[ Started: 2023-03-20 17:59:18 CET ]
[ progeny v1.17.3 for BioC-3.17 from https://github.com/saezlab/progeny@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/opt/R-devel/lib/R/library"     
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
  (2023-03-16 r83996)
Old packages: 'NMF'
trying URL 'https://cloud.r-project.org/src/contrib/NMF_0.26.tar.gz'
Content type 'application/x-gzip' length 1672812 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘NMF’ ...
** package ‘NMF’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c distance.cpp -o distance.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c divergence.cpp -o divergence.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c euclidean.cpp -o euclidean.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o NMF.so distance.o divergence.o euclidean.o registerDynamicSymbol.o utils.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-NMF/00new/NMF/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Setting package specific options: package:NMF:logger (1 default option(s))
Setting package specific options: package:NMF (10 default option(s))
Creating a generic function for ‘plot’ from ‘graphics’ in package ‘NMF’
    (from the saved implicit definition)
Creating meta registry in package 'NMF' ... OK
Creating registry 'extra_handler' in package 'NMF' ... OK
Creating registry 'extra_action' in package 'NMF' ... OK
Registering extra handler 'install.packages' [function] ... OK
Creating registry 'algorithm' in package 'NMF' ... OK
Registering NMF algorithm '.R#brunet' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'brunet' [NMFStrategyIterative] based on template '.R#brunet' ... OK
Registering NMF algorithm 'KL' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.R#lee' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'lee' [NMFStrategyIterative] based on template '.R#lee' ... OK
Registering NMF algorithm 'Frobenius' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.R#offset' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'offset' [NMFStrategyIterative] based on template '.R#offset' ... OK
Registering NMF algorithm '.R#nsNMF' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'nsNMF' [NMFStrategyIterative] based on template '.R#nsNMF' ... OK
Registering NMF algorithm 'ls-nmf' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'pe-nmf' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.siNMF' [NMFStrategyIterative] based on template 'lee' ... OK
Registering NMF algorithm 'siNMF' [NMFStrategyIterative] based on template 'lee' ... OK
Registering NMF algorithm 'snmf/r' [NMFStrategyFunction] ... OK
Registering NMF algorithm 'snmf/l' [NMFStrategyFunction] ... OK
Registering extra action 'bigmemory' for handler 'install.packages' ... OK
Registering extra action 'synchronicity' for handler 'install.packages' ... OK
Creating registry 'seed' in package 'NMF' ... OK
Registering NMF seeding method 'none' [NMFSeed] ... OK
Registering NMF seeding method 'random' [NMFSeed] ... OK
Registering NMF seeding method 'ica' [NMFSeed] ... OK
Registering NMF seeding method 'nndsvd' [NMFSeed] ... OK
** 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 (NMF)

The downloaded source packages are in
	‘/tmp/RtmpEAqTTO/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
  (2023-03-16 r83996)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 2 packages ahead of CRAN: tibble, FNN
[ Finished: 2023-03-20 17:59:39 CET ]