[ Started: 2024-11-03 12:19:05 CET ]
[ CARNIVAL v2.7.2 for BioC-3.20 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.20"
[3] "/home/omnipath/local/R/4.4"      "/usr/lib/R/library"             
trying URL 'https://cran.uni-muenster.de/src/contrib/Rcpp_1.0.13-1.tar.gz'
Content type 'application/x-gzip' length 3435726 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ 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../inst/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 api.cpp -o api.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/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 attributes.cpp -o attributes.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/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 barrier.cpp -o barrier.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/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 date.cpp -o date.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/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 module.cpp -o module.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/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 rcpp_init.cpp -o rcpp_init.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-Rcpp/00new/Rcpp/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 (Rcpp)

The downloaded source packages are in
	‘/tmp/Rtmpq4Cq7z/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)
Old packages: 'spatstat.utils', 'wppi'
trying URL 'https://cloud.r-project.org/src/contrib/spatstat.utils_3.1-1.tar.gz'
Content type 'application/x-gzip' length 102180 bytes (99 KB)
==================================================
downloaded 99 KB

trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/wppi_1.14.0.tar.gz'
Content type 'application/x-gzip' length 663228 bytes (647 KB)
==================================================
downloaded 647 KB

* installing *source* package ‘spatstat.utils’ ...
** package ‘spatstat.utils’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/usr/share/R/include" -DNDEBUG       -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 circxseg.c -o circxseg.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 distseg.c -o distseg.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 fastinterv.c -o fastinterv.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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
gcc -I"/usr/share/R/include" -DNDEBUG       -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 inxyp.c -o inxyp.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 matchindices.c -o matchindices.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 matchpoints.c -o matchpoints.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 ply.c -o ply.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 primefax.c -o primefax.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 revcum.c -o revcum.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o spatstat.utils.so circxseg.o distseg.o fastinterv.o init.o inxyp.o matchindices.o matchpoints.o ply.o primefax.o revcum.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-spatstat.utils/00new/spatstat.utils/libs
** 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
** 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 (spatstat.utils)
* installing *source* package ‘wppi’ ...
** package ‘wppi’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-11-03 12:19:40] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:40] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:40] [TRACE]   [OmnipathR] Cache locked: FALSE
Note: wrong number of arguments to '/' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:43] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:43] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:45] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-03 12:19:45] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)

The downloaded source packages are in
	‘/tmp/Rtmpq4Cq7z/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: 2024-11-03 12:19:51 CET ]