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/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/ad87j9w6kv679sj71dyv3vdxwr5yi5ia-r-rsamtools-2.6.0/site-library/:/gnu/store/b0bc60mqd508mql8q64clpxpa5hd23x7-r-s4vectors-0.28.1/site-library/:/gnu/store/mlsl0j769n3kmcs3ydc90n32snmj6jcb-r-summarizedexperiment-1.20.0/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/xzjl7y1kwsla3nj5kx4w3y4z9nqgqxgb-r-xvector-0.30.0/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/q12404513kffgf7x5w6p9x263xccng20-r-rhtslib-1.22.0/site-library/:/gnu/store/8jq1r3kfby23b4afadwfazal6in3saaw-r-bitops-1.0-7/site-library/:/gnu/store/1wj99kiwyhqj0r0lhl9g0ylckxa0ql76-r-matrixgenerics-1.2.1/site-library/:/gnu/store/sgkc3h839wijzlviiw425fxbjyq934hn-r-matrix-1.3-2/site-library/:/gnu/store/3waa589avdampx69ig0n7ddx3pm9hkr0-r-delayedarray-0.16.3/site-library/:/gnu/store/f8p8ljfd7hdiarqya52ixiq57kpv6f7d-r-biobase-2.50.0/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/aq46zkk2mjy3b96876zk4pmbcr8jjl33-r-zlibbioc-1.36.0/site-library/:/gnu/store/akd4jzjjwfmvr72vannj8aqdycgiw2zh-r-matrixstats-0.58.0/site-library/:/gnu/store/8gy419z0s3l4hbnkza4afpivp1434zmr-r-lattice-0.20-44/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/gfapkk5c6hvl1d94m4sqnhn7f9l5gqyh-linux-libre-headers-5.4.20/include:/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/include:/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/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/gfapkk5c6hvl1d94m4sqnhn7f9l5gqyh-linux-libre-headers-5.4.20/include:/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/include:/gnu/store/k9wmrk5m91599lk8gd4rc7h4df642qw0-curl-7.74.0/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' GenomicAlignments/DESCRIPTION GenomicAlignments/NAMESPACE GenomicAlignments/NEWS GenomicAlignments/R/ GenomicAlignments/R/GAlignmentPairs-class.R GenomicAlignments/R/GAlignments-class.R GenomicAlignments/R/GAlignmentsList-class.R GenomicAlignments/R/GappedReads-class.R GenomicAlignments/R/OverlapEncodings-class.R GenomicAlignments/R/cigar-utils.R GenomicAlignments/R/coordinate-mapping-methods.R GenomicAlignments/R/coverage-methods.R GenomicAlignments/R/encodeOverlaps-methods.R GenomicAlignments/R/findCompatibleOverlaps-methods.R GenomicAlignments/R/findMateAlignment.R GenomicAlignments/R/findOverlaps-methods.R GenomicAlignments/R/findSpliceOverlaps-methods.R GenomicAlignments/R/intra-range-methods.R GenomicAlignments/R/junctions-methods.R GenomicAlignments/R/pileLettersAt.R GenomicAlignments/R/readGAlignments.R GenomicAlignments/R/sequenceLayer.R GenomicAlignments/R/setops-methods.R GenomicAlignments/R/stackStringsFromGAlignments.R GenomicAlignments/R/summarizeOverlaps-methods.R GenomicAlignments/R/utils.R GenomicAlignments/R/zzz.R GenomicAlignments/README.md GenomicAlignments/build/ GenomicAlignments/build/vignette.rds GenomicAlignments/inst/ GenomicAlignments/inst/CITATION GenomicAlignments/inst/doc/ GenomicAlignments/inst/doc/GenomicAlignmentsIntroduction.R GenomicAlignments/inst/doc/GenomicAlignmentsIntroduction.Rnw GenomicAlignments/inst/doc/GenomicAlignmentsIntroduction.pdf GenomicAlignments/inst/doc/OverlapEncodings.R GenomicAlignments/inst/doc/OverlapEncodings.Rnw GenomicAlignments/inst/doc/OverlapEncodings.pdf GenomicAlignments/inst/doc/WorkingWithAlignedNucleotides.R GenomicAlignments/inst/doc/WorkingWithAlignedNucleotides.Rnw GenomicAlignments/inst/doc/WorkingWithAlignedNucleotides.pdf GenomicAlignments/inst/doc/summarizeOverlaps.R GenomicAlignments/inst/doc/summarizeOverlaps.Rnw GenomicAlignments/inst/doc/summarizeOverlaps.pdf GenomicAlignments/inst/extdata/ GenomicAlignments/inst/extdata/sm_treated1.bam GenomicAlignments/inst/extdata/sm_untreated1.bam GenomicAlignments/inst/unitTests/ GenomicAlignments/inst/unitTests/test_GAlignments-class.R GenomicAlignments/inst/unitTests/test_GAlignmentsList-class.R GenomicAlignments/inst/unitTests/test_cigar-utils.R GenomicAlignments/inst/unitTests/test_coordinate-mapping-methods.R GenomicAlignments/inst/unitTests/test_findSpliceOverlaps-methods.R GenomicAlignments/inst/unitTests/test_intra-range-methods.R GenomicAlignments/inst/unitTests/test_readGAlignmentPairs.R GenomicAlignments/inst/unitTests/test_readGAlignments.R GenomicAlignments/inst/unitTests/test_readGAlignmentsList.R GenomicAlignments/inst/unitTests/test_summarizeOverlaps-methods.R GenomicAlignments/man/ GenomicAlignments/man/GAlignmentPairs-class.Rd GenomicAlignments/man/GAlignments-class.Rd GenomicAlignments/man/GAlignmentsList-class.Rd GenomicAlignments/man/GappedReads-class.Rd GenomicAlignments/man/OverlapEncodings-class.Rd GenomicAlignments/man/cigar-utils.Rd GenomicAlignments/man/coordinate-mapping-methods.Rd GenomicAlignments/man/coverage-methods.Rd GenomicAlignments/man/encodeOverlaps-methods.Rd GenomicAlignments/man/findCompatibleOverlaps-methods.Rd GenomicAlignments/man/findMateAlignment.Rd GenomicAlignments/man/findOverlaps-methods.Rd GenomicAlignments/man/findSpliceOverlaps-methods.Rd GenomicAlignments/man/intra-range-methods.Rd GenomicAlignments/man/junctions-methods.Rd GenomicAlignments/man/pileLettersAt.Rd GenomicAlignments/man/readGAlignments.Rd GenomicAlignments/man/sequenceLayer.Rd GenomicAlignments/man/setops-methods.Rd GenomicAlignments/man/stackStringsFromGAlignments.Rd GenomicAlignments/man/summarizeOverlaps-methods.Rd GenomicAlignments/src/ GenomicAlignments/src/GenomicAlignments.h GenomicAlignments/src/IRanges_stubs.c GenomicAlignments/src/R_init_GenomicAlignments.c GenomicAlignments/src/S4Vectors_stubs.c GenomicAlignments/src/cigar_utils.c GenomicAlignments/src/coordinate_mapping_methods.c GenomicAlignments/src/encodeOverlaps_methods.c GenomicAlignments/tests/ GenomicAlignments/tests/run_unitTests.R GenomicAlignments/vignettes/ GenomicAlignments/vignettes/GenomicAlignmentsIntroduction.Rnw GenomicAlignments/vignettes/OverlapEncodings.Rnw GenomicAlignments/vignettes/WorkingWithAlignedNucleotides.Rnw GenomicAlignments/vignettes/precomputed_results/ GenomicAlignments/vignettes/precomputed_results/U1.sbcompHITSa.rda GenomicAlignments/vignettes/precomputed_results/U1.sbcompHITSb.rda GenomicAlignments/vignettes/precomputed_results/exbytx.rda GenomicAlignments/vignettes/summarizeOverlaps-modes.pdf GenomicAlignments/vignettes/summarizeOverlaps.Rnw 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' 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 ‘GenomicAlignments’ ... ** using staged installation ** libs gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -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/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -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/usr/local/include -fpic -g -O2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -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/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 -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/usr/local/include -fpic -g -O2 -c cigar_utils.c -o cigar_utils.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -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/usr/local/include -fpic -g -O2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o gcc -I"/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/include" -DNDEBUG -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/usr/local/include -fpic -g -O2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o gcc -shared -L/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/gnu/store/djxka8lxrllfbmnha6nnx9vl09hk8cz0-r-minimal-4.0.4/lib/R/lib -lR installing to /gnu/store/jvv6h2a578a9a46d129sf7jbfixfs55m-r-genomicalignments-1.26.0/site-library/00LOCK-GenomicAlignments/00new/GenomicAlignments/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 (GenomicAlignments) phase `install' succeeded after 43.2 seconds starting phase `check' Testing examples for package ‘GenomicAlignments’ phase `check' succeeded after 12.3 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