[ Started: 2025-01-22 12:22:13 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/clock_0.7.2.tar.gz'
Content type 'application/x-gzip' length 559601 bytes (546 KB)
==================================================
downloaded 546 KB
* installing *source* package ‘clock’ ...
** package ‘clock’ 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'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 duration.cpp -o duration.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 enums.cpp -o enums.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 format.cpp -o format.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 gregorian-year-day.cpp -o gregorian-year-day.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 gregorian-year-month-day.cpp -o gregorian-year-month-day.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 gregorian-year-month-weekday.cpp -o gregorian-year-month-weekday.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 iso-year-week-day.cpp -o iso-year-week-day.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 limits.cpp -o limits.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 naive-time.cpp -o naive-time.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 quarterly-year-quarter-day.cpp -o quarterly-year-quarter-day.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 rcrd.cpp -o rcrd.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 sys-time.cpp -o sys-time.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 time-point.cpp -o time-point.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 utils.cpp -o utils.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 week-year-week-day.cpp -o week-year-week-day.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 weekday.cpp -o weekday.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 zone.cpp -o zone.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/cpp11/include' -I'/home/omnipath/local/R/4.4-3.19/tzdb/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 zoned-time.cpp -o zoned-time.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o clock.so cpp11.o duration.o enums.o format.o gregorian-year-day.o gregorian-year-month-day.o gregorian-year-month-weekday.o iso-year-week-day.o limits.o naive-time.o quarterly-year-quarter-day.o rcrd.o sys-time.o time-point.o utils.o week-year-week-day.o weekday.o zone.o zoned-time.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-clock/00new/clock/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (clock)
The downloaded source packages are in
‘/tmp/RtmpVgt3q4/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: 2025-01-22 12:23:51 CET ]