[ Started: 2023-04-10 23:23:35 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-beta/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 4.3.0 beta (2023-04-08 r84203) Old packages: 'IRanges', 'S4Vectors' trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/IRanges_2.33.1.tar.gz' Content type 'application/x-gzip' length 480948 bytes (469 KB) ================================================== downloaded 469 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/S4Vectors_0.37.5.tar.gz' Content type 'application/x-gzip' length 837790 bytes (818 KB) ================================================== downloaded 818 KB * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c AEbufs.c -o AEbufs.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Hits_class.c -o Hits_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c LLint_class.c -o LLint_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c List_class.c -o List_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_class.c -o Rle_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_utils.c -o Rle_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SEXP_utils.c -o SEXP_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SimpleList_class.c -o SimpleList_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c character_utils.c -o character_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c eval_utils.c -o eval_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hash_utils.c -o hash_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c integer_utils.c -o integer_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c logical_utils.c -o logical_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c raw_utils.c -o raw_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c safe_arithm.c -o safe_arithm.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sort_utils.c -o sort_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c subsetting_utils.c -o subsetting_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c vector_utils.c -o vector_utils.o gcc -shared -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o installing to /home/omnipath/local/R/4.3-3.17/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List” Creating a new generic function for ‘unname’ in package ‘S4Vectors’ Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’ Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’ Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame” Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table” Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’ ** 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 (S4Vectors) * installing *source* package ‘IRanges’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c CompressedList_class.c -o CompressedList_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c Grouping_class.c -o Grouping_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c IRanges_class.c -o IRanges_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c IRanges_constructor.c -o IRanges_constructor.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c NCList.c -o NCList.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c R_init_IRanges.c -o R_init_IRanges.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c Ranges_class.c -o Ranges_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c RleViews_utils.c -o RleViews_utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c coverage_methods.c -o coverage_methods.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c extractListFragments.c -o extractListFragments.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c inter_range_methods.c -o inter_range_methods.o gcc -shared -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o installing to /home/omnipath/local/R/4.3-3.17/00LOCK-IRanges/00new/IRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ ** 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 (IRanges) The downloaded source packages are in ‘/tmp/RtmpUfhKvs/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 beta (2023-04-08 r84203) 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: 2023-04-10 23:24:36 CEST ]