[ Started: 2024-11-28 12:21:01 CET ]
[ CARNIVAL v2.14.0 for BioC-3.19 from https://git.bioconductor.org/packages/CARNIVAL@RELEASE_3_19 (bcf3cbc 2024-04-30 11:23:36) ]
[1] "Libraries: " "/home/omnipath/local/R/4.4-3.19"
[3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library"
trying URL 'https://cran.uni-muenster.de/src/contrib/later_1.4.1.tar.gz'
Content type 'application/x-gzip' length 69832 bytes (68 KB)
==================================================
downloaded 68 KB
trying URL 'https://cran.uni-muenster.de/src/contrib/promises_1.3.2.tar.gz'
Content type 'application/x-gzip' length 3168224 bytes (3.0 MB)
==================================================
downloaded 3.0 MB
* installing *source* package ‘later’ ...
** package ‘later’ successfully unpacked and MD5 sums checked
** using staged installation
Running configure script
-latomic linker flag not needed.
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 callback_registry.cpp -o callback_registry.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 debug.cpp -o debug.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 fd.cpp -o fd.o
gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 later.cpp -o later.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 later_posix.cpp -o later_posix.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 later_win32.cpp -o later_win32.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 timer_posix.cpp -o timer_posix.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 timestamp_unix.cpp -o timestamp_unix.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 timestamp_win32.cpp -o timestamp_win32.o
gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 tinycthread.c -o tinycthread.o
gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 wref.c -o wref.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o later.so RcppExports.o callback_registry.o debug.o fd.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o wref.o -pthread -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-later/00new/later/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (later)
* installing *source* package ‘promises’ ...
** package ‘promises’ 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'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/later/include' -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -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 promise_task.cpp -o promise_task.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o promises.so RcppExports.o promise_task.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-promises/00new/promises/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 (promises)
The downloaded source packages are in
‘/tmp/Rtmp4XNY3X/downloaded_packages’
Bioconductor version '3.19' is out-of-date; the current release version '3.20'
is available with R version '4.4'; see https://bioconductor.org/install
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (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: 2024-11-28 12:21:40 CET ]