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/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/bin:/gnu/store/hqysqhh80g7qy8287b8p2gwz0379vh50-tar-1.34/bin:/gnu/store/8rvnivj15gmirawhikgbjaang5b4w779-gzip-1.10/bin:/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/bin:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/bin:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/bin:/gnu/store/49j4cjqc8sckyh4qhf9j9dmc6anc8wk9-diffutils-3.8/bin:/gnu/store/znjj5y98lvi46fll85qg22ngz966gx1d-patch-2.7.6/bin:/gnu/store/yq3xalg1p2p5p5hfpw4v5jx0v86qw45w-findutils-4.8.0/bin:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/bin:/gnu/store/dsldg7i4y6hxdknh7cv93rbxbp17xm93-sed-4.8/bin:/gnu/store/4znchc8whjbs50mvxgc0skmkvyhy9xk1-grep-3.6/bin:/gnu/store/wllq3y3sl5bldm9vsx2fcwhcmks4i9ar-coreutils-8.32/bin:/gnu/store/zyhbjfyqh10yiw1dw1x1i7n70jm9ygdn-make-4.3/bin:/gnu/store/2an4h5ndc22dv62q3l985ciq862q4bj7-bash-minimal-5.1.8/bin:/gnu/store/g58zxpycy64m790vwjlzpadmbn065fia-ld-wrapper-0/bin:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/bin:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/bin:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/bin:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/sbin:/gnu/store/iv96qv3nm6xw999p1ni5xlsgkqzxm1y8-curl-7.79.1/bin' environment variable `R_LIBS_SITE' set to `/gnu/store/a4v41pybpghsfn9s5aaiap8ckkkfz06y-r-biocgenerics-0.40.0/site-library/:/gnu/store/9ljw57dz5xbkcrgmrp6lwm3l1w3sjkfc-r-biocparallel-1.28.3/site-library/:/gnu/store/g6c08ssixc0dkq04amx9hiyyad4mp83p-r-biostrings-2.62.0/site-library/:/gnu/store/fd067z0fvwbdxamjmmd1mchyi7kbwz34-r-genomeinfodb-1.30.0/site-library/:/gnu/store/whx7n74yy455k5jknpq10amj3kzgn86r-r-genomicranges-1.46.1/site-library/:/gnu/store/g0k56si5vikp7bwpqx43mlfl5is0n61p-r-iranges-2.28.0/site-library/:/gnu/store/4w039xvysc5kb0s4xsi9r70zqv3i0fc1-r-rsamtools-2.10.0/site-library/:/gnu/store/vygq99ll6pvzn2fvim1910b31a9cc1rz-r-s4vectors-0.32.3/site-library/:/gnu/store/zww65mzaw3hdixa54l905wmlwkzz4f2a-r-summarizedexperiment-1.24.0/site-library/:/gnu/store/jyabqyfl72i9cdr9aqi1gnl1xdx64ha0-r-bh-1.78.0-0/site-library/:/gnu/store/cyxjkp5jqci0c3wl86zaqmbcfhbfi0ab-r-snow-0.4-4/site-library/:/gnu/store/gfr4z2mj2p1xh44rh35p8k9vpsy7z97g-r-futile-logger-1.4.3/site-library/:/gnu/store/yymb9zm4878x840yak1pvm4r960nln92-r-xvector-0.34.0/site-library/:/gnu/store/lffs8k6jcggmkrmfzyv364z7jry8gqq8-r-crayon-1.4.2/site-library/:/gnu/store/gadrv3mrzp5r373394pm9r19vchb6la0-r-rcurl-1.95-0.1.2/site-library/:/gnu/store/izpkx7khyk0wlwhfyijl7ripvbikkrdn-r-genomeinfodbdata-1.2.0/site-library/:/gnu/store/sqqiy247p5p7ki3q0rd16kwhz256wf9j-r-rhtslib-1.26.0/site-library/:/gnu/store/p3i309aipfa94cb5cvpgqvwlyql8d004-r-bitops-1.0-7/site-library/:/gnu/store/d8nafd97qxb9iznpl4m5xblqzl0ngmbv-r-matrixgenerics-1.6.0/site-library/:/gnu/store/ads1ydlhj5v16jqng8hl2qb87yjc0ww6-r-matrix-1.4-0/site-library/:/gnu/store/m367vxqdin32ifa61s72gwmldiqrhdwd-r-delayedarray-0.20.0/site-library/:/gnu/store/s9hg4nlml3g6gplgfizwspyc5aihc3ps-r-biobase-2.54.0/site-library/:/gnu/store/wmxbjmnc6fw14azss2n89bkfc7zzsxjl-r-lambda-r-1.2.4/site-library/:/gnu/store/irpdqmgd9iirwi2ncwxnsk16s9g82gbc-r-futile-options-1.0.1/site-library/:/gnu/store/f3pqilw6x4hy2vjpsdj08mlwmdvaddq6-r-zlibbioc-1.40.0/site-library/:/gnu/store/ypcd1f79c1ifnsiycs4kcbq0a0v7ihc9-r-matrixstats-0.61.0/site-library/:/gnu/store/kwg7xzcnrra79r5fq8jz0hv0753q9ja7-r-lattice-0.20-45/site-library/:/gnu/store/xdmb1bwfyf3qx95h9p4xqw33s13ga389-r-formatr-1.11/site-library/' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/include:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/include:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/include:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/include:/gnu/store/zyhbjfyqh10yiw1dw1x1i7n70jm9ygdn-make-4.3/include:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/include:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/include:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/include:/gnu/store/k8xlwnnmhgmvzyxxfjq3z3fci73zx7x9-linux-libre-headers-5.10.35/include:/gnu/store/cahmfd1kbv06a8wwv7mm3ir847vn2s43-zlib-1.2.11/include:/gnu/store/iv96qv3nm6xw999p1ni5xlsgkqzxm1y8-curl-7.79.1/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/include:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/include:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/include:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/include:/gnu/store/zyhbjfyqh10yiw1dw1x1i7n70jm9ygdn-make-4.3/include:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/include:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/include/c++:/gnu/store/h88kd46c8br0wc4i6hq19cjby081ina4-gcc-10.3.0/include:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/include:/gnu/store/k8xlwnnmhgmvzyxxfjq3z3fci73zx7x9-linux-libre-headers-5.10.35/include:/gnu/store/cahmfd1kbv06a8wwv7mm3ir847vn2s43-zlib-1.2.11/include:/gnu/store/iv96qv3nm6xw999p1ni5xlsgkqzxm1y8-curl-7.79.1/include' environment variable `LIBRARY_PATH' set to `/gnu/store/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib:/gnu/store/64zk0izmaframq6cd0xlsmk0rxn3zc52-bzip2-1.0.8/lib:/gnu/store/z6bw81zw5b5jm3p02y906p0wnjbjqa7n-xz-5.2.5/lib:/gnu/store/jfmrxybjkd0nvh1n34hbzv0lwsnmxz1v-file-5.39/lib:/gnu/store/bgyr8c7bl1sqhpapm2kghiya0k6zvi51-gawk-5.1.0/lib:/gnu/store/cr38d3gvf52ckns2b01lwgw86hk3mvcc-binutils-2.37/lib:/gnu/store/mjdjgiz9k5rrbj440r16z6p5g33nr7d7-glibc-2.33/lib:/gnu/store/88bdm10sayqjnggrxlbdmk3rv1qqdrvl-glibc-2.33-static/lib:/gnu/store/y4x3whxg8i1p9w9vy67lz3cw8xfil8bh-glibc-utf8-locales-2.33/lib:/gnu/store/cahmfd1kbv06a8wwv7mm3ir847vn2s43-zlib-1.2.11/lib:/gnu/store/iv96qv3nm6xw999p1ni5xlsgkqzxm1y8-curl-7.79.1/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/y4x3whxg8i1p9w9vy67lz3cw8xfil8bh-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' 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/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I'/gnu/store/vygq99ll6pvzn2fvim1910b31a9cc1rz-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/g0k56si5vikp7bwpqx43mlfl5is0n61p-r-iranges-2.28.0/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/gnu/store/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I'/gnu/store/vygq99ll6pvzn2fvim1910b31a9cc1rz-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/g0k56si5vikp7bwpqx43mlfl5is0n61p-r-iranges-2.28.0/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/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I'/gnu/store/vygq99ll6pvzn2fvim1910b31a9cc1rz-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/g0k56si5vikp7bwpqx43mlfl5is0n61p-r-iranges-2.28.0/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/gnu/store/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I'/gnu/store/vygq99ll6pvzn2fvim1910b31a9cc1rz-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/g0k56si5vikp7bwpqx43mlfl5is0n61p-r-iranges-2.28.0/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -c cigar_utils.c -o cigar_utils.o gcc -I"/gnu/store/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I'/gnu/store/vygq99ll6pvzn2fvim1910b31a9cc1rz-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/g0k56si5vikp7bwpqx43mlfl5is0n61p-r-iranges-2.28.0/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/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I'/gnu/store/vygq99ll6pvzn2fvim1910b31a9cc1rz-r-s4vectors-0.32.3/site-library/S4Vectors/include' -I'/gnu/store/g0k56si5vikp7bwpqx43mlfl5is0n61p-r-iranges-2.28.0/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o gcc -shared -L/gnu/store/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/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/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib/R/lib -lR installing to /gnu/store/hl32n0g73im463zpianq9kyrki2bdjp1-r-genomicalignments-1.30.0/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 29.7 seconds starting phase `check' Testing examples for package ‘GenomicAlignments’ phase `check' succeeded after 8.9 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 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