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' environment variable `R_LIBS_SITE' set to `/gnu/store/cmxyq4zbmg1i43py5iwlhvf4q1rsy8j3-r-knitr-1.37/site-library/:/gnu/store/a4v41pybpghsfn9s5aaiap8ckkkfz06y-r-biocgenerics-0.40.0/site-library/:/gnu/store/fd067z0fvwbdxamjmmd1mchyi7kbwz34-r-genomeinfodb-1.30.0/site-library/:/gnu/store/g0k56si5vikp7bwpqx43mlfl5is0n61p-r-iranges-2.28.0/site-library/:/gnu/store/vygq99ll6pvzn2fvim1910b31a9cc1rz-r-s4vectors-0.32.3/site-library/:/gnu/store/yymb9zm4878x840yak1pvm4r960nln92-r-xvector-0.34.0/site-library/:/gnu/store/g318xp0lbn7mvcbjbdjzshiz0s18pq4q-r-yaml-2.2.1/site-library/:/gnu/store/qdvq4f6n1q469054glyihsggyamx4z0z-r-xfun-0.29/site-library/:/gnu/store/xsp9rs2dryj4p37r9kp81y2fyfx6jczb-r-stringr-1.4.0/site-library/:/gnu/store/kqxwskrp6ibs25c97rg9fkdmprjjjm6b-r-highr-0.9/site-library/:/gnu/store/a5ms2xqsialxlxx84qqqrlbzifm29z0d-r-evaluate-0.14/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/3926n38rv4wy355n8xxi4kf8s4im0dj0-r-stringi-1.7.6/site-library/:/gnu/store/fd4abysk2s9q3p76ab16rl402fccqxis-r-magrittr-2.0.1/site-library/:/gnu/store/n8p7yv81vwcddgba17ayrw3d7fkc5c5k-r-glue-1.6.0/site-library/:/gnu/store/p3i309aipfa94cb5cvpgqvwlyql8d004-r-bitops-1.0-7/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' 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' 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' environment variable `GUIX_LOCPATH' set to `/gnu/store/y4x3whxg8i1p9w9vy67lz3cw8xfil8bh-glibc-utf8-locales-2.33/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' GenomicRanges/DESCRIPTION GenomicRanges/NAMESPACE GenomicRanges/NEWS GenomicRanges/R/ GenomicRanges/R/DelegatingGenomicRanges-class.R GenomicRanges/R/GNCList-class.R GenomicRanges/R/GPos-class.R GenomicRanges/R/GRanges-class.R GenomicRanges/R/GRangesFactor-class.R GenomicRanges/R/GRangesList-class.R GenomicRanges/R/GenomicRanges-class.R GenomicRanges/R/GenomicRanges-comparison.R GenomicRanges/R/GenomicRangesList-class.R GenomicRanges/R/RangedData-methods.R GenomicRanges/R/absoluteRanges.R GenomicRanges/R/constraint.R GenomicRanges/R/coverage-methods.R GenomicRanges/R/findOverlaps-methods.R GenomicRanges/R/genomic-range-squeezers.R GenomicRanges/R/genomicvars.R GenomicRanges/R/inter-range-methods.R GenomicRanges/R/intra-range-methods.R GenomicRanges/R/makeGRangesFromDataFrame.R GenomicRanges/R/makeGRangesListFromDataFrame.R GenomicRanges/R/nearest-methods.R GenomicRanges/R/normarg-utils.R GenomicRanges/R/phicoef.R GenomicRanges/R/setops-methods.R GenomicRanges/R/strand-utils.R GenomicRanges/R/tile-methods.R GenomicRanges/R/tileGenome.R GenomicRanges/R/transcript-utils.R GenomicRanges/R/utils.R GenomicRanges/R/zzz.R GenomicRanges/README.md GenomicRanges/build/ GenomicRanges/build/vignette.rds GenomicRanges/inst/ GenomicRanges/inst/CITATION GenomicRanges/inst/doc/ GenomicRanges/inst/doc/ExtendingGenomicRanges.R GenomicRanges/inst/doc/ExtendingGenomicRanges.Rnw GenomicRanges/inst/doc/ExtendingGenomicRanges.pdf GenomicRanges/inst/doc/GRanges_and_GRangesList_slides.R GenomicRanges/inst/doc/GRanges_and_GRangesList_slides.Rnw GenomicRanges/inst/doc/GRanges_and_GRangesList_slides.pdf GenomicRanges/inst/doc/GenomicRangesHOWTOs.R GenomicRanges/inst/doc/GenomicRangesHOWTOs.Rnw GenomicRanges/inst/doc/GenomicRangesHOWTOs.pdf GenomicRanges/inst/doc/GenomicRangesIntroduction.R GenomicRanges/inst/doc/GenomicRangesIntroduction.Rmd GenomicRanges/inst/doc/GenomicRangesIntroduction.html GenomicRanges/inst/doc/Ten_things_slides.R GenomicRanges/inst/doc/Ten_things_slides.Rnw GenomicRanges/inst/doc/Ten_things_slides.pdf GenomicRanges/inst/extdata/ GenomicRanges/inst/extdata/feature_frags.txt GenomicRanges/inst/scripts/ GenomicRanges/inst/scripts/timing_overlaps.R GenomicRanges/inst/unitTests/ GenomicRanges/inst/unitTests/test_GNCList-class.R GenomicRanges/inst/unitTests/test_GRanges-class.R GenomicRanges/inst/unitTests/test_GRangesList-class.R GenomicRanges/inst/unitTests/test_GenomicRanges-comparison.R GenomicRanges/inst/unitTests/test_coverage-methods.R GenomicRanges/inst/unitTests/test_findOverlaps-methods.R GenomicRanges/inst/unitTests/test_inter-range-methods.R GenomicRanges/inst/unitTests/test_intra-range-methods.R GenomicRanges/inst/unitTests/test_makeGRangesFromDataFrame.R GenomicRanges/inst/unitTests/test_makeGRangesListFromDataFrame.R GenomicRanges/inst/unitTests/test_nearest-methods.R GenomicRanges/inst/unitTests/test_precede_follow.R GenomicRanges/inst/unitTests/test_setops-methods.R GenomicRanges/man/ GenomicRanges/man/DelegatingGenomicRanges-class.Rd GenomicRanges/man/GNCList-class.Rd GenomicRanges/man/GPos-class.Rd GenomicRanges/man/GRanges-class.Rd GenomicRanges/man/GRangesFactor-class.Rd GenomicRanges/man/GRangesList-class.Rd GenomicRanges/man/GenomicRanges-comparison.Rd GenomicRanges/man/GenomicRangesList-class.Rd GenomicRanges/man/absoluteRanges.Rd GenomicRanges/man/constraint.Rd GenomicRanges/man/coverage-methods.Rd GenomicRanges/man/findOverlaps-methods.Rd GenomicRanges/man/genomic-range-squeezers.Rd GenomicRanges/man/genomicvars.Rd GenomicRanges/man/inter-range-methods.Rd GenomicRanges/man/intra-range-methods.Rd GenomicRanges/man/makeGRangesFromDataFrame.Rd GenomicRanges/man/makeGRangesListFromDataFrame.Rd GenomicRanges/man/nearest-methods.Rd GenomicRanges/man/phicoef.Rd GenomicRanges/man/setops-methods.Rd GenomicRanges/man/strand-utils.Rd GenomicRanges/man/tile-methods.Rd GenomicRanges/man/tileGenome.Rd GenomicRanges/src/ GenomicRanges/src/GenomicRanges.h GenomicRanges/src/IRanges_stubs.c GenomicRanges/src/R_init_GenomicRanges.c GenomicRanges/src/S4Vectors_stubs.c GenomicRanges/src/transcript_utils.c GenomicRanges/tests/ GenomicRanges/tests/run_unitTests.R GenomicRanges/vignettes/ GenomicRanges/vignettes/ExtendingGenomicRanges.Rnw GenomicRanges/vignettes/GRanges_and_GRangesList_slides.Rnw GenomicRanges/vignettes/GenomicRanges.bib GenomicRanges/vignettes/GenomicRangesHOWTOs.Rnw GenomicRanges/vignettes/GenomicRangesIntroduction.Rmd GenomicRanges/vignettes/Ten_things_slides.Rnw GenomicRanges/vignettes/slides.sty phase `unpack' 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' 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 ‘GenomicRanges’ ... ** 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_GenomicRanges.c -o R_init_GenomicRanges.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 transcript_utils.c -o transcript_utils.o gcc -shared -L/gnu/store/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib/R/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/gnu/store/fpxfr4pxli6p3fx646agfln7hqy04l7r-r-minimal-4.1.2/lib/R/lib -lR installing to /gnu/store/whx7n74yy455k5jknpq10amj3kzgn86r-r-genomicranges-1.46.1/site-library/00LOCK-GenomicRanges/00new/GenomicRanges/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 (GenomicRanges) phase `install' succeeded after 33.6 seconds starting phase `check' Testing examples for package ‘GenomicRanges’ phase `check' succeeded after 6.9 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