[ Started: 2023-04-02 11:38:53 CEST ] [ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/opt/R-devel/lib/R/library" Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable) (2023-03-16 r83996) Old packages: 'BiocCheck', 'Biostrings', 'ComplexHeatmap' trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/BiocCheck_1.35.17.tar.gz' Content type 'application/x-gzip' length 4374124 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/Biostrings_2.67.2.tar.gz' Content type 'application/x-gzip' length 12446309 bytes (11.9 MB) ================================================== downloaded 11.9 MB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/ComplexHeatmap_2.15.3.tar.gz' Content type 'application/x-gzip' length 1454016 bytes (1.4 MB) ================================================== downloaded 1.4 MB * installing *source* package ‘BiocCheck’ ... ** 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 (BiocCheck) * installing *source* package ‘Biostrings’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c BAB_class.c -o BAB_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c BitMatrix.c -o BitMatrix.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c MIndex_class.c -o MIndex_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseList_utils.c -o SparseList_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c XStringSet_class.c -o XStringSet_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c XString_class.c -o XString_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c align_utils.c -o align_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c find_palindromes.c -o find_palindromes.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c gtestsim.c -o gtestsim.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c inject_code.c -o inject_code.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c letter_frequency.c -o letter_frequency.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_PWM.c -o match_PWM.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pattern.c -o match_pattern.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pattern_indels.c -o match_pattern_indels.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pdict.c -o match_pdict.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_pdict_utils.c -o match_pdict_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c match_reporting.c -o match_reporting.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c matchprobes.c -o matchprobes.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c pmatchPattern.c -o pmatchPattern.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c read_fasta_files.c -o read_fasta_files.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c read_fastq_files.c -o read_fastq_files.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c replaceAt.c -o replaceAt.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c replace_letter_at.c -o replace_letter_at.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c strutils.c -o strutils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c translate.c -o translate.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I'/home/omnipath/local/R/4.3-3.17/IRanges/include' -I'/home/omnipath/local/R/4.3-3.17/XVector/include' -I/usr/local/include -fpic -g -O2 -c xscat.c -o xscat.o gcc -shared -L/usr/local/lib -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 installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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 ‘ComplexHeatmap’ ... ** 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 (ComplexHeatmap) The downloaded source packages are in ‘/tmp/RtmpFbLGf0/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable) (2023-03-16 r83996) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 17 packages not available: BiocManager, yaml, rmarkdown, knitr, bookdown, sessioninfo, testthat, covr, RefManageR, rjson, tidyr, tibble, dplyr, igraph, lpSolve, stringr, readr [ Finished: 2023-04-02 11:39:42 CEST ]