[ Started: 2024-03-31 12:25:34 CEST ] [ CARNIVAL v2.7.2 for BioC-3.19 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.19" [3] "/home/omnipath/local/R/4.4" "/opt/R-devel/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/data.table_1.15.4.tar.gz' Content type 'application/x-gzip' length 5387593 bytes (5.1 MB) ================================================== downloaded 5.1 MB * installing *source* package ‘data.table’ ... ** package ‘data.table’ successfully unpacked and MD5 sums checked ** using staged installation gcc 11.4.0 zlib 1.2.11 is available ok R CMD SHLIB supports OpenMP without any extra hint ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/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/4.4-3.19/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) The downloaded source packages are in ‘/tmp/RtmpY0C52n/downloaded_packages’ Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable) (2024-03-23 r86179) Old packages: 'Biobase', 'wppi' trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/Biobase_2.63.1.tar.gz' Content type 'application/x-gzip' length 1796047 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.11.0.tar.gz' Content type 'application/x-gzip' length 662120 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘Biobase’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rinit.c -o Rinit.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 envir.c -o envir.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c matchpt.c -o matchpt.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowMedians.c -o rowMedians.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sublist_extract.c -o sublist_extract.o gcc -shared -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-Biobase/00new/Biobase/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 (Biobase) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-03-31 12:26:07] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-31 12:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:07] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-31 12:26:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:07] [TRACE] [OmnipathR] Contains 1 files. [2024-03-31 12:26:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-31 12:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-31 12:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:07] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-31 12:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-31 12:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-31 12:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-31 12:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-31 12:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:07] [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 [2024-03-31 12:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-31 12:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:09] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-31 12:26:09] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:09] [TRACE] [OmnipathR] Contains 1 files. [2024-03-31 12:26:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-31 12:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-31 12:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:09] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-31 12:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-31 12:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-31 12:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-31 12:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-31 12:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:09] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-03-31 12:26:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-31 12:26:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:11] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-31 12:26:11] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:11] [TRACE] [OmnipathR] Contains 1 files. [2024-03-31 12:26:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-31 12:26:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-31 12:26:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-31 12:26:11] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-31 12:26:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-31 12:26:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-31 12:26:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-31 12:26:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-31 12:26:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-31 12:26:11] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) The downloaded source packages are in ‘/tmp/RtmpY0C52n/downloaded_packages’ Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable) (2024-03-23 r86179) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 1 packages ahead of CRAN: BiocStyle [ Finished: 2024-03-31 12:26:14 CEST ]