[ Started: 2024-10-30 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: 'fs', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/fs_1.6.5.tar.gz' Content type 'application/x-gzip' length 1200455 bytes (1.1 MB) ================================================== downloaded 1.1 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 ‘fs’ ... ** package ‘fs’ 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./libuv-1.44.2/include -I. -pthread -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 dir.cc -o dir.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 error.cc -o error.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 file.cc -o file.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 fs.cc -o fs.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 getmode.cc -o getmode.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 id.cc -o id.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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.cc -o init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 link.cc -o link.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 path.cc -o path.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 utils.cc -o utils.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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/getmode.cc -o unix/getmode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 bsd/setmode.c -o bsd/setmode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 bsd/strmode.c -o bsd/strmode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 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="" CFLAGS="-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 -fpic -fvisibility=hidden -std=c99" AR="ar" RANLIB="ranlib" LDFLAGS="-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro" ./configure --quiet) make --directory=libuv-1.44.2 \ HAVE_DTRACE=0 make[1]: Entering directory '/tmp/Rtmpdij4QE/R.INSTALL33f7d455939f13/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/Rtmpdij4QE/R.INSTALL33f7d455939f13/fs/src/libuv-1.44.2' g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -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.a -pthread -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-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 ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-10-30 12:19:47] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-30 12:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:47] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-30 12:19:47] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:47] [TRACE] [OmnipathR] Contains 1 files. [2024-10-30 12:19:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-30 12:19:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-30 12:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:47] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-30 12:19:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-30 12:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-30 12:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-30 12:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-30 12:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:47] [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 [2024-10-30 12:19:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-30 12:19:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:49] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-30 12:19:49] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:49] [TRACE] [OmnipathR] Contains 1 files. [2024-10-30 12:19:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-30 12:19:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-30 12:19:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:49] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-30 12:19:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-30 12:19:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-30 12:19:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-30 12:19:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-30 12:19:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:50] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-10-30 12:19:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-30 12:19:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:52] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-30 12:19:52] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:52] [TRACE] [OmnipathR] Contains 1 files. [2024-10-30 12:19:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-30 12:19:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-30 12:19:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-30 12:19:52] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-30 12:19:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-30 12:19:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-30 12:19:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-30 12:19:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-30 12:19:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-30 12:19:52] [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/RtmpBlLOmx/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 2 packages ahead of CRAN: fs, BiocStyle [ Finished: 2024-10-30 12:19:58 CET ]