[ Started: 2024-11-15 12:21:02 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/reticulate_1.40.0.tar.gz'
Content type 'application/x-gzip' length 1640550 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘reticulate’ ...
** package ‘reticulate’ 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/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/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 event_loop.cpp -o event_loop.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -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 libpython.cpp -o libpython.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -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 output.cpp -o output.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -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 pending_py_calls_notifier.cpp -o pending_py_calls_notifier.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -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 python.cpp -o python.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -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 readline.cpp -o readline.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -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 signals.cpp -o signals.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o reticulate.so RcppExports.o event_loop.o libpython.o output.o pending_py_calls_notifier.o python.o readline.o signals.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-reticulate/00new/reticulate/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 (reticulate)

The downloaded source packages are in
	‘/tmp/RtmptoBwaq/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)
Old packages: 'spatstat.data'
trying URL 'https://cloud.r-project.org/src/contrib/spatstat.data_3.1-4.tar.gz'
Content type 'application/x-gzip' length 2943340 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

* installing *source* package ‘spatstat.data’ ...
** package ‘spatstat.data’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (spatstat.data)

The downloaded source packages are in
	‘/tmp/RtmptoBwaq/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 3.19 (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: 2024-11-15 12:21:40 CET ]