[ Started: 2025-02-25 00:08:04 CET ]
[ 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: 'ggnewscale', 'iml', 'R.utils', 'reticulate', 'uwot'
trying URL 'https://cloud.r-project.org/src/contrib/ggnewscale_0.5.1.tar.gz'
Content type 'application/x-gzip' length 415146 bytes (405 KB)
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downloaded 405 KB

trying URL 'https://cloud.r-project.org/src/contrib/iml_0.11.4.tar.gz'
Content type 'application/x-gzip' length 164941 bytes (161 KB)
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downloaded 161 KB

trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.13.0.tar.gz'
Content type 'application/x-gzip' length 367225 bytes (358 KB)
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downloaded 358 KB

trying URL 'https://cloud.r-project.org/src/contrib/reticulate_1.41.0.tar.gz'
Content type 'application/x-gzip' length 1676690 bytes (1.6 MB)
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downloaded 1.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/uwot_0.2.3.tar.gz'
Content type 'application/x-gzip' length 614317 bytes (599 KB)
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downloaded 599 KB

* installing *source* package ‘ggnewscale’ ...
** package ‘ggnewscale’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (ggnewscale)
* installing *source* package ‘iml’ ...
** package ‘iml’ successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (iml)
* installing *source* package ‘R.utils’ ...
** package ‘R.utils’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function warnings to warnings.default, which was defined in environment R.utils.
Warning in setGenericS3.default("use") :
  Renamed the preexisting function use to use.default, which was defined in environment R.utils.
Warning in setMethodS3.default("use", "default", function(pkg = "R.utils",  :
  Method already existed and was overwritten: use.default
** 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 (R.utils)
* installing *source* package ‘reticulate’ ...
** package ‘reticulate’ 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/4.4-3.20/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/4.4-3.20/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/4.4-3.20/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/4.4-3.20/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/4.4-3.20/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/4.4-3.20/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/4.4-3.20/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/4.4-3.20/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/4.4-3.20/00LOCK-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)
* installing *source* package ‘uwot’ ...
** package ‘uwot’ 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../inst/include/ -I'/home/omnipath/local/R/4.4-3.20/dqrng/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.20/RcppProgress/include'    -DRCPP_NO_RTTI -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../inst/include/ -I'/home/omnipath/local/R/4.4-3.20/dqrng/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.20/RcppProgress/include'    -DRCPP_NO_RTTI -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 connected_components.cpp -o connected_components.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.20/dqrng/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.20/RcppProgress/include'    -DRCPP_NO_RTTI -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 nn_parallel.cpp -o nn_parallel.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.20/dqrng/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.20/RcppProgress/include'    -DRCPP_NO_RTTI -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 perplexity.cpp -o perplexity.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.20/dqrng/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.20/RcppProgress/include'    -DRCPP_NO_RTTI -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 r_uwot.cpp -o r_uwot.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.20/dqrng/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.20/RcppProgress/include'    -DRCPP_NO_RTTI -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 smooth_knn.cpp -o smooth_knn.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.20/dqrng/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.20/RcppProgress/include'    -DRCPP_NO_RTTI -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 supervised.cpp -o supervised.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.20/dqrng/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.20/RcppProgress/include'    -DRCPP_NO_RTTI -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 thread.cpp -o thread.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.4-3.20/dqrng/include' -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.20/RcppAnnoy/include' -I'/home/omnipath/local/R/4.4-3.20/RcppProgress/include'    -DRCPP_NO_RTTI -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 transform.cpp -o transform.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o uwot.so RcppExports.o connected_components.o nn_parallel.o perplexity.o r_uwot.o smooth_knn.o supervised.o thread.o transform.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-uwot/00new/uwot/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 (uwot)

The downloaded source packages are in
	‘/tmp/RtmpV8JHON/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 1 packages ahead of CRAN: BiocStyle
[ Finished: 2025-02-25 00:09:47 CET ]