starting phase `separate-from-pid1'
build process now running as PID 18
phase `separate-from-pid1' succeeded after 0.0 seconds
starting phase `set-SOURCE-DATE-EPOCH'
phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds
starting phase `set-paths'
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environment variable `BASH_LOADABLES_PATH' unset
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environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include/c++:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include:/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/31xynhn10x499sqsigjqr67z02zng5r7-curl-8.6.0/include'
environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include:/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/31xynhn10x499sqsigjqr67z02zng5r7-curl-8.6.0/include'
environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/include:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/include:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/include:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/include:/gnu/store/jkxm9drwlxkmb53zn1sd7w2wxdvpbj32-make-4.4.1/include:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/include:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include/c++:/gnu/store/wssvk5s5akbx78kx92bdkirrry87jvbj-gcc-14.3.0/include:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/include:/gnu/store/90qwxdmdw7jdf0dkkgdgxln6b5a57kzx-linux-libre-headers-6.12.17/include:/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/include:/gnu/store/31xynhn10x499sqsigjqr67z02zng5r7-curl-8.6.0/include'
environment variable `LIBRARY_PATH' set to `/gnu/store/3yagih0jifj7d8sksmrvslv7gn2gjw18-r-minimal-4.5.2/lib:/gnu/store/j2bib9ysq7f3369gjg6hv1kp24g07472-bzip2-1.0.8/lib:/gnu/store/plifc9akxxfyjjbnh10dj350nxbhc399-file-5.46/lib:/gnu/store/xmqvvby6vlmhbi3q913ck5marh6p86av-gawk-5.3.0/lib:/gnu/store/gd41pn8r5723cyd6d79q9riqjbi070zz-xz-5.4.5/lib:/gnu/store/c8mp7qq5az7cbnvmxgj2bjkscsf5h9ri-binutils-2.44/lib:/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/lib:/gnu/store/q1s19kv8bdq9ssfdgznzgkmfmj90vdfd-glibc-2.41-static/lib:/gnu/store/a2jnc1avp7jdyp01r9kpp8q1i72kk8g0-zlib-1.3.1/lib:/gnu/store/31xynhn10x499sqsigjqr67z02zng5r7-curl-8.6.0/lib'
environment variable `GUIX_LOCPATH' set to `/gnu/store/yj053cys0724p7vs9kir808x7fivz17m-glibc-2.41/lib/locale'
environment variable `TZDIR' unset
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 'C.UTF-8' locale for category "LC_ALL"
phase `install-locale' succeeded after 0.0 seconds
starting phase `unpack'
BaalChIP/DESCRIPTION
BaalChIP/MD5
BaalChIP/NAMESPACE
BaalChIP/NEWS
BaalChIP/R/
BaalChIP/R/BaalChIP-checks.R
BaalChIP/R/BaalChIP-class.R
BaalChIP/R/BaalChIP-generics.R
BaalChIP/R/BaalChIP-methods.R
BaalChIP/R/Bayes_report.R
BaalChIP/R/QCIntBias.R
BaalChIP/R/QCmerged.R
BaalChIP/R/QCperBam.R
BaalChIP/R/allASBbias.R
BaalChIP/R/alleleCounts.R
BaalChIP/R/allplots.R
BaalChIP/R/allsummary.R
BaalChIP/R/applyBayes.R
BaalChIP/README.md
BaalChIP/build/
BaalChIP/build/vignette.rds
BaalChIP/data/
BaalChIP/data/ENCODEexample.RData
BaalChIP/data/FAIREexample.RData
BaalChIP/data/UniqueMappability50bp_hg19.RData
BaalChIP/data/baalObject.RData
BaalChIP/data/blacklist_hg19.RData
BaalChIP/data/datalist
BaalChIP/data/pickrell2011cov1_hg19.RData
BaalChIP/inst/
BaalChIP/inst/CITATION
BaalChIP/inst/doc/
BaalChIP/inst/doc/BaalChIP.R
BaalChIP/inst/doc/BaalChIP.Rmd
BaalChIP/inst/doc/BaalChIP.html
BaalChIP/inst/extra/
BaalChIP/inst/extra/get.overlaps.v2_chrXY.perl
BaalChIP/inst/extra/run_simulations.sh
BaalChIP/inst/test/
BaalChIP/inst/test/AMOVC_hetSNP.txt
BaalChIP/inst/test/GM12891_hetSNP.txt
BaalChIP/inst/test/MCF7_hetSNP.txt
BaalChIP/inst/test/TaT1_hetSNP.txt
BaalChIP/inst/test/bamFiles/
BaalChIP/inst/test/bamFiles/AMOVC_1.test.bam
BaalChIP/inst/test/bamFiles/AMOVC_1.test.bam.bai
BaalChIP/inst/test/bamFiles/AMOVC_1_gDNA.test.bam
BaalChIP/inst/test/bamFiles/AMOVC_1_gDNA.test.bam.bai
BaalChIP/inst/test/bamFiles/AMOVC_2.test.bam
BaalChIP/inst/test/bamFiles/AMOVC_2.test.bam.bai
BaalChIP/inst/test/bamFiles/AMOVC_2_gDNA.test.bam
BaalChIP/inst/test/bamFiles/AMOVC_2_gDNA.test.bam.bai
BaalChIP/inst/test/bamFiles/GM12891_PAX5_Rep1.bam
BaalChIP/inst/test/bamFiles/GM12891_PAX5_Rep1.bam.bai
BaalChIP/inst/test/bamFiles/GM12891_PAX5_Rep2.bam
BaalChIP/inst/test/bamFiles/GM12891_PAX5_Rep2.bam.bai
BaalChIP/inst/test/bamFiles/GM12891_POL2_Rep1.bam
BaalChIP/inst/test/bamFiles/GM12891_POL2_Rep1.bam.bai
BaalChIP/inst/test/bamFiles/GM12891_POL2_Rep2.bam
BaalChIP/inst/test/bamFiles/GM12891_POL2_Rep2.bam.bai
BaalChIP/inst/test/bamFiles/GM12891_PU1_Rep1.bam
BaalChIP/inst/test/bamFiles/GM12891_PU1_Rep1.bam.bai
BaalChIP/inst/test/bamFiles/GM12891_PU1_Rep2.bam
BaalChIP/inst/test/bamFiles/GM12891_PU1_Rep2.bam.bai
BaalChIP/inst/test/bamFiles/GM12891_TAF1_Rep1.bam
BaalChIP/inst/test/bamFiles/GM12891_TAF1_Rep1.bam.bai
BaalChIP/inst/test/bamFiles/GM12891_TAF1_Rep2.bam
BaalChIP/inst/test/bamFiles/GM12891_TAF1_Rep2.bam.bai
BaalChIP/inst/test/bamFiles/MCF7_POL2_Rep1.bam
BaalChIP/inst/test/bamFiles/MCF7_POL2_Rep1.bam.bai
BaalChIP/inst/test/bamFiles/MCF7_POL2_Rep2.bam
BaalChIP/inst/test/bamFiles/MCF7_POL2_Rep2.bam.bai
BaalChIP/inst/test/bamFiles/MCF7_STAT3_Rep1.bam
BaalChIP/inst/test/bamFiles/MCF7_STAT3_Rep1.bam.bai
BaalChIP/inst/test/bamFiles/MCF7_STAT3_Rep2.bam
BaalChIP/inst/test/bamFiles/MCF7_STAT3_Rep2.bam.bai
BaalChIP/inst/test/bamFiles/MCF7_cFOS_Rep1.bam
BaalChIP/inst/test/bamFiles/MCF7_cFOS_Rep1.bam.bai
BaalChIP/inst/test/bamFiles/MCF7_cFOS_Rep2.bam
BaalChIP/inst/test/bamFiles/MCF7_cFOS_Rep2.bam.bai
BaalChIP/inst/test/bamFiles/MCF7_cMYC_Rep1.bam
BaalChIP/inst/test/bamFiles/MCF7_cMYC_Rep1.bam.bai
BaalChIP/inst/test/bamFiles/MCF7_cMYC_Rep2.bam
BaalChIP/inst/test/bamFiles/MCF7_cMYC_Rep2.bam.bai
BaalChIP/inst/test/bamFiles/TaT1_1.test.bam
BaalChIP/inst/test/bamFiles/TaT1_1.test.bam.bai
BaalChIP/inst/test/bamFiles/TaT1_1_gDNA.test.bam
BaalChIP/inst/test/bamFiles/TaT1_1_gDNA.test.bam.bai
BaalChIP/inst/test/bamFiles/TaT1_2.test.bam
BaalChIP/inst/test/bamFiles/TaT1_2.test.bam.bai
BaalChIP/inst/test/bamFiles/TaT1_2_gDNA.test.bam
BaalChIP/inst/test/bamFiles/TaT1_2_gDNA.test.bam.bai
BaalChIP/inst/test/bedFiles/
BaalChIP/inst/test/bedFiles/AMOVC_peaks_example.bed
BaalChIP/inst/test/bedFiles/GM12891_PAX5.bed
BaalChIP/inst/test/bedFiles/GM12891_POL2.bed
BaalChIP/inst/test/bedFiles/GM12891_POU2F2.bed
BaalChIP/inst/test/bedFiles/GM12891_PU1.bed
BaalChIP/inst/test/bedFiles/GM12891_TAF1.bed
BaalChIP/inst/test/bedFiles/GM12891_YY1.bed
BaalChIP/inst/test/bedFiles/MCF7_POL2.bed
BaalChIP/inst/test/bedFiles/MCF7_STAT3.bed
BaalChIP/inst/test/bedFiles/MCF7_cFOS.bed
BaalChIP/inst/test/bedFiles/MCF7_cMYC.bed
BaalChIP/inst/test/bedFiles/TaT1_peaks_example.bed
BaalChIP/inst/test/exampleChIP.tsv
BaalChIP/inst/test/exampleChIP1.tsv
BaalChIP/inst/test/exampleChIP2.tsv
BaalChIP/inst/test/simuloutput/
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln32.bam
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln32.bam.bai
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln32.fasta
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln32.fasta.sam
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln32_snplist.txt
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln34.bam
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln34.bam.bai
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln34.fasta
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln34.fasta.sam
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln36.bam
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln36.bam.bai
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln36.fasta
BaalChIP/inst/test/simuloutput/c67c6ec6c433_aln36.fasta.sam
BaalChIP/inst/test/simuloutput/c67c6ec6c433_snplist.txt
BaalChIP/inst/unitTests/
BaalChIP/inst/unitTests/test_get_allele_counts.R
BaalChIP/man/
BaalChIP/man/BaalChIP.Rd
BaalChIP/man/BaalChIP.get.Rd
BaalChIP/man/BaalChIP.report.Rd
BaalChIP/man/BaalChIP.run.Rd
BaalChIP/man/BaalObject.Rd
BaalChIP/man/ENCODEexample.Rd
BaalChIP/man/FAIREexample.Rd
BaalChIP/man/QCfilter.Rd
BaalChIP/man/UniqueMappability50bp_hg19.Rd
BaalChIP/man/adjustmentBaalPlot.Rd
BaalChIP/man/alleleCounts.Rd
BaalChIP/man/blacklist_hg19.Rd
BaalChIP/man/filter1allele.Rd
BaalChIP/man/filterIntbias.Rd
BaalChIP/man/getASB.Rd
BaalChIP/man/mergePerGroup.Rd
BaalChIP/man/pickrell2011cov1_hg19.Rd
BaalChIP/man/plotQC.Rd
BaalChIP/man/plotSimul.Rd
BaalChIP/man/summaryASB.Rd
BaalChIP/man/summaryQC.Rd
BaalChIP/tests/
BaalChIP/tests/runTests.R
BaalChIP/vignettes/
BaalChIP/vignettes/BaalChIP-vignette.bib
BaalChIP/vignettes/BaalChIP.Rmd
BaalChIP/vignettes/baal.png
BaalChIP/vignettes/biomed-central.csl
phase `unpack' succeeded after 0.3 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/extra/get.overlaps.v2_chrXY.perl: warning: no binary for interpreter `perl' found in $PATH
patch-shebang: ./inst/extra/run_simulations.sh: changing `/bin/sh' to `/gnu/store/k66i68s5l93n1lgxp29vn2292nsywp1v-bash-minimal-5.2.37/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 ‘BaalChIP’ ...
** this is package ‘BaalChIP’ version ‘1.36.0’
file ‘inst/extra/run_simulations.sh’ has the wrong MD5 checksum
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BaalChIP)
phase `install' succeeded after 84.7 seconds
starting phase `check'
Running specific tests for package ‘BaalChIP’
  Running ‘runTests.R’
Running vignettes for package ‘BaalChIP’
phase `check' succeeded after 20.3 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 `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