[ Started: 2025-03-08 00:07:21 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: 'readxl'
trying URL 'https://cloud.r-project.org/src/contrib/readxl_1.4.5.tar.gz'
Content type 'application/x-gzip' length 1636512 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘readxl’ ...
** package ‘readxl’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 XlsWorkBook.cpp -o XlsWorkBook.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 XlsxWorkBook.cpp -o XlsxWorkBook.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 zip.cpp -o zip.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 Read.cpp -o Read.o
gcc -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 cran.c -o cran.o
gcc -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 libxls/xlstool.c -o libxls/xlstool.o
gcc -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 libxls/endian.c -o libxls/endian.o
gcc -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 libxls/ole.c -o libxls/ole.o
gcc -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 libxls/xls.c -o libxls/xls.o
gcc -I"/usr/share/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.4-3.20/cpp11/include' -I'/home/omnipath/local/R/4.4-3.20/progress/include'    -fvisibility=hidden -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 libxls/locale.c -o libxls/locale.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o readxl.so cpp11.o XlsWorkBook.o XlsxWorkBook.o zip.o Read.o cran.o libxls/xlstool.o libxls/endian.o libxls/ole.o libxls/xls.o libxls/locale.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-readxl/00new/readxl/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 (readxl)

The downloaded source packages are in
	‘/tmp/RtmpKRW0nt/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: 2025-03-08 00:07:46 CET ]