[ Started: 2024-11-19 12:19:10 CET ] [ CARNIVAL v2.7.2 for BioC-3.20 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.20" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/graphlayouts_1.2.1.tar.gz' Content type 'application/x-gzip' length 2049895 bytes (2.0 MB) ================================================== downloaded 2.0 MB * installing *source* package ‘graphlayouts’ ... ** package ‘graphlayouts’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppArmadillo/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppArmadillo/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c constrained_stress.cpp -o constrained_stress.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppArmadillo/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c constrained_stress3D.cpp -o constrained_stress3D.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppArmadillo/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c metroLayout.cpp -o metroLayout.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppArmadillo/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c reweight.cpp -o reweight.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppArmadillo/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c sparseStress.cpp -o sparseStress.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppArmadillo/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c stress.cpp -o stress.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppArmadillo/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c stress3D.cpp -o stress3D.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o graphlayouts.so RcppExports.o constrained_stress.o constrained_stress3D.o metroLayout.o reweight.o sparseStress.o stress.o stress3D.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-graphlayouts/00new/graphlayouts/libs ** 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 ** 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 (graphlayouts) The downloaded source packages are in ‘/tmp/RtmpD8yQbn/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Old packages: 'wppi' trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/wppi_1.14.0.tar.gz' Content type 'application/x-gzip' length 663228 bytes (647 KB) ================================================== downloaded 647 KB * installing *source* package ‘wppi’ ... ** package ‘wppi’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-11-19 12:19:54] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 12:19:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:54] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-19 12:19:54] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:54] [TRACE] [OmnipathR] Contains 1 files. [2024-11-19 12:19:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-19 12:19:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 12:19:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:54] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-19 12:19:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-19 12:19:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-19 12:19:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-19 12:19:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-19 12:19:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:55] [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 [2024-11-19 12:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 12:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:57] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-19 12:19:57] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:57] [TRACE] [OmnipathR] Contains 1 files. [2024-11-19 12:19:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-19 12:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 12:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:57] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-19 12:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-19 12:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-19 12:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-19 12:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-19 12:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:57] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-11-19 12:19:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 12:19:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:59] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-19 12:19:59] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:59] [TRACE] [OmnipathR] Contains 1 files. [2024-11-19 12:19:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-19 12:19:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 12:19:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-19 12:19:59] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-19 12:19:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-19 12:19:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-19 12:19:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-19 12:19:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-19 12:19:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 12:19:59] [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/RtmpD8yQbn/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) 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: 2024-11-19 12:20:06 CET ]