[ Started: 2025-02-23 00:05:26 CET ] [ CARNIVAL v2.7.2 for BioC-3.21 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/opt/R-devel/lib/R/library" Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Old packages: 'BiocCheck', 'Biostrings', 'data.table', 'wppi', 'zoo' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/BiocCheck_1.43.12.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/Biostrings_2.75.4.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/data.table_1.17.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/zoo_1.8-13.tar.gz' * installing *source* package ‘BiocCheck’ ... ** this is package ‘BiocCheck’ version ‘1.43.12’ ** 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’ ... ** this is package ‘Biostrings’ version ‘2.75.4’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/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 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/4.5-3.21/00LOCK-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 ‘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’ ... ** this is package ‘data.table’ version ‘1.17.0’ ** package ‘data.table’ successfully unpacked and MD5 sums checked ** using staged installation gcc 13.3.0 zlib 1.3 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c assign.c -o assign.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c between.c -o between.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c bmerge.c -o bmerge.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c chmatch.c -o chmatch.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c cj.c -o cj.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c coalesce.c -o coalesce.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c dogroups.c -o dogroups.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fastmean.c -o fastmean.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fcast.c -o fcast.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fifelse.c -o fifelse.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fmelt.c -o fmelt.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c forder.c -o forder.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c frank.c -o frank.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fread.c -o fread.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c freadR.c -o freadR.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c froll.c -o froll.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c frollR.c -o frollR.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c frolladaptive.c -o frolladaptive.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fsort.c -o fsort.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fwrite.c -o fwrite.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c fwriteR.c -o fwriteR.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c gsumm.c -o gsumm.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c idatetime.c -o idatetime.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c ijoin.c -o ijoin.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c inrange.c -o inrange.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c nafill.c -o nafill.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c negate.c -o negate.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c nqrecreateindices.c -o nqrecreateindices.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c openmp-utils.c -o openmp-utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c programming.c -o programming.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c quickselect.c -o quickselect.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c rbindlist.c -o rbindlist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c reorder.c -o reorder.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c shift.c -o shift.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c snprintf.c -o snprintf.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c subset.c -o subset.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c transpose.c -o transpose.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c types.c -o types.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c uniqlist.c -o uniqlist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c vecseq.c -o vecseq.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c wrappers.c -o wrappers.o gcc -shared -L/usr/local/lib -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 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/4.5-3.21/00LOCK-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) * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.15.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2025-02-23 00:06:25] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-23 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:25] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-22 00:02:54 UTC; omnipath [2025-02-23 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-23 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-22 00:02:55 UTC; unix [2025-02-23 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-23 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-23 00:06:25] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-23 00:06:25] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-02-23 00:06:25] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-02-23 00:06:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-23 00:06:25] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:25] [TRACE] [OmnipathR] Contains 1 files. [2025-02-23 00:06:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-23 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-23 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:25] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-23 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-23 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-23 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-23 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-23 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:25] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-02-23 00:06:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-23 00:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:28] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:28] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-22 00:02:54 UTC; omnipath [2025-02-23 00:06:28] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-23 00:06:28] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-22 00:02:55 UTC; unix [2025-02-23 00:06:28] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-23 00:06:28] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-23 00:06:28] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-23 00:06:28] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-02-23 00:06:28] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-02-23 00:06:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-23 00:06:28] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:28] [TRACE] [OmnipathR] Contains 1 files. [2025-02-23 00:06:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-23 00:06:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-23 00:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:28] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-23 00:06:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-23 00:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-23 00:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-23 00:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-23 00:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:28] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-23 00:06:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-23 00:06:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:30] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-22 00:02:54 UTC; omnipath [2025-02-23 00:06:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-23 00:06:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-22 00:02:55 UTC; unix [2025-02-23 00:06:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-23 00:06:30] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-23 00:06:31] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-23 00:06:31] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-02-23 00:06:31] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-02-23 00:06:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-23 00:06:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:31] [TRACE] [OmnipathR] Contains 1 files. [2025-02-23 00:06:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-23 00:06:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-23 00:06:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-23 00:06:31] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-23 00:06:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-23 00:06:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-23 00:06:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-23 00:06:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-23 00:06:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-23 00:06:31] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘zoo’ ... ** this is package ‘zoo’ version ‘1.8-13’ ** package ‘zoo’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I/usr/local/include -fpic -g -O2 -c coredata.c -o coredata.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I/usr/local/include -fpic -g -O2 -c lag.c -o lag.o gcc -shared -L/usr/local/lib -o zoo.so coredata.o init.o lag.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-zoo/00new/zoo/libs ** R ** demo ** 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 (zoo) The downloaded source packages are in ‘/tmp/Rtmpar2ugT/downloaded_packages’ Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2025-02-23 00:06:38 CET ]