[ Started: 2025-04-12 22:27:00 CEST ]
[ CARNIVAL v2.16.0 for BioC-3.20 from https://git.bioconductor.org/packages/CARNIVAL@RELEASE_3_20 (a7305b3 2024-10-29 10:46:30) ]
[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', 'ps'
trying URL 'https://cloud.r-project.org/src/contrib/fs_1.6.6.tar.gz'
Content type 'application/x-gzip' length 1201011 bytes (1.1 MB)
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downloaded 1.1 MB
trying URL 'https://cloud.r-project.org/src/contrib/ps_1.9.1.tar.gz'
Content type 'application/x-gzip' length 167920 bytes (163 KB)
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downloaded 163 KB
* installing *source* package ‘fs’ ...
** 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"/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/RtmpfIjtGT/R.INSTALL96aba6ed4220d/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/RtmpfIjtGT/R.INSTALL96aba6ed4220d/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.pa -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 ‘ps’ ...
** 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 -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 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’ 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 px.c:83:9,
inlined from ‘main’ at px.c:203:11:
/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 -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 api-common.c -o api-common.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 common.c -o common.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 extra.c -o extra.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 dummy.c -o dummy.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 error-codes.c -o error-codes.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 -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 posix.c -o posix.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 api-posix.c -o api-posix.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 linux.c -o linux.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 api-linux.c -o api-linux.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -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 -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /home/omnipath/local/R/4.4-3.20/00LOCK-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)
The downloaded source packages are in
‘/tmp/RtmpANFozx/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 3 packages ahead of CRAN: ps, fs, BiocStyle
[ Finished: 2025-04-12 22:27:43 CEST ]