[ Started: 2023-06-12 23:02:57 CEST ] [ decoupleR v2.5.1 for BioC-3.17 from https://github.com/saezlab/decoupleR@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 1.30.21), R 4.3.0 (2023-04-21) Bioconductor version 3.17 (BiocManager 1.30.21), 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' magick (NA -> 2.7.4 ) [CRAN] OmnipathR (7a3c0de23... -> 19fc47cbd...) [GitHub] Skipping 1 packages ahead of CRAN: scattermore Installing 1 packages: magick trying URL 'https://cran.uni-muenster.de/src/contrib/magick_2.7.4.tar.gz' Content type 'application/x-gzip' length 4754217 bytes (4.5 MB) ================================================== downloaded 4.5 MB * installing *source* package ‘magick’ ... ** package ‘magick’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 Using PKG_LIBS=-lMagick++-6.Q16 -lMagickWand-6.Q16 -lMagickCore-6.Q16 ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c animation.cpp -o animation.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c attributes.cpp -o attributes.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c base.cpp -o base.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c color.cpp -o color.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c composite.cpp -o composite.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c config.cc -o config.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c convolve.cpp -o convolve.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c device.cpp -o device.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c edges.cpp -o edges.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c edit.cpp -o edit.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fonts.cpp -o fonts.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c options.cpp -o options.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c properties.cpp -o properties.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c resize.cpp -o resize.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c segment.cpp -o segment.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c transformations.cpp -o transformations.o g++ -std=gnu++17 -shared -L/usr/local/lib -o magick.so RcppExports.o animation.o attributes.o base.o color.o composite.o config.o convolve.o device.o edges.o edit.o fonts.o options.o properties.o resize.o segment.o transformations.o -lMagick++-6.Q16 -lMagickWand-6.Q16 -lMagickCore-6.Q16 installing to /home/omnipath/local/R/4.3-3.17/00LOCK-magick/00new/magick/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 (magick) The downloaded source packages are in ‘/tmp/RtmpFhSVhl/downloaded_packages’ Downloading GitHub repo saezlab/OmnipathR@HEAD ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpFhSVhl/remotes3710819692dcb/saezlab-OmnipathR-19fc47c/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 * looking to see if a ‘data/datalist’ file should be added * building ‘OmnipathR_3.9.6.tar.gz’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** 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 [2023-06-12 23:04:23] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2023-06-12 23:04:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-12 23:04:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:23] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-06-12 23:04:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-06-12 23:04:23] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-06-12 23:04:23] [TRACE] [OmnipathR] Contains 1 files. [2023-06-12 23:04:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-06-12 23:04:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-12 23:04:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-06-12 23:04:23] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-06-12 23:04:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-06-12 23:04:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-06-12 23:04:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-06-12 23:04:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-06-12 23:04:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:23] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-06-12 23:04:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-12 23:04:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:24] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-06-12 23:04:24] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-06-12 23:04:24] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-06-12 23:04:24] [TRACE] [OmnipathR] Contains 1 files. [2023-06-12 23:04:24] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-06-12 23:04:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-06-12 23:04:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-06-12 23:04:24] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-06-12 23:04:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-06-12 23:04:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-06-12 23:04:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-06-12 23:04:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-06-12 23:04:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-06-12 23:04:24] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) [ Finished: 2023-06-12 23:04:24 CEST ]