[ Started: 2024-05-13 15:19:49 CEST ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.18" [3] "/home/omnipath/local/R/4.3" "/usr/lib/R/library" Bioconductor version '3.18' is out-of-date; the current release version '3.19' is available with R version '4.4'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29) Old packages: 'farver', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/farver_2.1.2.tar.gz' Content type 'application/x-gzip' length 1275981 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/wppi_1.10.0.tar.gz' Content type 'application/x-gzip' length 662114 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘farver’ ... ** package ‘farver’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ColorSpace.cpp -o ColorSpace.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Comparison.cpp -o Comparison.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Conversion.cpp -o Conversion.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c encode.cpp -o encode.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c farver.cpp -o farver.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o farver.so ColorSpace.o Comparison.o Conversion.o encode.o farver.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-farver/00new/farver/libs ** R ** 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 (farver) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-05-13 15:20:17] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-13 15:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:17] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:17] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-13 15:20:17] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:17] [TRACE] [OmnipathR] Contains 1 files. [2024-05-13 15:20:17] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-13 15:20:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-13 15:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:17] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-13 15:20:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-13 15:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-13 15:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-13 15:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-13 15:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:17] [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 [2024-05-13 15:20:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-13 15:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:19] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-13 15:20:19] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:19] [TRACE] [OmnipathR] Contains 1 files. [2024-05-13 15:20:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-13 15:20:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-13 15:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:19] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-13 15:20:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-13 15:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-13 15:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-13 15:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-13 15:20:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:19] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-13 15:20:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-13 15:20:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:21] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:21] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-13 15:20:21] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:21] [TRACE] [OmnipathR] Contains 1 files. [2024-05-13 15:20:21] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-13 15:20:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-13 15:20:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-13 15:20:21] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-13 15:20:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-13 15:20:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-13 15:20:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-13 15:20:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-13 15:20:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-13 15:20:21] [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/Rtmpam16f0/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29) 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: 2024-05-13 15:20:30 CEST ]