[ Started: 2024-11-26 12:19:17 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" '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: 'later', 'promises', 'usethis', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/later_1.4.0.tar.gz' Content type 'application/x-gzip' length 69382 bytes (67 KB) ================================================== downloaded 67 KB trying URL 'https://cloud.r-project.org/src/contrib/promises_1.3.1.tar.gz' Content type 'application/x-gzip' length 3166648 bytes (3.0 MB) ================================================== downloaded 3.0 MB trying URL 'https://cloud.r-project.org/src/contrib/usethis_3.1.0.tar.gz' Content type 'application/x-gzip' length 384582 bytes (375 KB) ================================================== downloaded 375 KB 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 ‘later’ ... ** package ‘later’ successfully unpacked and MD5 sums checked ** using staged installation Running configure script -latomic linker flag not needed. ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 callback_registry.cpp -o callback_registry.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 debug.cpp -o debug.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 fd.cpp -o fd.o gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 init.c -o init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 later.cpp -o later.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 later_posix.cpp -o later_posix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 later_win32.cpp -o later_win32.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 timer_posix.cpp -o timer_posix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 timestamp_unix.cpp -o timestamp_unix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 timestamp_win32.cpp -o timestamp_win32.o gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 tinycthread.c -o tinycthread.o gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 wref.c -o wref.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o later.so RcppExports.o callback_registry.o debug.o fd.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o wref.o -pthread -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-later/00new/later/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 (later) * installing *source* package ‘usethis’ ... ** package ‘usethis’ 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 ** 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 (usethis) * 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 [2024-11-26 12:19:48] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-26 12:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:48] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-26 12:19:48] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:48] [TRACE] [OmnipathR] Contains 1 files. [2024-11-26 12:19:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-26 12:19:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-26 12:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:48] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-26 12:19:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-26 12:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-26 12:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-26 12:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-26 12:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:48] [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 [2024-11-26 12:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-26 12:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:51] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-26 12:19:51] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:51] [TRACE] [OmnipathR] Contains 1 files. [2024-11-26 12:19:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-26 12:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-26 12:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:51] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-26 12:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-26 12:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-26 12:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-26 12:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-26 12:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:51] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-11-26 12:19:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-26 12:19:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:53] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-26 12:19:53] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:53] [TRACE] [OmnipathR] Contains 1 files. [2024-11-26 12:19:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-26 12:19:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-26 12:19:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-26 12:19:53] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-26 12:19:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-26 12:19:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-26 12:19:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-26 12:19:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-26 12:19:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-26 12:19:53] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘promises’ ... ** package ‘promises’ 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 -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 -I'/home/omnipath/local/R/4.4-3.20/later/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/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 promise_task.cpp -o promise_task.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o promises.so RcppExports.o promise_task.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-promises/00new/promises/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 (promises) The downloaded source packages are in ‘/tmp/RtmpW1OuAF/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: 2024-11-26 12:20:07 CET ]