[ Started: 2025-02-13 19:41:29 CET ] [ cosmosR v1.9.1 for BioC-3.21 from https://github.com/saezlab/cosmosR@master (81d1a7f 2024-07-23 10:15:19) ] [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) 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' formatR (NA -> 1.14 ) [CRAN] futile.op... (NA -> 1.0.1 ) [CRAN] lambda.r (NA -> 1.2.4 ) [CRAN] snow (NA -> 0.4-4 ) [CRAN] futile.lo... (NA -> 1.4.3 ) [CRAN] cowplot (NA -> 1.1.3 ) [CRAN] BiocParallel (NA -> 1.41.0) [CRAN] statmod (NA -> 1.5.0 ) [CRAN] limma (NA -> 3.63.3) [CRAN] sets (NA -> 1.0-25) [CRAN] slam (NA -> 0.1-55) [CRAN] caTools (NA -> 1.18.3) [CRAN] gtools (NA -> 3.9.5 ) [CRAN] GenomeInf... (NA -> 1.2.13) [CRAN] UCSC.utils (NA -> 1.3.1 ) [CRAN] GenomeInfoDb (NA -> 1.43.4) [CRAN] XVector (NA -> 0.47.2) [CRAN] Biostrings (NA -> 2.75.3) [CRAN] png (NA -> 0.1-8 ) [CRAN] KEGGREST (NA -> 1.47.0) [CRAN] S4Vectors (NA -> 0.45.4) [CRAN] IRanges (NA -> 2.41.3) [CRAN] Annotatio... (NA -> 1.69.0) [CRAN] parallelly (NA -> 1.42.0) [CRAN] broom (NA -> 1.0.7 ) [CRAN] visNetwork (NA -> 2.1.2 ) [CRAN] shinydash... (NA -> 0.7.2 ) [CRAN] shinyjs (NA -> 2.1.0 ) [CRAN] DT (NA -> 0.33 ) [CRAN] fgsea (NA -> 1.33.2) [CRAN] marray (NA -> 1.85.0) [CRAN] relations (NA -> 0.6-14) [CRAN] gplots (NA -> 3.2.0 ) [CRAN] annotate (NA -> 1.85.0) [CRAN] decoupleR (NA -> 2.13.0) [CRAN] bcellViper (NA -> 1.43.0) [CRAN] reshape2 (NA -> 1.4.4 ) [CRAN] piano (NA -> 2.23.0) [CRAN] markdown (NA -> 1.13 ) [CRAN] GSEABase (NA -> 1.69.1) [CRAN] dorothea (NA -> 1.19.0) [CRAN] Skipping 1 packages ahead of CRAN: cli Installing 41 packages: formatR, futile.options, lambda.r, snow, futile.logger, cowplot, BiocParallel, statmod, limma, sets, slam, caTools, gtools, GenomeInfoDbData, UCSC.utils, GenomeInfoDb, XVector, Biostrings, png, KEGGREST, S4Vectors, IRanges, AnnotationDbi, parallelly, broom, visNetwork, shinydashboard, shinyjs, DT, fgsea, marray, relations, gplots, annotate, decoupleR, bcellViper, reshape2, piano, markdown, GSEABase, dorothea trying URL 'https://cran.uni-muenster.de/src/contrib/formatR_1.14.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/futile.options_1.0.1.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/lambda.r_1.2.4.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/snow_0.4-4.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/futile.logger_1.4.3.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/cowplot_1.1.3.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/BiocParallel_1.41.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/statmod_1.5.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/limma_3.63.3.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/sets_1.0-25.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/slam_0.1-55.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/caTools_1.18.3.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/gtools_3.9.5.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/data/annotation/src/contrib/GenomeInfoDbData_1.2.13.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/UCSC.utils_1.3.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/GenomeInfoDb_1.43.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/XVector_0.47.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/Biostrings_2.75.3.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/png_0.1-8.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/KEGGREST_1.47.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/S4Vectors_0.45.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/IRanges_2.41.3.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/AnnotationDbi_1.69.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/parallelly_1.42.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/broom_1.0.7.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/visNetwork_2.1.2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/shinydashboard_0.7.2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/shinyjs_2.1.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/DT_0.33.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/fgsea_1.33.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/marray_1.85.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/relations_0.6-14.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/gplots_3.2.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/annotate_1.85.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/decoupleR_2.13.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/data/experiment/src/contrib/bcellViper_1.43.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/reshape2_1.4.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/piano_2.23.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/markdown_1.13.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/GSEABase_1.69.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/data/experiment/src/contrib/dorothea_1.19.0.tar.gz' * installing *source* package ‘formatR’ ... ** this is package ‘formatR’ version ‘1.14’ ** package ‘formatR’ 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 (formatR) * installing *source* package ‘futile.options’ ... ** this is package ‘futile.options’ version ‘1.0.1’ ** package ‘futile.options’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (futile.options) * installing *source* package ‘snow’ ... ** this is package ‘snow’ version ‘0.4-4’ ** package ‘snow’ 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 ** 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 (snow) * installing *source* package ‘cowplot’ ... ** this is package ‘cowplot’ version ‘1.1.3’ ** package ‘cowplot’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (cowplot) * installing *source* package ‘statmod’ ... ** this is package ‘statmod’ version ‘1.5.0’ ** package ‘statmod’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c expectedDeviance.c -o expectedDeviance.o gfortran -fpic -g -O2 -c gaussq2.f -o gaussq2.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/usr/local/lib -o statmod.so expectedDeviance.o gaussq2.o init.o -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.5-3.21/00LOCK-statmod/00new/statmod/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (statmod) * installing *source* package ‘sets’ ... ** this is package ‘sets’ version ‘1.0-25’ ** package ‘sets’ 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/usr/local/include -fpic -g -O2 -c closure.c -o closure.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -shared -L/usr/local/lib -o sets.so closure.o init.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-sets/00new/sets/libs ** R ** data ** 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 (sets) * installing *source* package ‘slam’ ... ** this is package ‘slam’ version ‘0.1-55’ ** package ‘slam’ 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/usr/local/include -fpic -g -O2 -c apply.c -o apply.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dll.c -o dll.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c grouped.c -o grouped.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sparse.c -o sparse.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c util.c -o util.o gcc -shared -L/usr/local/lib -o slam.so apply.o dll.o grouped.o sparse.o util.o -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.5-3.21/00LOCK-slam/00new/slam/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (slam) * installing *source* package ‘caTools’ ... ** this is package ‘caTools’ version ‘1.18.3’ ** package ‘caTools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Gif2R.cpp -o Gif2R.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c GifTools.cpp -o GifTools.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c caTools_init.c -o caTools_init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c runfunc.c -o runfunc.o g++ -std=gnu++17 -shared -L/usr/local/lib -o caTools.so Gif2R.o GifTools.o caTools_init.o runfunc.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-caTools/00new/caTools/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (caTools) * installing *source* package ‘gtools’ ... ** this is package ‘gtools’ version ‘3.9.5’ ** package ‘gtools’ 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/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c roman2int.c -o roman2int.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c setTCPNoDelay.c -o setTCPNoDelay.o gcc -shared -L/usr/local/lib -o gtools.so init.o roman2int.o setTCPNoDelay.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-gtools/00new/gtools/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (gtools) * installing *source* package ‘GenomeInfoDbData’ ... ** this is package ‘GenomeInfoDbData’ version ‘1.2.13’ ** using staged installation ** data ** inst ** help *** installing help indices ** building package indices ** 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 (GenomeInfoDbData) * installing *source* package ‘png’ ... ** this is package ‘png’ version ‘0.1-8’ ** package ‘png’ 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/usr/local/include `libpng-config --cflags` -fpic -g -O2 -c dummy.c -o dummy.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -c read.c -o read.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -c write.c -o write.o gcc -shared -L/usr/local/lib -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm installing to /home/omnipath/local/R/4.5-3.21/00LOCK-png/00new/png/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (png) * installing *source* package ‘S4Vectors’ ... ** this is package ‘S4Vectors’ version ‘0.45.4’ ** 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/usr/local/include -fpic -g -O2 -c AEbufs.c -o AEbufs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Hits_class.c -o Hits_class.o In file included from /usr/include/string.h:548, from /opt/R-devel/lib/R/include/R_ext/RS.h:34, from /opt/R-devel/lib/R/include/Rdefines.h:38, from ../inst/include/S4Vectors_defines.h:18, from S4Vectors.h:1, from Hits_class.c:4: In function ‘memcpy’, inlined from ‘tsort_hits’ at Hits_class.c:113:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c LLint_class.c -o LLint_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c List_class.c -o List_class.o gcc -I"/opt/R-devel/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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_class.c -o Rle_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_utils.c -o Rle_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SEXP_utils.c -o SEXP_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SimpleList_class.c -o SimpleList_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c character_utils.c -o character_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c eval_utils.c -o eval_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hash_utils.c -o hash_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c integer_utils.c -o integer_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c logical_utils.c -o logical_utils.o gcc -I"/opt/R-devel/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-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c raw_utils.c -o raw_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c safe_arithm.c -o safe_arithm.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sort_utils.c -o sort_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c subsetting_utils.c -o subsetting_utils.o gcc -I"/opt/R-devel/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/4.5-3.21/00LOCK-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’ 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 ‘parallelly’ ... ** this is package ‘parallelly’ version ‘1.42.0’ ** package ‘parallelly’ 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/usr/local/include -fpic -g -O2 -c 000.init.c -o 000.init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c calc-serialized-size.c -o calc-serialized-size.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c test_tcp_port.c -o test_tcp_port.o gcc -shared -L/usr/local/lib -o parallelly.so 000.init.o calc-serialized-size.o test_tcp_port.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-parallelly/00new/parallelly/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (parallelly) * installing *source* package ‘broom’ ... ** this is package ‘broom’ version ‘1.0.7’ ** package ‘broom’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (broom) * installing *source* package ‘visNetwork’ ... ** this is package ‘visNetwork’ version ‘2.1.2’ ** package ‘visNetwork’ 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 (visNetwork) * installing *source* package ‘shinydashboard’ ... ** this is package ‘shinydashboard’ version ‘0.7.2’ ** package ‘shinydashboard’ 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 ** 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 (shinydashboard) * installing *source* package ‘shinyjs’ ... ** this is package ‘shinyjs’ version ‘2.1.0’ ** package ‘shinyjs’ 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 (shinyjs) * installing *source* package ‘DT’ ... ** this is package ‘DT’ version ‘0.33’ ** package ‘DT’ 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 (DT) * installing *source* package ‘bcellViper’ ... ** this is package ‘bcellViper’ version ‘1.43.0’ ** using staged installation ** data ** inst ** 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 (bcellViper) * installing *source* package ‘reshape2’ ... ** this is package ‘reshape2’ version ‘1.4.4’ ** package ‘reshape2’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c melt.cpp -o melt.o g++ -std=gnu++17 -shared -L/usr/local/lib -o reshape2.so RcppExports.o melt.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-reshape2/00new/reshape2/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (reshape2) * installing *source* package ‘markdown’ ... ** this is package ‘markdown’ version ‘1.13’ ** package ‘markdown’ 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 ** 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 (markdown) * installing *source* package ‘lambda.r’ ... ** this is package ‘lambda.r’ version ‘1.2.4’ ** package ‘lambda.r’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (lambda.r) * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.63.3’ ** 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/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-limma/00new/limma/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 (limma) * installing *source* package ‘UCSC.utils’ ... ** this is package ‘UCSC.utils’ version ‘1.3.1’ ** 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 (UCSC.utils) * installing *source* package ‘IRanges’ ... ** this is package ‘IRanges’ version ‘2.41.3’ ** 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/usr/local/include -fpic -g -O2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c CompressedList_class.c -o CompressedList_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c Grouping_class.c -o Grouping_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c IRanges_class.c -o IRanges_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c IRanges_constructor.c -o IRanges_constructor.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c NCList.c -o NCList.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c R_init_IRanges.c -o R_init_IRanges.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c Ranges_class.c -o Ranges_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c RleViews_utils.c -o RleViews_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/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/usr/local/include -fpic -g -O2 -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c coverage_methods.c -o coverage_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c extractListFragments.c -o extractListFragments.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/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/4.5-3.21/00LOCK-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) * installing *source* package ‘relations’ ... ** this is package ‘relations’ version ‘0.6-14’ ** package ‘relations’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (relations) * installing *source* package ‘gplots’ ... ** this is package ‘gplots’ version ‘3.2.0’ ** package ‘gplots’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (gplots) * installing *source* package ‘futile.logger’ ... ** this is package ‘futile.logger’ version ‘1.4.3’ ** package ‘futile.logger’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (futile.logger) * installing *source* package ‘GenomeInfoDb’ ... ** this is package ‘GenomeInfoDb’ version ‘1.43.4’ ** 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 (GenomeInfoDb) * installing *source* package ‘XVector’ ... ** this is package ‘XVector’ version ‘0.47.2’ ** 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/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/usr/local/include -fpic -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.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/usr/local/include -fpic -g -O2 -c RDS_random_access.c -o RDS_random_access.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/usr/local/include -fpic -g -O2 -c R_init_XVector.c -o R_init_XVector.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/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/usr/local/include -fpic -g -O2 -c SharedDouble_class.c -o SharedDouble_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/usr/local/include -fpic -g -O2 -c SharedInteger_class.c -o SharedInteger_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/usr/local/include -fpic -g -O2 -c SharedRaw_class.c -o SharedRaw_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/usr/local/include -fpic -g -O2 -c SharedVector_class.c -o SharedVector_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/usr/local/include -fpic -g -O2 -c XDouble_class.c -o XDouble_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/usr/local/include -fpic -g -O2 -c XInteger_class.c -o XInteger_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/usr/local/include -fpic -g -O2 -c XRawList_comparison.c -o XRawList_comparison.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/usr/local/include -fpic -g -O2 -c XRaw_class.c -o XRaw_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/usr/local/include -fpic -g -O2 -c XVectorList_class.c -o XVectorList_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/usr/local/include -fpic -g -O2 -c XVector_class.c -o XVector_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/usr/local/include -fpic -g -O2 -c io_utils.c -o io_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/usr/local/include -fpic -g -O2 -c slice_methods.c -o slice_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/usr/local/include -fpic -g -O2 -c vector_copy.c -o vector_copy.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/usr/local/include -fpic -g -O2 -c view_summarization_methods.c -o view_summarization_methods.o gcc -shared -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz installing to /home/omnipath/local/R/4.5-3.21/00LOCK-XVector/00new/XVector/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (XVector) * installing *source* package ‘marray’ ... ** this is package ‘marray’ version ‘1.85.0’ ** using staged installation ** R ** data ** 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 (marray) * installing *source* package ‘BiocParallel’ ... ** this is package ‘BiocParallel’ version ‘1.41.0’ ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking for library containing shm_open... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/mman.h... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ipcmutex.cpp -o ipcmutex.o g++ -std=gnu++11 -shared -L/usr/local/lib -o BiocParallel.so cpp11.o ipcmutex.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-BiocParallel/00new/BiocParallel/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 (BiocParallel) * installing *source* package ‘Biostrings’ ... ** this is package ‘Biostrings’ version ‘2.75.3’ ** 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 ‘KEGGREST’ ... ** this is package ‘KEGGREST’ version ‘1.47.0’ ** 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 (KEGGREST) * installing *source* package ‘fgsea’ ... ** this is package ‘fgsea’ version ‘1.33.2’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c ScoreCalculation.cpp -o ScoreCalculation.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c ScoreRuler.cpp -o ScoreRuler.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c esCalculation.cpp -o esCalculation.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c fastGSEA.cpp -o fastGSEA.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c fgseaMultilevel.cpp -o fgseaMultilevel.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c geseca.cpp -o geseca.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c util.cpp -o util.o g++ -std=gnu++17 -shared -L/usr/local/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-fgsea/00new/fgsea/libs ** R ** data *** moving datasets to lazyload DB ** 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 (fgsea) * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.13.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (decoupleR) * installing *source* package ‘AnnotationDbi’ ... ** this is package ‘AnnotationDbi’ version ‘1.69.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’ ** 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 (AnnotationDbi) * installing *source* package ‘piano’ ... ** this is package ‘piano’ version ‘2.23.0’ ** using staged installation ** R ** data ** 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 (piano) * installing *source* package ‘dorothea’ ... ** this is package ‘dorothea’ version ‘1.19.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (dorothea) * installing *source* package ‘annotate’ ... ** this is package ‘annotate’ version ‘1.85.0’ ** using staged installation ** R ** data ** 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 (annotate) * installing *source* package ‘GSEABase’ ... ** this is package ‘GSEABase’ version ‘1.69.1’ ** 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 (GSEABase) The downloaded source packages are in ‘/tmp/Rtmp54IHBA/downloaded_packages’ [ Finished: 2025-02-13 19:46:43 CET ]