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/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/bin:/gnu/store/ikc2qn1h260f8mdhjz2cwndv2i7n753z-tar-1.34/bin:/gnu/store/v5l2251ck0r4n3w2rjw3l5dzyqsb9zj1-gzip-1.10/bin:/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/bin:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/bin:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/bin:/gnu/store/s49sxmz9g4xmzz222cay9k04ziy3qgmj-diffutils-3.8/bin:/gnu/store/m96snvbl92ivkd32giqh5f3d21bc2n5x-patch-2.7.6/bin:/gnu/store/l8l2y2dlya5rs9hfypmcb4saay7iwn0q-findutils-4.8.0/bin:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/bin:/gnu/store/7cddr79rydhc1m4hxr921mq17pz1jj3z-sed-4.8/bin:/gnu/store/ldkm5jwql0qsrfh3ax6rljjsrk0jzv7z-grep-3.6/bin:/gnu/store/25gv43v5rm05i26z39ajrd6nsxa5r461-coreutils-8.32/bin:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/bin:/gnu/store/vx6vfbmmazvfi7vp8xyjn2mcyylvw9gn-bash-minimal-5.1.8/bin:/gnu/store/k452f0r5bk6n0cbsf5ndxbp5qcf6bpfw-ld-wrapper-0/bin:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/bin:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/bin:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/sbin:/gnu/store/6r82375s1fx3363k6wk5f16z8xvwzmj0-curl-7.79.1/bin' environment variable `R_LIBS_SITE' set to `/gnu/store/drxhpk02mipa2c32hsyabzjhvbg9dhsl-r-biocgenerics-0.40.0/site-library/:/gnu/store/9glyi6mj3swv7bdfnpivhmxjb12yy8ls-r-biocparallel-1.28.3/site-library/:/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/:/gnu/store/srx83l9sis96gvals5096wshbgnp3a04-r-bitops-1.0-7/site-library/:/gnu/store/k1c9p1zgsq151hw94d58yv9k56mmf1b2-r-genomeinfodb-1.30.0/site-library/:/gnu/store/v2cs3a5kfi3i8jm6nvk9abzjpckaq8r4-r-genomicranges-1.46.1/site-library/:/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/:/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/:/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/:/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/:/gnu/store/rnp9gnw0wnik8zsw335b307nq43d2mzq-r-bh-1.78.0-0/site-library/:/gnu/store/dbi804fi6afli4k3h91sd81dk1bc4akn-r-snow-0.4-4/site-library/:/gnu/store/w7v75lxdscadvcs1ib0k5rnhwgcvf5li-r-futile-logger-1.4.3/site-library/:/gnu/store/dy1gxq50zwjkjra1in8mjw4n7g73q0f0-r-crayon-1.4.2/site-library/:/gnu/store/cy8ff46y25km96d5gcsr26gmgaiga4ps-r-rcurl-1.95-0.1.2/site-library/:/gnu/store/3nq8hfik9mmlwc4j4hwil6awbjz348x7-r-genomeinfodbdata-1.2.0/site-library/:/gnu/store/vzz31h3h6i3s2bwx1grdcnsbbx6102h9-r-zlibbioc-1.40.0/site-library/:/gnu/store/0gxq4547vip1q7jnl38hzic5cmq33c3d-r-lambda-r-1.2.4/site-library/:/gnu/store/dwc1ix6dmpxc9g7rwxa0nylrk8fm9m5z-r-futile-options-1.0.1/site-library/:/gnu/store/r18cy9q86li6v24vj39ngx7kdkmly6ix-r-formatr-1.11/site-library/' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/include:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/include:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/include:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/include:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/include:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/include:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/include:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/include:/gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/include:/gnu/store/6r82375s1fx3363k6wk5f16z8xvwzmj0-curl-7.79.1/include:/gnu/store/99a2njzz22dkzd8pz75fsi5nbgv9ww0x-linux-libre-headers-5.10.35/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/include:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/include:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/include:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/include:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/include:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/include:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/include/c++:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/include:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/include:/gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/include:/gnu/store/6r82375s1fx3363k6wk5f16z8xvwzmj0-curl-7.79.1/include:/gnu/store/99a2njzz22dkzd8pz75fsi5nbgv9ww0x-linux-libre-headers-5.10.35/include' environment variable `LIBRARY_PATH' set to `/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib:/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/lib:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/lib:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/lib:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/lib:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/lib:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/lib:/gnu/store/3ywv7s8d38rgcq7ljmc1s084358a2m3h-glibc-2.33-static/lib:/gnu/store/0brdikxqk59hdr47qabcm3sya001d8vf-glibc-utf8-locales-2.33/lib:/gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/lib:/gnu/store/6r82375s1fx3363k6wk5f16z8xvwzmj0-curl-7.79.1/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/0brdikxqk59hdr47qabcm3sya001d8vf-glibc-utf8-locales-2.33/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 0.0 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/vx6vfbmmazvfi7vp8xyjn2mcyylvw9gn-bash-minimal-5.1.8/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/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/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/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o g++ -std=gnu++14 -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c PileupBuffer.cpp -o PileupBuffer.o g++ -std=gnu++14 -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c PosCacheColl.cpp -o PosCacheColl.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o g++ -std=gnu++14 -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c ResultManager.cpp -o ResultManager.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c as_bam.c -o as_bam.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bam.c -o bam.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bam_data.c -o bam_data.o g++ -std=gnu++14 -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/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/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include/sam.h:29, 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/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/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] 57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ~~~~~~~~~^~~~~~~~~~~~~~ BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’ 138 | (void) bam_seek(bfile, pos, SEEK_SET); | ^~~~~~~~ BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’: /gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/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] 57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ~~~~~~~~~^~~~~~~~~~~~~~ BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’ 87 | (void) bam_seek(bfile, 0, 0); | ^~~~~~~~ gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bam_plbuf.c -o bam_plbuf.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bam_sort.c -o bam_sort.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bambuffer.c -o bambuffer.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/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:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 168 | (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c bcffile.c -o bcffile.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c encode.c -o encode.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c fafile.c -o fafile.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c idxstats.c -o idxstats.o In file included from /gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include/sam.h:29, from bamfile.h:5, from idxstats.c:1: idxstats.c: In function ‘idxstats_bamfile’: /gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ^~~~~~~~~~~~~~~~~~~~~~~ idxstats.c:20:12: note: in expansion of macro ‘bam_seek’ 20 | (void) bam_seek(fp, 0, 0); | ^~~~~~~~ gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/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/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include/sam.h:29, from io_sam.c:2: io_sam.c: In function ‘_scan_bam_all’: /gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ^~~~~~~~~~~~~~~~~~~~~~~ io_sam.c:304:12: note: in expansion of macro ‘bam_seek’ 304 | (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET); | ^~~~~~~~ g++ -std=gnu++14 -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o g++ -std=gnu++14 -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c pileup.cpp -o pileup.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c pileupbam.c -o pileupbam.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c sam.c -o sam.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c sam_opts.c -o sam_opts.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c sam_utils.c -o sam_utils.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c samtools_patch.c -o samtools_patch.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/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/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/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] 190 | if (bgzf_is_bgzf(fn) != 1) | ^~ In file included from tabixfile.c:3: /gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here 243 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); | ^~~~~~~~~~~~ gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c tagfilter.c -o tagfilter.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c utilities.c -o utilities.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/gnu/store/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/include' -I'/gnu/store/g91jilkd37bw87y81cqhad8v6hyzcllr-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/p6z338ra1p1wn980rr5gdda9b8qxxyi1-r-iranges-2.28.0/site-library/IRanges/include' -I'/gnu/store/vpw525flj10dr9fkrpkzf5zfxfdkckvq-r-xvector-0.34.0/site-library/XVector/include' -I'/gnu/store/7ibdzrf3wfik14b5jihqqbsqdrwmkv98-r-biostrings-2.62.0/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -c zip_compression.c -o zip_compression.o g++ -std=gnu++14 -shared -L/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/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/kdf3lkr5m1d5jahbk415cfphvb0lx4j8-r-rhtslib-1.26.0/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/lib -lR installing to /gnu/store/286sxhpmg35lz4578g2ghj5r4d9qnzmz-r-rsamtools-2.10.0/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 33.3 seconds starting phase `check' Testing examples for package ‘Rsamtools’ phase `check' succeeded after 4.5 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 `make-dynamic-linker-cache' phase `make-dynamic-linker-cache' 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