[ Started: 2024-10-27 12:19:09 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: 'edgeR', 'wppi' trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/edgeR_4.3.21.tar.gz' Content type 'application/x-gzip' length 3439955 bytes (3.3 MB) ================================================== downloaded 3.3 MB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/wppi_1.13.0.tar.gz' Content type 'application/x-gzip' length 662273 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘edgeR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -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 R_exports.c -o R_exports.o gcc -I"/usr/share/R/include" -DNDEBUG -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 R_process_hairpin_reads.c -o R_process_hairpin_reads.o gcc -I"/usr/share/R/include" -DNDEBUG -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 add_prior_count.c -o add_prior_count.o gcc -I"/usr/share/R/include" -DNDEBUG -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 clowess.c -o clowess.o gcc -I"/usr/share/R/include" -DNDEBUG -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 compute_apl.c -o compute_apl.o gcc -I"/usr/share/R/include" -DNDEBUG -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 compute_cpm.c -o compute_cpm.o gcc -I"/usr/share/R/include" -DNDEBUG -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 compute_nbdev.c -o compute_nbdev.o gcc -I"/usr/share/R/include" -DNDEBUG -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 exact_test_by_dev.c -o exact_test_by_dev.o gcc -I"/usr/share/R/include" -DNDEBUG -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 fmm_spline.c -o fmm_spline.o gcc -I"/usr/share/R/include" -DNDEBUG -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 glm.c -o glm.o gcc -I"/usr/share/R/include" -DNDEBUG -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 good_turing.c -o good_turing.o gcc -I"/usr/share/R/include" -DNDEBUG -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 gcc -I"/usr/share/R/include" -DNDEBUG -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 interpolator.c -o interpolator.o gcc -I"/usr/share/R/include" -DNDEBUG -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 loess_by_col.c -o loess_by_col.o gcc -I"/usr/share/R/include" -DNDEBUG -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 object.c -o object.o gcc -I"/usr/share/R/include" -DNDEBUG -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 ql_glm.c -o ql_glm.o gcc -I"/usr/share/R/include" -DNDEBUG -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 ql_weights.c -o ql_weights.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o edgeR.so R_exports.o R_process_hairpin_reads.o add_prior_count.o clowess.o compute_apl.o compute_cpm.o compute_nbdev.o exact_test_by_dev.o fmm_spline.o glm.o good_turing.o init.o interpolator.o loess_by_col.o object.o ql_glm.o ql_weights.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-edgeR/00new/edgeR/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 (edgeR) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-10-27 12:19:26] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-27 12:19:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:26] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-27 12:19:26] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:26] [TRACE] [OmnipathR] Contains 1 files. [2024-10-27 12:19:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-27 12:19:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-27 12:19:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:26] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-27 12:19:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-27 12:19:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-27 12:19:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-27 12:19:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-27 12:19:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:26] [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 [2024-10-27 12:19:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-27 12:19:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:29] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-27 12:19:29] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:29] [TRACE] [OmnipathR] Contains 1 files. [2024-10-27 12:19:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-27 12:19:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-27 12:19:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:29] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-27 12:19:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-27 12:19:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-27 12:19:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-27 12:19:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-27 12:19:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:29] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-10-27 12:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-27 12:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:31] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-27 12:19:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:31] [TRACE] [OmnipathR] Contains 1 files. [2024-10-27 12:19:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-27 12:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-27 12:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-27 12:19:31] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-27 12:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-27 12:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-27 12:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-27 12:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-27 12:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-27 12:19:31] [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/RtmpeXHCFB/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: 2024-10-27 12:19:37 CET ]