[ Started: 2023-10-13 07:51:01 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/opt/R-devel/lib/R/library"     
trying URL 'https://cran.uni-muenster.de/src/contrib/ggplot2_3.4.4.tar.gz'
Content type 'application/x-gzip' length 3159578 bytes (3.0 MB)
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downloaded 3.0 MB

trying URL 'https://cran.uni-muenster.de/src/contrib/ggrepel_0.9.4.tar.gz'
Content type 'application/x-gzip' length 149991 bytes (146 KB)
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downloaded 146 KB

trying URL 'https://cran.uni-muenster.de/src/contrib/reticulate_1.34.0.tar.gz'
Content type 'application/x-gzip' length 1605758 bytes (1.5 MB)
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downloaded 1.5 MB

trying URL 'https://cran.uni-muenster.de/src/contrib/vctrs_0.6.4.tar.gz'
Content type 'application/x-gzip' length 968450 bytes (945 KB)
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downloaded 945 KB

* installing *source* package ‘reticulate’ ...
** package ‘reticulate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c event_loop.cpp -o event_loop.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c libpython.cpp -o libpython.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c output.cpp -o output.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c python.cpp -o python.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c readline.cpp -o readline.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c signals.cpp -o signals.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o reticulate.so RcppExports.o event_loop.o libpython.o output.o python.o readline.o signals.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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 ‘vctrs’ ...
** package ‘vctrs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c altrep-lazy-character.c -o altrep-lazy-character.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c altrep-rle.c -o altrep-rle.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c altrep.c -o altrep.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c arg-counter.c -o arg-counter.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c arg.c -o arg.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c assert.c -o assert.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c bind.c -o bind.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c c-unchop.c -o c-unchop.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c c.c -o c.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c callables.c -o callables.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c cast-bare.c -o cast-bare.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c cast-dispatch.c -o cast-dispatch.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c cast.c -o cast.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c compare.c -o compare.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c complete.c -o complete.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c conditions.c -o conditions.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c dictionary.c -o dictionary.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c dim.c -o dim.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c empty.c -o empty.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c equal.c -o equal.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c expand.c -o expand.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c fields.c -o fields.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c fill.c -o fill.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c globals.c -o globals.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c group.c -o group.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c growable.c -o growable.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c hash.c -o hash.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c interval.c -o interval.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c match-joint.c -o match-joint.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c match.c -o match.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c missing.c -o missing.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c names.c -o names.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c order-collate.c -o order-collate.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c order-groups.c -o order-groups.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c order-sortedness.c -o order-sortedness.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c order-truelength.c -o order-truelength.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c order.c -o order.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c poly-op.c -o poly-op.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c proxy-restore.c -o proxy-restore.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c proxy.c -o proxy.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c ptype-common.c -o ptype-common.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c ptype.c -o ptype.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c ptype2-dispatch.c -o ptype2-dispatch.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c ptype2.c -o ptype2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c rank.c -o rank.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c rep.c -o rep.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c rlang-dev.c -o rlang-dev.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c rlang.c -o rlang.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c runs.c -o runs.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c set.c -o set.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c shape.c -o shape.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c size-common.c -o size-common.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c size.c -o size.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c slice-array.c -o slice-array.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c slice-assign-array.c -o slice-assign-array.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c slice-assign.c -o slice-assign.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c slice-chop.c -o slice-chop.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c slice-interleave.c -o slice-interleave.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c slice.c -o slice.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c split.c -o split.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c subscript-loc.c -o subscript-loc.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c subscript.c -o subscript.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c translate.c -o translate.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c type-data-frame.c -o type-data-frame.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c type-date-time.c -o type-date-time.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c type-factor.c -o type-factor.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c type-info.c -o type-info.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c type-integer64.c -o type-integer64.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c type-tibble.c -o type-tibble.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c typeof2-s3.c -o typeof2-s3.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c typeof2.c -o typeof2.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c unspecified.c -o unspecified.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c utils-dispatch.c -o utils-dispatch.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c utils.c -o utils.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c vctrs-core.c -o vctrs-core.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -c version.c -o version.o
gcc -shared -L/usr/local/lib -o vctrs.so altrep-lazy-character.o altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-vctrs/00new/vctrs/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 (vctrs)
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ 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
*** 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 (ggplot2)
* installing *source* package ‘ggrepel’ ...
** package ‘ggrepel’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c repel_boxes.cpp -o repel_boxes.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o ggrepel.so RcppExports.o repel_boxes.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-ggrepel/00new/ggrepel/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 (ggrepel)

The downloaded source packages are in
	‘/tmp/RtmpZq1Xxn/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21)
Old packages: 'tinytex'
trying URL 'https://cloud.r-project.org/src/contrib/tinytex_0.48.tar.gz'
Content type 'application/x-gzip' length 33463 bytes (32 KB)
==================================================
downloaded 32 KB

* installing *source* package ‘tinytex’ ...
** package ‘tinytex’ successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tinytex)

The downloaded source packages are in
	‘/tmp/RtmpZq1Xxn/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21)
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: tinytex
[ Finished: 2023-10-13 07:52:17 CEST ]