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/krpyb0zi700dcrg9cc8932w4v0qivdg9-pkg-config-0.29.2/bin:/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/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' environment variable `R_LIBS_SITE' set to `/gnu/store/kqi92357ksc7fjmrpr0s663ywzr0dm8q-r-knitr-1.33/site-library/:/gnu/store/aq46zkk2mjy3b96876zk4pmbcr8jjl33-r-zlibbioc-1.36.0/site-library/:/gnu/store/gl2pj9r7qi2xxr6lvfibwml6j1xcwz6l-r-yaml-2.2.1/site-library/:/gnu/store/k281zzn108xxkrzwdih0v71hf1vj4d5a-r-xfun-0.22/site-library/:/gnu/store/z35808jrbgah5y4h8gys74c9ja8fgk9b-r-stringr-1.4.0/site-library/:/gnu/store/qg128fx6brs8a28dwry5hnznfmvf1rw2-r-markdown-1.1/site-library/:/gnu/store/r41mca76fiqwmxc37izjifzhy380l81p-r-highr-0.9/site-library/:/gnu/store/k1x81c0my01w1pjhfzx312dxza1jxxd9-r-evaluate-0.14/site-library/:/gnu/store/dgizz42xg36mrb4607sxlqzr075vqy50-r-stringi-1.5.3/site-library/:/gnu/store/29bairzdrm91sxmbrsm5px8b7djq1n5y-r-magrittr-2.0.1/site-library/:/gnu/store/sx59njjib4m9d2x8vw80vczsb59vgl6a-r-glue-1.4.2/site-library/:/gnu/store/6lgjwi8m3lagbd79vn1fkp0pwhrl180p-r-mime-0.10/site-library/' environment variable `PKG_CONFIG_PATH' set to `/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/pkgconfig:/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/lib/pkgconfig:/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/lib/pkgconfig:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/lib/pkgconfig' environment variable `SSL_CERT_DIR' unset environment variable `SSL_CERT_FILE' unset environment variable `CURL_CA_BUNDLE' unset environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/include:/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/include:/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/gfapkk5c6hvl1d94m4sqnhn7f9l5gqyh-linux-libre-headers-5.4.20/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/include:/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/include:/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/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/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/lib:/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/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' environment variable `GUIX_LOCPATH' set to `/gnu/store/hwcky7446s952w0mwchhmm211ll07zrq-glibc-utf8-locales-2.31/lib/locale' 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' Rhtslib/DESCRIPTION Rhtslib/NAMESPACE Rhtslib/NEWS Rhtslib/R/ Rhtslib/R/zzz.R Rhtslib/README.md Rhtslib/build/ Rhtslib/build/vignette.rds Rhtslib/inst/ Rhtslib/inst/doc/ Rhtslib/inst/doc/Rhtslib.R Rhtslib/inst/doc/Rhtslib.Rmd Rhtslib/inst/doc/Rhtslib.html Rhtslib/inst/include/ Rhtslib/inst/include/README Rhtslib/inst/include/bam.c Rhtslib/inst/include/bam.h Rhtslib/inst/include/bam_aux.c Rhtslib/inst/include/bam_cat.c Rhtslib/inst/include/bam_endian.h Rhtslib/inst/include/bam_plbuf.c Rhtslib/inst/include/bam_plbuf.h Rhtslib/inst/include/bam_sort.c Rhtslib/inst/include/sam.c Rhtslib/inst/include/sam.h Rhtslib/inst/include/sam_header.h Rhtslib/inst/include/sam_opts.c Rhtslib/inst/include/sam_opts.h Rhtslib/inst/include/sam_utils.c Rhtslib/inst/include/samtools.h Rhtslib/inst/include/version.h Rhtslib/man/ Rhtslib/man/Rhtslib-package.Rd Rhtslib/man/pkgconfig.Rd Rhtslib/src/ Rhtslib/src/Makevars Rhtslib/src/Makevars.common Rhtslib/src/Makevars.win Rhtslib/src/R_init_Rhtslib.c Rhtslib/src/htslib-1.7/ Rhtslib/src/htslib-1.7/.appveyor.yml Rhtslib/src/htslib-1.7/INSTALL Rhtslib/src/htslib-1.7/LICENSE Rhtslib/src/htslib-1.7/Makefile Rhtslib/src/htslib-1.7/Makefile.Rhtslib Rhtslib/src/htslib-1.7/Makefile.Rhtslib.win Rhtslib/src/htslib-1.7/NEWS Rhtslib/src/htslib-1.7/README Rhtslib/src/htslib-1.7/bcf_sr_sort.c Rhtslib/src/htslib-1.7/bcf_sr_sort.h Rhtslib/src/htslib-1.7/bgzf.c Rhtslib/src/htslib-1.7/bgzip.c Rhtslib/src/htslib-1.7/config.h Rhtslib/src/htslib-1.7/config.h.in Rhtslib/src/htslib-1.7/config.mk.in Rhtslib/src/htslib-1.7/configure Rhtslib/src/htslib-1.7/configure.ac Rhtslib/src/htslib-1.7/cram/ Rhtslib/src/htslib-1.7/cram/cram.h Rhtslib/src/htslib-1.7/cram/cram_codecs.c Rhtslib/src/htslib-1.7/cram/cram_codecs.h Rhtslib/src/htslib-1.7/cram/cram_decode.c Rhtslib/src/htslib-1.7/cram/cram_decode.h Rhtslib/src/htslib-1.7/cram/cram_encode.c Rhtslib/src/htslib-1.7/cram/cram_encode.h Rhtslib/src/htslib-1.7/cram/cram_external.c Rhtslib/src/htslib-1.7/cram/cram_index.c Rhtslib/src/htslib-1.7/cram/cram_index.h Rhtslib/src/htslib-1.7/cram/cram_io.c Rhtslib/src/htslib-1.7/cram/cram_io.h Rhtslib/src/htslib-1.7/cram/cram_samtools.c Rhtslib/src/htslib-1.7/cram/cram_samtools.h Rhtslib/src/htslib-1.7/cram/cram_stats.c Rhtslib/src/htslib-1.7/cram/cram_stats.h Rhtslib/src/htslib-1.7/cram/cram_structs.h Rhtslib/src/htslib-1.7/cram/files.c Rhtslib/src/htslib-1.7/cram/mFILE.c Rhtslib/src/htslib-1.7/cram/mFILE.h Rhtslib/src/htslib-1.7/cram/misc.h Rhtslib/src/htslib-1.7/cram/open_trace_file.c Rhtslib/src/htslib-1.7/cram/open_trace_file.h Rhtslib/src/htslib-1.7/cram/os.h Rhtslib/src/htslib-1.7/cram/pooled_alloc.c Rhtslib/src/htslib-1.7/cram/pooled_alloc.h Rhtslib/src/htslib-1.7/cram/rANS_byte.h Rhtslib/src/htslib-1.7/cram/rANS_static.c Rhtslib/src/htslib-1.7/cram/rANS_static.h Rhtslib/src/htslib-1.7/cram/sam_header.c Rhtslib/src/htslib-1.7/cram/sam_header.h Rhtslib/src/htslib-1.7/cram/string_alloc.c Rhtslib/src/htslib-1.7/cram/string_alloc.h Rhtslib/src/htslib-1.7/errmod.c Rhtslib/src/htslib-1.7/faidx.5 Rhtslib/src/htslib-1.7/faidx.c Rhtslib/src/htslib-1.7/hfile.c Rhtslib/src/htslib-1.7/hfile_gcs.c Rhtslib/src/htslib-1.7/hfile_internal.h Rhtslib/src/htslib-1.7/hfile_libcurl.c Rhtslib/src/htslib-1.7/hfile_net.c Rhtslib/src/htslib-1.7/hfile_s3.c Rhtslib/src/htslib-1.7/hts.c Rhtslib/src/htslib-1.7/hts_internal.h Rhtslib/src/htslib-1.7/hts_os.c Rhtslib/src/htslib-1.7/htsfile.1 Rhtslib/src/htslib-1.7/htsfile.c Rhtslib/src/htslib-1.7/htslib/ Rhtslib/src/htslib-1.7/htslib.mk Rhtslib/src/htslib-1.7/htslib.pc.in Rhtslib/src/htslib-1.7/htslib/bgzf.h Rhtslib/src/htslib-1.7/htslib/cram.h Rhtslib/src/htslib-1.7/htslib/faidx.h Rhtslib/src/htslib-1.7/htslib/hfile.h Rhtslib/src/htslib-1.7/htslib/hts.h Rhtslib/src/htslib-1.7/htslib/hts_defs.h Rhtslib/src/htslib-1.7/htslib/hts_endian.h Rhtslib/src/htslib-1.7/htslib/hts_log.h Rhtslib/src/htslib-1.7/htslib/hts_os.h 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Rhtslib/src/htslib-1.7/os/lzma_stub.h Rhtslib/src/htslib-1.7/os/rand.c Rhtslib/src/htslib-1.7/plugin.c Rhtslib/src/htslib-1.7/probaln.c Rhtslib/src/htslib-1.7/realn.c Rhtslib/src/htslib-1.7/regidx.c Rhtslib/src/htslib-1.7/sam.5 Rhtslib/src/htslib-1.7/sam.c Rhtslib/src/htslib-1.7/synced_bcf_reader.c Rhtslib/src/htslib-1.7/tabix.1 Rhtslib/src/htslib-1.7/tabix.c Rhtslib/src/htslib-1.7/tbx.c Rhtslib/src/htslib-1.7/test/ Rhtslib/src/htslib-1.7/test/auxf#values.sam Rhtslib/src/htslib-1.7/test/auxf#values_java.cram Rhtslib/src/htslib-1.7/test/auxf.fa Rhtslib/src/htslib-1.7/test/auxf.fa.fai Rhtslib/src/htslib-1.7/test/bgziptest.txt Rhtslib/src/htslib-1.7/test/bgziptest.txt.gz Rhtslib/src/htslib-1.7/test/bgziptest.txt.gz.gzi Rhtslib/src/htslib-1.7/test/c1#bounds.sam Rhtslib/src/htslib-1.7/test/c1#clip.sam Rhtslib/src/htslib-1.7/test/c1#noseq.sam Rhtslib/src/htslib-1.7/test/c1#pad1.sam Rhtslib/src/htslib-1.7/test/c1#pad2.sam Rhtslib/src/htslib-1.7/test/c1#pad3.sam Rhtslib/src/htslib-1.7/test/c1#unknown.sam Rhtslib/src/htslib-1.7/test/c1.fa Rhtslib/src/htslib-1.7/test/c1.fa.fai Rhtslib/src/htslib-1.7/test/c2#pad.sam Rhtslib/src/htslib-1.7/test/c2.fa Rhtslib/src/htslib-1.7/test/c2.fa.fai Rhtslib/src/htslib-1.7/test/ce#1.sam Rhtslib/src/htslib-1.7/test/ce#2.sam Rhtslib/src/htslib-1.7/test/ce#5.sam Rhtslib/src/htslib-1.7/test/ce#5b.sam Rhtslib/src/htslib-1.7/test/ce#5b_java.cram Rhtslib/src/htslib-1.7/test/ce#large_seq.sam Rhtslib/src/htslib-1.7/test/ce#supp.sam Rhtslib/src/htslib-1.7/test/ce#tag_depadded.sam Rhtslib/src/htslib-1.7/test/ce#tag_padded.sam Rhtslib/src/htslib-1.7/test/ce#unmap.sam Rhtslib/src/htslib-1.7/test/ce#unmap1.sam Rhtslib/src/htslib-1.7/test/ce#unmap2.sam Rhtslib/src/htslib-1.7/test/ce.fa Rhtslib/src/htslib-1.7/test/ce.fa.fai Rhtslib/src/htslib-1.7/test/compare_sam.pl Rhtslib/src/htslib-1.7/test/cross_validate.sh Rhtslib/src/htslib-1.7/test/faidx.fa Rhtslib/src/htslib-1.7/test/fieldarith.c Rhtslib/src/htslib-1.7/test/fieldarith.sam Rhtslib/src/htslib-1.7/test/formatcols.vcf Rhtslib/src/htslib-1.7/test/formatmissing-out.vcf Rhtslib/src/htslib-1.7/test/formatmissing.vcf Rhtslib/src/htslib-1.7/test/hfile.c Rhtslib/src/htslib-1.7/test/hts_endian.c Rhtslib/src/htslib-1.7/test/md#1.sam Rhtslib/src/htslib-1.7/test/md.fa Rhtslib/src/htslib-1.7/test/md.fa.fai Rhtslib/src/htslib-1.7/test/noroundtrip-out.vcf Rhtslib/src/htslib-1.7/test/noroundtrip.vcf Rhtslib/src/htslib-1.7/test/sam.c Rhtslib/src/htslib-1.7/test/tabix/ Rhtslib/src/htslib-1.7/test/tabix/bed_file.Y.100200.out Rhtslib/src/htslib-1.7/test/tabix/bed_file.bed Rhtslib/src/htslib-1.7/test/tabix/gff_file.X.2934832.2935190.out Rhtslib/src/htslib-1.7/test/tabix/gff_file.gff Rhtslib/src/htslib-1.7/test/tabix/large_chr.20.1.2147483647.out Rhtslib/src/htslib-1.7/test/tabix/large_chr.vcf Rhtslib/src/htslib-1.7/test/tabix/tabix.tst Rhtslib/src/htslib-1.7/test/tabix/test-tabix.sh Rhtslib/src/htslib-1.7/test/tabix/vcf_file.1.3000151.out Rhtslib/src/htslib-1.7/test/tabix/vcf_file.2.3199812.out Rhtslib/src/htslib-1.7/test/tabix/vcf_file.vcf Rhtslib/src/htslib-1.7/test/test-bcf-sr.c Rhtslib/src/htslib-1.7/test/test-bcf-sr.pl Rhtslib/src/htslib-1.7/test/test-bcf-translate.c Rhtslib/src/htslib-1.7/test/test-bcf-translate.out Rhtslib/src/htslib-1.7/test/test-logging.pl Rhtslib/src/htslib-1.7/test/test-regidx.c Rhtslib/src/htslib-1.7/test/test-vcf-api.c Rhtslib/src/htslib-1.7/test/test-vcf-api.out Rhtslib/src/htslib-1.7/test/test-vcf-hdr-in.vcf Rhtslib/src/htslib-1.7/test/test-vcf-hdr.out Rhtslib/src/htslib-1.7/test/test-vcf-sweep.c Rhtslib/src/htslib-1.7/test/test-vcf-sweep.out Rhtslib/src/htslib-1.7/test/test.pl Rhtslib/src/htslib-1.7/test/test_bgzf.c Rhtslib/src/htslib-1.7/test/test_view.c Rhtslib/src/htslib-1.7/test/thrash_threads1.c Rhtslib/src/htslib-1.7/test/thrash_threads2.c Rhtslib/src/htslib-1.7/test/thrash_threads3.c Rhtslib/src/htslib-1.7/test/thrash_threads4.c Rhtslib/src/htslib-1.7/test/thrash_threads5.c Rhtslib/src/htslib-1.7/test/thrash_threads6.c Rhtslib/src/htslib-1.7/test/thread_pool.md Rhtslib/src/htslib-1.7/test/xx#blank.sam Rhtslib/src/htslib-1.7/test/xx#large_aux.sam Rhtslib/src/htslib-1.7/test/xx#large_aux2.sam Rhtslib/src/htslib-1.7/test/xx#large_aux_java.cram Rhtslib/src/htslib-1.7/test/xx#minimal.sam Rhtslib/src/htslib-1.7/test/xx#pair.sam Rhtslib/src/htslib-1.7/test/xx#repeated.sam Rhtslib/src/htslib-1.7/test/xx#rg.sam Rhtslib/src/htslib-1.7/test/xx#tlen.sam Rhtslib/src/htslib-1.7/test/xx#tlen2.sam Rhtslib/src/htslib-1.7/test/xx#triplet.sam Rhtslib/src/htslib-1.7/test/xx#unsorted.sam Rhtslib/src/htslib-1.7/test/xx.fa Rhtslib/src/htslib-1.7/test/xx.fa.fai Rhtslib/src/htslib-1.7/textutils.c Rhtslib/src/htslib-1.7/textutils_internal.h Rhtslib/src/htslib-1.7/thread_pool.c Rhtslib/src/htslib-1.7/thread_pool_internal.h Rhtslib/src/htslib-1.7/vcf.5 Rhtslib/src/htslib-1.7/vcf.c Rhtslib/src/htslib-1.7/vcf_sweep.c Rhtslib/src/htslib-1.7/vcfutils.c Rhtslib/src/htslib-1.7/version.sh Rhtslib/vignettes/ Rhtslib/vignettes/Rhtslib.Rmd phase `unpack' succeeded after 0.1 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' patch-shebang: ./src/htslib-1.7/configure: changing `/bin/sh' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/sh' patch-shebang: ./src/htslib-1.7/test/compare_sam.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./src/htslib-1.7/test/cross_validate.sh: changing `/bin/sh' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/sh' patch-shebang: ./src/htslib-1.7/test/tabix/test-tabix.sh: changing `/bin/sh' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/sh' patch-shebang: ./src/htslib-1.7/test/test-bcf-sr.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./src/htslib-1.7/test/test-logging.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./src/htslib-1.7/test/test.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./src/htslib-1.7/version.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' patch-shebang: ./src/htslib-1.7/test/compare_sam.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./src/htslib-1.7/test/test-bcf-sr.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./src/htslib-1.7/test/test-logging.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./src/htslib-1.7/test/test.pl: warning: no binary for interpreter `perl' found in $PATH phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs cd "htslib-1.7" && make -f "/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/etc/Makeconf" -f "Makefile.Rhtslib" make[1]: Entering directory '/tmp/guix-build-r-rhtslib-1.22.0.drv-0/Rhtslib/src/htslib-1.7' Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o' /gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/etc/Makeconf:172: warning: ignoring old recipe for target '.c.o' gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.7"' > version.h gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o ranlib libhts.a gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.pico kfunc.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.pico knetfile.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.pico kstring.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.pico bgzf.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.pico errmod.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.pico faidx.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.pico hfile.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.pico hfile_net.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.pico hts.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.pico hts_os.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.pico md5.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.pico multipart.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.pico probaln.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.pico realn.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.pico regidx.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.pico sam.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.pico tbx.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.pico textutils.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.pico thread_pool.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.pico vcf.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.pico vcfutils.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.pico cram/files.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.pico cram/sam_header.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.pico hfile_libcurl.c gcc -shared -Wl,-soname,libhts.so.2 -L/usr/local/lib -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread ln -sf libhts.so libhts.so.2 make[1]: Leaving directory '/tmp/guix-build-r-rhtslib-1.22.0.drv-0/Rhtslib/src/htslib-1.7' mkdir -p "/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/htslib" cd "htslib-1.7/htslib" && cp * "/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/include" 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/aq46zkk2mjy3b96876zk4pmbcr8jjl33-r-zlibbioc-1.36.0/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/usrlib" cd "htslib-1.7" && cp libhts.so libhts.a "/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/usrlib" cd "/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2 gcc -shared -L/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/lib -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.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 mkdir -p "/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/testdata/tabix" cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /gnu/store/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/Rhtslib/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rhtslib) phase `install' succeeded after 65.6 seconds starting phase `check' phase `check' succeeded after 0.0 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 0 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