[ Started: 2025-07-19 19:59:59 CEST ]
[ dorothea v1.20.0 for BioC-3.21 from https://git.bioconductor.org/packages/dorothea@RELEASE_3_21 (109bfa1 2025-04-15 10:14:54) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.5-3.21"
[3] "/home/omnipath/local/R/4.5"      "/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 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13)
Old packages: 'enrichplot', 'ggtree', 'wppi'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.4.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.16.3.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz'
* installing *source* package ‘ggtree’ ...
** this is package ‘ggtree’ version ‘3.16.3’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/omnipath/local/R/4.5-3.21/ape/libs/ape.so':
  libRblas.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘ggtree’
* removing ‘/home/omnipath/local/R/4.5-3.21/ggtree’
* restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggtree’
* installing *source* package ‘wppi’ ...
** this is package ‘wppi’ version ‘1.16.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so':
  libRblas.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘wppi’
* removing ‘/home/omnipath/local/R/4.5-3.21/wppi’
* restoring previous ‘/home/omnipath/local/R/4.5-3.21/wppi’
* installing *source* package ‘enrichplot’ ...
** this is package ‘enrichplot’ version ‘1.28.4’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so':
  libRblas.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘enrichplot’
* removing ‘/home/omnipath/local/R/4.5-3.21/enrichplot’
* restoring previous ‘/home/omnipath/local/R/4.5-3.21/enrichplot’

The downloaded source packages are in
	‘/tmp/RtmpDjwabc/downloaded_packages’
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘ggtree’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘wppi’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘enrichplot’ had non-zero exit status
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13)
Old packages: 'enrichplot', 'ggtree', 'wppi'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.4.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.16.3.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz'
* installing *source* package ‘ggtree’ ...
** this is package ‘ggtree’ version ‘3.16.3’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/omnipath/local/R/4.5-3.21/ape/libs/ape.so':
  libRblas.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘ggtree’
* removing ‘/home/omnipath/local/R/4.5-3.21/ggtree’
* restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggtree’
* installing *source* package ‘wppi’ ...
** this is package ‘wppi’ version ‘1.16.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so':
  libRblas.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘wppi’
* removing ‘/home/omnipath/local/R/4.5-3.21/wppi’
* restoring previous ‘/home/omnipath/local/R/4.5-3.21/wppi’
* installing *source* package ‘enrichplot’ ...
** this is package ‘enrichplot’ version ‘1.28.4’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so':
  libRblas.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘enrichplot’
* removing ‘/home/omnipath/local/R/4.5-3.21/enrichplot’
* restoring previous ‘/home/omnipath/local/R/4.5-3.21/enrichplot’

The downloaded source packages are in
	‘/tmp/RtmpDjwabc/downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘ggtree’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘wppi’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘enrichplot’ had non-zero exit status
OmnipathR (ee6fdf167... -> a7f3b9dda...) [GitHub]
Downloading GitHub repo saezlab/OmnipathR@HEAD

── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpDjwabc/remotes2c1cb8ded8681/saezlab-OmnipathR-a7f3b9d/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘OmnipathR/.github’
* looking to see if a ‘data/datalist’ file should be added
* building ‘OmnipathR_3.17.4.tar.gz’

* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.17.4’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so':
  libRblas.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘OmnipathR’
* removing ‘/home/omnipath/local/R/4.5-3.21/OmnipathR’
* restoring previous ‘/home/omnipath/local/R/4.5-3.21/OmnipathR’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpDjwabc/file2c1cb82790e046/OmnipathR_3.17.4.tar.gz’ had non-zero exit status
[ Finished: 2025-07-19 20:00:27 CEST ]