[ Started: 2025-04-12 22:25:08 CEST ] [ CARNIVAL v2.7.2 for BioC-3.21 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/opt/R-devel/lib/R/library" Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Old packages: 'fs', 'ps', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/fs_1.6.6.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/ps_1.9.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz' * installing *source* package ‘fs’ ... ** this is package ‘fs’ version ‘1.6.6’ ** package ‘fs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c dir.cc -o dir.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c error.cc -o error.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c file.cc -o file.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c fs.cc -o fs.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c getmode.cc -o getmode.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c id.cc -o id.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c init.cc -o init.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c link.cc -o link.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c path.cc -o path.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c utils.cc -o utils.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c unix/getmode.cc -o unix/getmode.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c bsd/setmode.c -o bsd/setmode.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c bsd/strmode.c -o bsd/strmode.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c bsd/reallocarray.c -o bsd/reallocarray.o touch libuv-1.44.2/aclocal.m4 && touch libuv-1.44.2/configure && touch libuv-1.44.2/Makefile.in (cd libuv-1.44.2 \ && CC="gcc" CPPFLAGS="-I/usr/local/include" CFLAGS="-g -O2 -fpic -fvisibility=hidden -std=c99" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/lib" ./configure --quiet) make --directory=libuv-1.44.2 \ HAVE_DTRACE=0 make[1]: Entering directory '/tmp/Rtmpa5hZas/R.INSTALL94fae3c332204/fs/src/libuv-1.44.2' CC src/libuv_la-fs-poll.lo CC src/libuv_la-idna.lo CC src/libuv_la-inet.lo CC src/libuv_la-random.lo CC src/libuv_la-strscpy.lo CC src/libuv_la-threadpool.lo CC src/libuv_la-timer.lo CC src/libuv_la-uv-data-getter-setters.lo CC src/libuv_la-uv-common.lo In file included from src/uv-common.h:42, from src/uv-common.c:23: src/uv-common.c: In function 'uv_walk': src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_13(D) + 16B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/uv-common.c:507:3: note: in expansion of macro 'QUEUE_MOVE' 507 | QUEUE_MOVE(&loop->handle_queue, &queue); | ^~~~~~~~~~ src/uv-common.c:503:9: note: 'queue' declared here 503 | QUEUE queue; | ^~~~~ src/uv-common.c:502:25: note: 'loop' declared here 502 | void uv_walk(uv_loop_t* loop, uv_walk_cb walk_cb, void* arg) { | ~~~~~~~~~~~^~~~ CC src/libuv_la-version.lo CC src/libuv_la-strtok.lo CC src/unix/libuv_la-async.lo In file included from ./src/uv-common.h:42, from src/unix/internal.h:25, from src/unix/async.c:26: src/unix/async.c: In function 'uv__async_io.part.0': ./src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_6(D) + 432B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/async.c:149:3: note: in expansion of macro 'QUEUE_MOVE' 149 | QUEUE_MOVE(&loop->async_handles, &queue); | ^~~~~~~~~~ src/unix/async.c:125:9: note: 'queue' declared here 125 | QUEUE queue; | ^~~~~ src/unix/async.c:122:37: note: 'loop' declared here 122 | static void uv__async_io(uv_loop_t* loop, uv__io_t* w, unsigned int events) { | ~~~~~~~~~~~^~~~ CC src/unix/libuv_la-core.lo In file included from ./src/uv-common.h:42, from src/unix/internal.h:25, from src/unix/core.c:22: src/unix/core.c: In function 'uv__run_pending': ./src/queue.h:68:19: warning: storing the address of local variable 'pq' in '((void * (**)[2])MEM[(void *[2] * *)loop_11(D) + 72B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/core.c:803:3: note: in expansion of macro 'QUEUE_MOVE' 803 | QUEUE_MOVE(&loop->pending_queue, &pq); | ^~~~~~~~~~ src/unix/core.c:800:9: note: 'pq' declared here 800 | QUEUE pq; | ^~ src/unix/core.c:798:40: note: 'loop' declared here 798 | static void uv__run_pending(uv_loop_t* loop) { | ~~~~~~~~~~~^~~~ CC src/unix/libuv_la-dl.lo CC src/unix/libuv_la-fs.lo CC src/unix/libuv_la-getaddrinfo.lo CC src/unix/libuv_la-getnameinfo.lo CC src/unix/libuv_la-loop-watcher.lo In file included from ./src/uv-common.h:42, from src/unix/internal.h:25, from src/unix/loop-watcher.c:23: src/unix/loop-watcher.c: In function 'uv__run_prepare': ./src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_12(D) + 384B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/loop-watcher.c:52:5: note: in expansion of macro 'QUEUE_MOVE' 52 | QUEUE_MOVE(&loop->name##_handles, &queue); \ | ^~~~~~~~~~ src/unix/loop-watcher.c:66:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 66 | UV_LOOP_WATCHER_DEFINE(prepare, PREPARE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:50:11: note: 'queue' declared here 50 | QUEUE queue; \ | ^~~~~ src/unix/loop-watcher.c:66:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 66 | UV_LOOP_WATCHER_DEFINE(prepare, PREPARE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:48:34: note: 'loop' declared here 48 | void uv__run_##name(uv_loop_t* loop) { \ | ~~~~~~~~~~~^~~~ src/unix/loop-watcher.c:66:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 66 | UV_LOOP_WATCHER_DEFINE(prepare, PREPARE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c: In function 'uv__run_check': ./src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_12(D) + 400B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/loop-watcher.c:52:5: note: in expansion of macro 'QUEUE_MOVE' 52 | QUEUE_MOVE(&loop->name##_handles, &queue); \ | ^~~~~~~~~~ src/unix/loop-watcher.c:67:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 67 | UV_LOOP_WATCHER_DEFINE(check, CHECK) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:50:11: note: 'queue' declared here 50 | QUEUE queue; \ | ^~~~~ src/unix/loop-watcher.c:67:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 67 | UV_LOOP_WATCHER_DEFINE(check, CHECK) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:48:34: note: 'loop' declared here 48 | void uv__run_##name(uv_loop_t* loop) { \ | ~~~~~~~~~~~^~~~ src/unix/loop-watcher.c:67:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 67 | UV_LOOP_WATCHER_DEFINE(check, CHECK) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c: In function 'uv__run_idle': ./src/queue.h:68:19: warning: storing the address of local variable 'queue' in '((void * (**)[2])MEM[(void *[2] * *)loop_12(D) + 416B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/loop-watcher.c:52:5: note: in expansion of macro 'QUEUE_MOVE' 52 | QUEUE_MOVE(&loop->name##_handles, &queue); \ | ^~~~~~~~~~ src/unix/loop-watcher.c:68:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 68 | UV_LOOP_WATCHER_DEFINE(idle, IDLE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:50:11: note: 'queue' declared here 50 | QUEUE queue; \ | ^~~~~ src/unix/loop-watcher.c:68:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 68 | UV_LOOP_WATCHER_DEFINE(idle, IDLE) | ^~~~~~~~~~~~~~~~~~~~~~ src/unix/loop-watcher.c:48:34: note: 'loop' declared here 48 | void uv__run_##name(uv_loop_t* loop) { \ | ~~~~~~~~~~~^~~~ src/unix/loop-watcher.c:68:1: note: in expansion of macro 'UV_LOOP_WATCHER_DEFINE' 68 | UV_LOOP_WATCHER_DEFINE(idle, IDLE) | ^~~~~~~~~~~~~~~~~~~~~~ CC src/unix/libuv_la-loop.lo CC src/unix/libuv_la-pipe.lo CC src/unix/libuv_la-poll.lo CC src/unix/libuv_la-process.lo CC src/unix/libuv_la-random-devurandom.lo CC src/unix/libuv_la-signal.lo CC src/unix/libuv_la-stream.lo In file included from ./src/uv-common.h:42, from src/unix/internal.h:25, from src/unix/stream.c:23: src/unix/stream.c: In function 'uv__write_callbacks': ./src/queue.h:68:19: warning: storing the address of local variable 'pq' in '((void * (**)[2])MEM[(void *[2] * *)stream_23(D) + 208B])[1]' [-Wdangling-pointer=] 68 | QUEUE_PREV(q) = (n); \ | ^ ./src/queue.h:78:7: note: in expansion of macro 'QUEUE_SPLIT' 78 | QUEUE_SPLIT(h, q, n); \ | ^~~~~~~~~~~ src/unix/stream.c:941:3: note: in expansion of macro 'QUEUE_MOVE' 941 | QUEUE_MOVE(&stream->write_completed_queue, &pq); | ^~~~~~~~~~ src/unix/stream.c:936:9: note: 'pq' declared here 936 | QUEUE pq; | ^~ src/unix/stream.c:933:46: note: 'stream' declared here 933 | static void uv__write_callbacks(uv_stream_t* stream) { | ~~~~~~~~~~~~~^~~~~~ CC src/unix/libuv_la-tcp.lo CC src/unix/libuv_la-thread.lo CC src/unix/libuv_la-tty.lo CC src/unix/libuv_la-udp.lo CC src/unix/libuv_la-linux-core.lo CC src/unix/libuv_la-linux-inotify.lo CC src/unix/libuv_la-linux-syscalls.lo CC src/unix/libuv_la-procfs-exepath.lo CC src/unix/libuv_la-proctitle.lo CC src/unix/libuv_la-random-getrandom.lo CC src/unix/libuv_la-random-sysctl-linux.lo CC src/unix/libuv_la-epoll.lo CCLD libuv.la make[1]: Leaving directory '/tmp/Rtmpa5hZas/R.INSTALL94fae3c332204/fs/src/libuv-1.44.2' g++ -std=gnu++17 -shared -L/usr/local/lib -o fs.so dir.o error.o file.o fs.o getmode.o id.o init.o link.o path.o utils.o unix/getmode.o bsd/setmode.o bsd/strmode.o bsd/reallocarray.o ./libuv-1.44.2/.libs/libuv.pa -pthread installing to /home/omnipath/local/R/4.5-3.21/00LOCK-fs/00new/fs/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 (fs) * installing *source* package ‘ps’ ... ** this is package ‘ps’ version ‘1.9.1’ ** package ‘ps’ 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 -L/usr/local/lib -Wall px.c -o px In file included from /usr/include/features.h:502, from /usr/include/unistd.h:25, from px.c:6: In function ‘read’, inlined from ‘echo_from_fd’ at px.c:83:9: /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 ‘echo_from_fd’: /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 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-common.c -o api-common.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c common.c -o common.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c extra.c -o extra.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dummy.c -o dummy.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c error-codes.c -o error-codes.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cleancall.c -o cleancall.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c posix.c -o posix.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-posix.c -o api-posix.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c linux.c -o linux.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-linux.c -o api-linux.o gcc -shared -L/usr/local/lib -o ps.so init.o api-common.o common.o extra.o dummy.o error-codes.o cleancall.o posix.o api-posix.o linux.o api-linux.o installing via 'install.libs.R' to /home/omnipath/local/R/4.5-3.21/00LOCK-ps/00new/ps ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (ps) * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.15.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2025-04-12 22:25:47] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-12 22:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:47] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:47] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-11 21:35:20 UTC; omnipath [2025-04-12 22:25:47] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-12 22:25:47] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-11 21:35:21 UTC; unix [2025-04-12 22:25:47] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-12 22:25:47] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-12 22:25:47] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-12; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-12 22:25:47] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-12 22:25:47] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-11); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.15.0(2024-10-29); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-12 22:25:47] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-12 22:25:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-12 22:25:47] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:47] [TRACE] [OmnipathR] Contains 1 files. [2025-04-12 22:25:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-12 22:25:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-12 22:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:47] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-12 22:25:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-12 22:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-12 22:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-12 22:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-12 22:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:47] [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 [2025-04-12 22:25:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-12 22:25:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:50] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-11 21:35:20 UTC; omnipath [2025-04-12 22:25:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-12 22:25:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-11 21:35:21 UTC; unix [2025-04-12 22:25:50] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-12 22:25:50] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-12 22:25:50] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-12; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-12 22:25:50] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-12 22:25:50] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-11); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.15.0(2024-10-29); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-12 22:25:50] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-12 22:25:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-12 22:25:50] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:50] [TRACE] [OmnipathR] Contains 1 files. [2025-04-12 22:25:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-12 22:25:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-12 22:25:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:50] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-12 22:25:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-12 22:25:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-12 22:25:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-12 22:25:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-12 22:25:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:50] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-04-12 22:25:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-12 22:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:52] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-11 21:35:20 UTC; omnipath [2025-04-12 22:25:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-12 22:25:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-11 21:35:21 UTC; unix [2025-04-12 22:25:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.99 [2025-04-12 22:25:52] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-12 22:25:53] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-12; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-12 22:25:53] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-04-12 22:25:53] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.99(2025-04-11); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.15.0(2024-10-29); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-12 22:25:53] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-12 22:25:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-12 22:25:53] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:53] [TRACE] [OmnipathR] Contains 1 files. [2025-04-12 22:25:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-12 22:25:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-12 22:25:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-12 22:25:53] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-12 22:25:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-12 22:25:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-12 22:25:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-12 22:25:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-12 22:25:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-12 22:25:53] [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/RtmppiREyK/downloaded_packages’ Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 2 packages ahead of CRAN: ps, fs [ Finished: 2025-04-12 22:25:56 CEST ]