8/bin:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/bin:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/bin:/gnu/store/n4n560pfvvw50a9369axw5vj5rrqfj1n-diffutils-3.7/bin:/gnu/store/cd5qf3kcnlq35p9k392pjdpdzpsnds70-patch-2.7.6/bin:/gnu/store/hic7snhayfl7m6cpfqqr73nmm19bpqkg-findutils-4.7.0/bin:/gnu/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/bin:/gnu/store/ishk7fswcs4gkwcp8mh788z4mvvl9bxh-sed-4.8/bin:/gnu/store/bhs4rj58v8j1narb2454raan2ps38xd8-grep-3.4/bin:/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/bin:/gnu/store/hm40bxnv8jxmbc1lpb7zfimii4xm9m81-make-4.3/bin:/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin:/gnu/store/mpa04aq8lblbcviyxywxcsb1zbi0mf39-ld-wrapper-0/bin:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7gkcg3m4-binutils-2.34/bin:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0/bin:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/bin:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/sbin:/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/bin' environment variable `R_LIBS_SITE' set to `/gnu/store/qh6zfmrmb7srqb1h9hgm64gbhp7cm4fg-r-biocgenerics-0.36.1/site-library/:/gnu/store/875k6jgk7jf4ill2q30rb88lpqg2xdf1-r-biocparallel-1.24.1/site-library/:/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/:/gnu/store/8jq1r3kfby23b4afadwfazal6in3saaw-r-bitops-1.0-7/site-library/:/gnu/store/f4dwcz12gdz2xzxr55wz0xnyqq4sm30f-r-genomeinfodb-1.26.7/site-library/:/gnu/store/6sb85f0rv9v0bnqqxfzsn4x42k38bclm-r-genomicranges-1.42.0/site-library/:/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/:/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/:/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/:/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/:/gnu/store/dkh819jzf86ljdm0xf2377zwapd8sg6i-r-bh-1.75.0-0/site-library/:/gnu/store/qpvfkj7bls7jrslk1zxdvwf5hvswk6dw-r-snow-0.4-3/site-library/:/gnu/store/slwl3ygc8wxvzv1q4rp0pvx74k9j4h3a-r-futile-logger-1.4.3/site-library/:/gnu/store/086qgd6pmyrgg3w8q65iyilxc5i8mzvw-r-crayon-1.4.1/site-library/:/gnu/store/ngmpbsrslskyihfi4p64wk618j1cc1yz-r-rcurl-1.95-0.1.2/site-library/:/gnu/store/raqrx9blyby4ldgsa8ay679kdm4j6i53-r-genomeinfodbdata-1.2.0/site-library/:/gnu/store/aq46zkk2mjy3b96876zk4pmbcr8jjl33-r-zlibbioc-1.36.0/site-library/:/gnu/store/ldbi2cnikqpvmq7snd2l5lsi9h7mvgj2-r-lambda-r-1.2.4/site-library/:/gnu/store/8616cafavm8c1gjam26vg0v7x5cxrr21-r-futile-options-1.0.1/site-library/:/gnu/store/q61g7q8jf1kggzpbxnpk8m5nyb6a01li-r-formatr-1.9/site-library/' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w48v-bzip2-1.0.8/include:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/include:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/include:/gnu/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/include:/gnu/store/hm40bxnv8jxmbc1lpb7zfimii4xm9m81-make-4.3/include:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7gkcg3m4-binutils-2.34/include:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0/include:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/include:/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/include:/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/include:/gnu/store/gfapkk5c6hvl1d94m4sqnhn7f9l5gqyh-linux-libre-headers-5.4.20/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w48v-bzip2-1.0.8/include:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/include:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/include:/gnu/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/include:/gnu/store/hm40bxnv8jxmbc1lpb7zfimii4xm9m81-make-4.3/include:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7gkcg3m4-binutils-2.34/include:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0/include/c++:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0/include:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/include:/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/include:/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/include:/gnu/store/gfapkk5c6hvl1d94m4sqnhn7f9l5gqyh-linux-libre-headers-5.4.20/include' environment variable `LIBRARY_PATH' set to `/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib:/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w48v-bzip2-1.0.8/lib:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/lib:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/lib:/gnu/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/lib:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7gkcg3m4-binutils-2.34/lib:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib:/gnu/store/s3dcqzwqaakv1yx37by9chksdbkgih17-glibc-2.31-static/lib:/gnu/store/hwcky7446s952w0mwchhmm211ll07zrq-glibc-utf8-locales-2.31/lib:/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/lib:/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/hwcky7446s952w0mwchhmm211ll07zrq-glibc-utf8-locales-2.31/lib/locale' environment variable `SSL_CERT_DIR' unset environment variable `SSL_CERT_FILE' unset environment variable `CURL_CA_BUNDLE' unset phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'en_US.utf8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' Rsamtools/DESCRIPTION Rsamtools/LICENSE Rsamtools/NAMESPACE Rsamtools/NEWS Rsamtools/R/ Rsamtools/R/AllClasses.R Rsamtools/R/AllGenerics.R Rsamtools/R/asBam.R Rsamtools/R/countBam.R Rsamtools/R/filterBam.R Rsamtools/R/idxstatsBam.R Rsamtools/R/indexBam.R Rsamtools/R/io_bam.R Rsamtools/R/mergeBam.R Rsamtools/R/methods-ApplyPileupsParam.R Rsamtools/R/methods-BamFile.R Rsamtools/R/methods-BamFileList.R Rsamtools/R/methods-BamSampler.R Rsamtools/R/methods-BamViews.R Rsamtools/R/methods-BcfFile.R Rsamtools/R/methods-FaFile.R Rsamtools/R/methods-PileupFiles.R Rsamtools/R/methods-RsamtoolsFile.R Rsamtools/R/methods-RsamtoolsFileList.R Rsamtools/R/methods-ScanBVcfParam.R Rsamtools/R/methods-ScanBamParam.R Rsamtools/R/methods-TabixFile.R Rsamtools/R/phred2ASCIIOffset.R Rsamtools/R/pileup.R Rsamtools/R/pkgconfig.R Rsamtools/R/quickBamFlagSummary.R Rsamtools/R/readPileup.R Rsamtools/R/scanBam.R Rsamtools/R/scanBamHeader.R Rsamtools/R/scanBcf.R Rsamtools/R/scanBcfHeader.R Rsamtools/R/sortBam.R Rsamtools/R/testPairedEndBam.R Rsamtools/R/utilities.R Rsamtools/R/zip_compression.R Rsamtools/R/zzz.R Rsamtools/README.md Rsamtools/build/ Rsamtools/build/vignette.rds Rsamtools/inst/ Rsamtools/inst/doc/ Rsamtools/inst/doc/Rsamtools-Overview.R Rsamtools/inst/doc/Rsamtools-Overview.Rnw Rsamtools/inst/doc/Rsamtools-Overview.pdf Rsamtools/inst/extdata/ Rsamtools/inst/extdata/ce2dict1.fa Rsamtools/inst/extdata/ce2dict1.fa.fai Rsamtools/inst/extdata/ex1.bam Rsamtools/inst/extdata/ex1.bam.bai Rsamtools/inst/extdata/ex1.bcf.gz Rsamtools/inst/extdata/ex1.bcf.gz.csi Rsamtools/inst/extdata/ex1.sam Rsamtools/inst/extdata/ex1.vcf.gz Rsamtools/inst/extdata/ex1.vcf.gz.csi Rsamtools/inst/extdata/example.gtf.gz Rsamtools/inst/extdata/example.gtf.gz.tbi Rsamtools/inst/extdata/example_from_SAM_Spec.bam Rsamtools/inst/extdata/example_from_SAM_Spec.bam.bai Rsamtools/inst/extdata/example_from_SAM_Spec.sam Rsamtools/inst/extdata/no_which_buffered_pileup.bam Rsamtools/inst/extdata/no_which_buffered_pileup.bam.bai Rsamtools/inst/extdata/no_which_buffered_pileup.sam Rsamtools/inst/extdata/no_which_whole_file.bam Rsamtools/inst/extdata/no_which_whole_file.bam.bai Rsamtools/inst/extdata/no_which_whole_file.sam Rsamtools/inst/extdata/olaps.Rda Rsamtools/inst/extdata/pileup.txt Rsamtools/inst/extdata/querybins.bam Rsamtools/inst/extdata/querybins.bam.bai Rsamtools/inst/extdata/querybins.sam Rsamtools/inst/extdata/revbins.bam Rsamtools/inst/extdata/revbins.bam.bai Rsamtools/inst/extdata/revbins.sam Rsamtools/inst/extdata/samtools-github.txt Rsamtools/inst/extdata/slxMaq09_urls.txt Rsamtools/inst/extdata/tagfilter.bam Rsamtools/inst/extdata/tagfilter.bam.bai Rsamtools/inst/extdata/tagfilter.sam Rsamtools/inst/extdata/tiny.bam Rsamtools/inst/extdata/tiny.bam.bai Rsamtools/inst/extdata/tiny.sam Rsamtools/inst/extdata/tophat/ Rsamtools/inst/extdata/tophat/README Rsamtools/inst/extdata/tophat/accepted_hits.sam Rsamtools/inst/extdata/tophat/coverage.wig Rsamtools/inst/extdata/tophat/junctions.bed Rsamtools/inst/scripts/ Rsamtools/inst/scripts/BamViews-1000g.R Rsamtools/inst/scripts/features.R Rsamtools/inst/scripts/remote_test.R Rsamtools/inst/scripts/update-samtools.sh Rsamtools/inst/unitTests/ Rsamtools/inst/unitTests/cases/ Rsamtools/inst/unitTests/cases/RNEXT.bam Rsamtools/inst/unitTests/cases/ex1.sam.gz Rsamtools/inst/unitTests/cases/ex1_noindex.bam Rsamtools/inst/unitTests/cases/ex1_shuf1000.bam Rsamtools/inst/unitTests/cases/ex1_shuf1000.bam.bai Rsamtools/inst/unitTests/cases/ex1_unsort.bam Rsamtools/inst/unitTests/cases/ex1_zero_index.bam.bai Rsamtools/inst/unitTests/cases/no_SAMPLE_header.vcf.gz Rsamtools/inst/unitTests/cases/no_header_line.vcf.gz Rsamtools/inst/unitTests/cases/pileup-no-stars.txt Rsamtools/inst/unitTests/cases/plp_refskip.bam Rsamtools/inst/unitTests/cases/plp_refskip.bam.bai Rsamtools/inst/unitTests/test_BamFile.R Rsamtools/inst/unitTests/test_BamViews.R Rsamtools/inst/unitTests/test_BcfFile.R Rsamtools/inst/unitTests/test_FaFile.R Rsamtools/inst/unitTests/test_RsamtoolsFile.R Rsamtools/inst/unitTests/test_TabixFile.R Rsamtools/inst/unitTests/test_applyPileups.R Rsamtools/inst/unitTests/test_asBam.R Rsamtools/inst/unitTests/test_bam.R Rsamtools/inst/unitTests/test_bam_count.R Rsamtools/inst/unitTests/test_bam_header.R Rsamtools/inst/unitTests/test_compression.R Rsamtools/inst/unitTests/test_mapqfilter.R Rsamtools/inst/unitTests/test_phred2ASCIIOffset.R Rsamtools/inst/unitTests/test_pileup_nowhich.R Rsamtools/inst/unitTests/test_pileup_querybins.R Rsamtools/inst/unitTests/test_pileup_revbins.R Rsamtools/inst/unitTests/test_pileup_single_range.R Rsamtools/inst/unitTests/test_readPileup.R Rsamtools/inst/unitTests/test_scanBamFlag.R Rsamtools/inst/unitTests/test_sortBam_test.R Rsamtools/inst/unitTests/test_tagfilter.R Rsamtools/inst/unitTests/test_testPairedEndBam.R Rsamtools/inst/unitTests/test_utilities.R Rsamtools/man/ Rsamtools/man/ApplyPileupsParam-class.Rd Rsamtools/man/BamFile-class.Rd Rsamtools/man/BamViews-class.Rd Rsamtools/man/BcfFile-class.Rd Rsamtools/man/FaFile-class.Rd Rsamtools/man/PileupFiles-class.Rd Rsamtools/man/Rsamtools-package.Rd Rsamtools/man/RsamtoolsFile-class.Rd Rsamtools/man/RsamtoolsFileList-class.Rd Rsamtools/man/ScanBamParam-class.Rd Rsamtools/man/ScanBcfParam-class.Rd Rsamtools/man/TabixFile-class.Rd Rsamtools/man/applyPileups.Rd Rsamtools/man/defunct.Rd Rsamtools/man/deprecated.Rd Rsamtools/man/headerTabix.Rd Rsamtools/man/indexTabix.Rd Rsamtools/man/pileup.Rd Rsamtools/man/quickBamFlagSummary.Rd Rsamtools/man/readPileup.Rd Rsamtools/man/scanBam.Rd Rsamtools/man/scanBcf.Rd Rsamtools/man/scanFa.Rd Rsamtools/man/scanTabix.Rd Rsamtools/man/seqnamesTabix.Rd Rsamtools/man/testPairedEndBam.Rd Rsamtools/man/zip.Rd Rsamtools/migration_notes.md Rsamtools/src/ Rsamtools/src/BamFileIterator.h Rsamtools/src/BamIterator.h Rsamtools/src/BamRangeIterator.h Rsamtools/src/Biostrings_stubs.c Rsamtools/src/COMPAT_bcf_hdr_read.c Rsamtools/src/COMPAT_bcf_hdr_read.h Rsamtools/src/GenomicPosition.h Rsamtools/src/IRanges_stubs.c Rsamtools/src/Makevars Rsamtools/src/PileupBuffer.cpp Rsamtools/src/PileupBuffer.h Rsamtools/src/PileupBufferShim.h Rsamtools/src/PosCache.h Rsamtools/src/PosCacheColl.cpp Rsamtools/src/PosCacheColl.h Rsamtools/src/R_init_Rsamtools.c Rsamtools/src/ResultManager.cpp Rsamtools/src/ResultManager.h Rsamtools/src/S4Vectors_stubs.c Rsamtools/src/Template.h Rsamtools/src/XVector_stubs.c Rsamtools/src/as_bam.c Rsamtools/src/as_bam.h Rsamtools/src/bam.c Rsamtools/src/bam_data.c Rsamtools/src/bam_data.h Rsamtools/src/bam_mate_iter.cpp Rsamtools/src/bam_mate_iter.h Rsamtools/src/bam_plbuf.c Rsamtools/src/bam_sort.c Rsamtools/src/bambuffer.c Rsamtools/src/bambuffer.h Rsamtools/src/bamfile.c Rsamtools/src/bamfile.h Rsamtools/src/bcffile.c Rsamtools/src/bcffile.h Rsamtools/src/encode.c Rsamtools/src/encode.h Rsamtools/src/fafile.c Rsamtools/src/fafile.h Rsamtools/src/idxstats.c Rsamtools/src/idxstats.h Rsamtools/src/io_sam.c Rsamtools/src/io_sam.h Rsamtools/src/pbuffer_wrapper.cpp Rsamtools/src/pbuffer_wrapper.h Rsamtools/src/pileup.cpp Rsamtools/src/pileup.h Rsamtools/src/pileupbam.c Rsamtools/src/pileupbam.h Rsamtools/src/sam.c Rsamtools/src/sam_opts.c Rsamtools/src/sam_utils.c Rsamtools/src/samtools_patch.c Rsamtools/src/samtools_patch.h Rsamtools/src/scan_bam_data.c Rsamtools/src/scan_bam_data.h Rsamtools/src/tabixfile.c Rsamtools/src/tabixfile.h Rsamtools/src/tagfilter.c Rsamtools/src/tagfilter.h Rsamtools/src/utilities.c Rsamtools/src/utilities.h Rsamtools/src/zip_compression.c Rsamtools/src/zip_compression.h Rsamtools/tests/ Rsamtools/tests/Rsamtools_unit_tests.R Rsamtools/vignettes/ Rsamtools/vignettes/Rsamtools-Overview.Rnw phase `unpack' succeeded after 0.1 seconds starting phase `use-system-zlib' phase `use-system-zlib' succeeded after 0.0 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' patch-shebang: ./inst/scripts/update-samtools.sh: changing `/bin/sh' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/sh' phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' * installing *source* package ‘Rsamtools’ ... ** using staged installation ** libs gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o g++ -std=gnu++11 -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c PileupBuffer.cpp -o PileupBuffer.o g++ -std=gnu++11 -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c PosCacheColl.cpp -o PosCacheColl.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o g++ -std=gnu++11 -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c ResultManager.cpp -o ResultManager.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c as_bam.c -o as_bam.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bam.c -o bam.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bam_data.c -o bam_data.o g++ -std=gnu++11 -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bam_mate_iter.cpp -o bam_mate_iter.o In file included from /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/sam.h:29:0, from Template.h:9, from BamIterator.h:10, from BamRangeIterator.h:7, from bam_mate_iter.cpp:2: BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’: /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result] #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) ~~~~~~~~~^~~~~~~~~~~~~~ BamRangeIterator.h:138:9: note: in expansion of macro ‘bam_seek’ bam_seek(bfile, pos, SEEK_SET); ^~~~~~~~ BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’: /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result] #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) ~~~~~~~~~^~~~~~~~~~~~~~ BamIterator.h:87:9: note: in expansion of macro ‘bam_seek’ bam_seek(bfile, 0, 0); ^~~~~~~~ gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bam_plbuf.c -o bam_plbuf.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bam_sort.c -o bam_sort.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bambuffer.c -o bambuffer.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bamfile.c -o bamfile.o bamfile.c: In function ‘bamfile_isincomplete’: bamfile.c:168:13: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] bgzf_seek(bfile->file->x.bam, offset, SEEK_SET); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bcffile.c -o bcffile.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c encode.c -o encode.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c fafile.c -o fafile.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c idxstats.c -o idxstats.o In file included from /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/sam.h:29:0, from bamfile.h:5, from idxstats.c:1: idxstats.c: In function ‘idxstats_bamfile’: /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) ^~~~~~~~~~~~~~~~~~~~~~~ idxstats.c:20:5: note: in expansion of macro ‘bam_seek’ bam_seek(fp, 0, 0); ^~~~~~~~ gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c io_sam.c -o io_sam.o In file included from /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/sam.h:29:0, from io_sam.c:2: io_sam.c: In function ‘_scan_bam_all’: /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) ^~~~~~~~~~~~~~~~~~~~~~~ io_sam.c:304:5: note: in expansion of macro ‘bam_seek’ bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET); ^~~~~~~~ g++ -std=gnu++11 -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o g++ -std=gnu++11 -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c pileup.cpp -o pileup.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c pileupbam.c -o pileupbam.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c sam.c -o sam.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c sam_opts.c -o sam_opts.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c sam_utils.c -o sam_utils.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c samtools_patch.c -o samtools_patch.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c scan_bam_data.c -o scan_bam_data.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c tabixfile.c -o tabixfile.o tabixfile.c: In function ‘index_tabix’: tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations] if (bgzf_is_bgzf(fn) != 1) ^~ In file included from tabixfile.c:3:0: /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); ^~~~~~~~~~~~ gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c tagfilter.c -o tagfilter.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c utilities.c -o utilities.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include' -I'/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/S4Vectors/include' -I'/gnu/store/i4hzw1q7b6mwd7qvvgib35v9lj4l1gaf-r-iranges-2.24.1/site-library/IRanges/include' -I'/gnu/store/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/site-library/XVector/include' -I'/gnu/store/4299v5359zqkjwsmlldnj8sjjjsdc4zi-r-biostrings-2.58.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c zip_compression.c -o zip_compression.o g++ -std=gnu++11 -shared -L/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/lib -L/usr/local/lib -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/lib -lR installing to /gnu/store/ad87j9w6kv679sj71dyv3vdxwr5yi5ia-r-rsamtools-2.6.0/site-library/00LOCK-Rsamtools/00new/Rsamtools/libs ** R ** inst ** tests ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsamtools) phase `install' succeeded after 57.2 seconds starting phase `check' Testing examples for package ‘Rsamtools’ phase `check' succeeded after 7.8 seconds starting phase `patch-shebangs' phase `patch-shebangs' succeeded after 0.0 seconds starting phase `strip' phase `strip' succeeded after 0.0 seconds starting phase `validate-runpath' phase `validate-runpath' succeeded after 0.0 seconds starting phase `validate-documentation-location' phase `validate-documentation-location' succeeded after 0.0 seconds starting phase `delete-info-dir-file' phase `delete-info-dir-file' succeeded after 0.0 seconds starting phase `patch-dot-desktop-files' phase `patch-dot-desktop-files' succeeded after 0.0 seconds starting phase `install-license-files' installing 1 license files from '.' phase `install-license-files' succeeded after 0.0 seconds starting phase `reset-gzip-timestamps' phase `reset-gzip-timestamps' succeeded after 0.0 seconds starting phase `compress-documentation' phase `compress-documentation' succeeded after 0.0 seconds