[ Started: 2024-01-30 11:51:15 CET ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.18" [3] "/home/omnipath/local/R/4.3" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/listenv_0.9.1.tar.gz' Content type 'application/x-gzip' length 36600 bytes (35 KB) ================================================== downloaded 35 KB * installing *source* package ‘listenv’ ... ** package ‘listenv’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 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 (listenv) The downloaded source packages are in ‘/tmp/RtmpkKq34z/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Old packages: 'Biostrings', 'data.table' trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Biostrings_2.70.2.tar.gz' Content type 'application/x-gzip' length 12741368 bytes (12.2 MB) ================================================== downloaded 12.2 MB trying URL 'https://cloud.r-project.org/src/contrib/data.table_1.15.0.tar.gz' Content type 'application/x-gzip' length 5385187 bytes (5.1 MB) ================================================== downloaded 5.1 MB * installing *source* package ‘Biostrings’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c BAB_class.c -o BAB_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c BitMatrix.c -o BitMatrix.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MIndex_class.c -o MIndex_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SparseList_utils.c -o SparseList_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XStringSet_class.c -o XStringSet_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XString_class.c -o XString_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c align_needwunsQS.c -o align_needwunsQS.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c align_utils.c -o align_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c find_palindromes.c -o find_palindromes.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gtestsim.c -o gtestsim.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c inject_code.c -o inject_code.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c letter_frequency.c -o letter_frequency.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_PWM.c -o match_PWM.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pattern.c -o match_pattern.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pattern_indels.c -o match_pattern_indels.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pdict.c -o match_pdict.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pdict_utils.c -o match_pdict_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_reporting.c -o match_reporting.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c matchprobes.c -o matchprobes.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pmatchPattern.c -o pmatchPattern.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_fasta_files.c -o read_fasta_files.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_fastq_files.c -o read_fastq_files.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceAt.c -o replaceAt.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replace_letter_at.c -o replace_letter_at.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c strutils.c -o strutils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c translate.c -o translate.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.18/IRanges/include' -I'/home/omnipath/local/R/4.3-3.18/XVector/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c xscat.c -o xscat.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-Biostrings/00new/Biostrings/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet” Creating a new generic function for ‘strsplit’ in package ‘Biostrings’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’ Creating a new generic function for ‘pattern’ in package ‘Biostrings’ Creating a new generic function for ‘offset’ in package ‘Biostrings’ ** 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 (Biostrings) * installing *source* package ‘data.table’ ... ** package ‘data.table’ successfully unpacked and MD5 sums checked ** using staged installation gcc 11.4.0 zlib 1.2.11 is available ok R CMD SHLIB supports OpenMP without any extra hint ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c assign.c -o assign.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c between.c -o between.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bmerge.c -o bmerge.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c chmatch.c -o chmatch.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cj.c -o cj.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c coalesce.c -o coalesce.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dogroups.c -o dogroups.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fastmean.c -o fastmean.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fcast.c -o fcast.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fifelse.c -o fifelse.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fmelt.c -o fmelt.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c forder.c -o forder.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c frank.c -o frank.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fread.c -o fread.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c freadR.c -o freadR.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c froll.c -o froll.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c frollR.c -o frollR.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c frolladaptive.c -o frolladaptive.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fsort.c -o fsort.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fwrite.c -o fwrite.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fwriteR.c -o fwriteR.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gsumm.c -o gsumm.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c idatetime.c -o idatetime.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ijoin.c -o ijoin.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c inrange.c -o inrange.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nafill.c -o nafill.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c negate.c -o negate.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nqrecreateindices.c -o nqrecreateindices.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c openmp-utils.c -o openmp-utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c programming.c -o programming.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c quickselect.c -o quickselect.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rbindlist.c -o rbindlist.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c reorder.c -o reorder.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c shift.c -o shift.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c snprintf.c -o snprintf.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c subset.c -o subset.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c transpose.c -o transpose.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c types.c -o types.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c uniqlist.c -o uniqlist.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vecseq.c -o vecseq.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c wrappers.c -o wrappers.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/usr/lib/R/lib -lR PKG_CFLAGS = -fopenmp PKG_LIBS = -fopenmp -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /home/omnipath/local/R/4.3-3.18/00LOCK-data.table/00new/data.table/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 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 (data.table) The downloaded source packages are in ‘/tmp/RtmpkKq34z/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2024-01-30 11:52:08 CET ]