[ Started: 2025-02-19 01:30:54 CET ] [ progeny v1.17.3 for BioC-3.21 from https://github.com/saezlab/progeny@master (cad6be0 2023-01-30 11:01:10) ] [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: 'ps' trying URL 'https://cloud.r-project.org/src/contrib/ps_1.9.0.tar.gz' Content type 'application/x-gzip' length 167599 bytes (163 KB) ================================================== downloaded 163 KB * installing *source* package ‘ps’ ... ** this is package ‘ps’ version ‘1.9.0’ ** 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) The downloaded source packages are in ‘/tmp/RtmpaRAeYq/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 1 packages ahead of CRAN: ps [ Finished: 2025-02-19 01:31:05 CET ]