[ Started: 2025-01-09 12:19:26 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/processx_3.8.5.tar.gz' Content type 'application/x-gzip' length 165103 bytes (161 KB) ================================================== downloaded 161 KB * installing *source* package ‘processx’ ... ** package ‘processx’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wall tools/px.c -o tools/px In file included from /usr/include/features.h:502, from /usr/include/unistd.h:25, from tools/px.c:11: In function ‘read’, inlined from ‘echo_from_fd’ at tools/px.c:93:9: /usr/include/x86_64-linux-gnu/bits/unistd.h:28:10: warning: ‘*read’ specified size 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 28 | return __glibc_fortify (read, __nbytes, sizeof (char), | ^~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/unistd-decl.h: In function ‘echo_from_fd’: /usr/include/x86_64-linux-gnu/bits/unistd-decl.h:29:16: note: in a call to function ‘*read’ declared with attribute ‘access (write_only, 2, 3)’ 29 | extern ssize_t __REDIRECT_FORTIFY (__read_alias, (int __fd, void *__buf, | ^~~~~~~~~~~~~~~~~~ In function ‘read’, inlined from ‘echo_from_fd’ at tools/px.c:93:9, inlined from ‘main’ at tools/px.c:201:11: /usr/include/x86_64-linux-gnu/bits/unistd.h:28:10: warning: ‘__read_alias’ specified size 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 28 | return __glibc_fortify (read, __nbytes, sizeof (char), | ^ /usr/include/x86_64-linux-gnu/bits/unistd-decl.h: In function ‘main’: /usr/include/x86_64-linux-gnu/bits/unistd-decl.h:29:16: note: in a call to function ‘__read_alias’ declared with attribute ‘access (write_only, 2, 3)’ 29 | extern ssize_t __REDIRECT_FORTIFY (__read_alias, (int __fd, void *__buf, | ^ gcc -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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -I../inst/include -Wall tools/sock.c -o tools/sock gcc -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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro supervisor/supervisor.c \ supervisor/utils.c -o supervisor/supervisor 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 base64.c -o base64.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 client.c -o client.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 errors.c -o errors.o gcc -shared -L"/usr/lib/R/lib" -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o client.so base64.o client.o errors.o \ -L"/usr/lib/R/lib" -lR 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 poll.c -o poll.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 processx-connection.c -o processx-connection.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 processx-vector.c -o processx-vector.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 create-time.c -o create-time.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 unix/childlist.c -o unix/childlist.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 unix/connection.c -o unix/connection.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 unix/processx.c -o unix/processx.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 unix/sigchld.c -o unix/sigchld.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 unix/utils.c -o unix/utils.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 unix/named_pipe.c -o unix/named_pipe.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 cleancall.c -o cleancall.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o processx.so init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o cleancall.o -L/usr/lib/R/lib -lR installing via 'install.libs.R' to /home/omnipath/local/R/4.4-3.20/00LOCK-processx/00new/processx ** 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 ** 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 (processx) The downloaded source packages are in ‘/tmp/Rtmp8V603d/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 [2025-01-09 12:19:38] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-09 12:19:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:38] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-09 12:19:38] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:38] [TRACE] [OmnipathR] Contains 1 files. [2025-01-09 12:19:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-09 12:19:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-09 12:19:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:38] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-01-09 12:19:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-09 12:19:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-09 12:19:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-09 12:19:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-09 12:19:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:38] [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 [2025-01-09 12:19:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-09 12:19:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:41] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-09 12:19:41] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:41] [TRACE] [OmnipathR] Contains 1 files. [2025-01-09 12:19:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-09 12:19:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-09 12:19:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:41] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-01-09 12:19:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-09 12:19:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-09 12:19:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-09 12:19:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-09 12:19:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:41] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-01-09 12:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-09 12:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:43] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-09 12:19:43] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:43] [TRACE] [OmnipathR] Contains 1 files. [2025-01-09 12:19:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-09 12:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-09 12:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-01-09 12:19:43] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-01-09 12:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-09 12:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-09 12:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-09 12:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-09 12:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-09 12:19:43] [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/Rtmp8V603d/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: 2025-01-09 12:19:49 CET ]