[ Started: 2025-03-21 00:05:10 CET ] [ CARNIVAL v2.7.2 for BioC-3.21 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/opt/R-devel/lib/R/library" Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Old packages: 'basilisk', 'emmeans', 'GSVA', 'SparseArray', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/basilisk_1.19.2.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/emmeans_1.11.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/GSVA_2.1.9.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/SparseArray_1.7.7.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz' * installing *source* package ‘basilisk’ ... ** this is package ‘basilisk’ version ‘1.19.2’ ** using non-staged installation via StagedInstall field ** 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 * DONE (basilisk) * installing *source* package ‘emmeans’ ... ** this is package ‘emmeans’ version ‘1.11.0’ ** package ‘emmeans’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (emmeans) * installing *source* package ‘GSVA’ ... ** this is package ‘GSVA’ version ‘2.1.9’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cli/include' -I/usr/local/include -fpic -g -O2 -c ecdfvals.c -o ecdfvals.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cli/include' -I/usr/local/include -fpic -g -O2 -c kcdfvals.c -o kcdfvals.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cli/include' -I/usr/local/include -fpic -g -O2 -c kernel_estimation.c -o kernel_estimation.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cli/include' -I/usr/local/include -fpic -g -O2 -c ks_test.c -o ks_test.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cli/include' -I/usr/local/include -fpic -g -O2 -c register_cmethods.c -o register_cmethods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/cli/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -shared -L/usr/local/lib -o GSVA.so ecdfvals.o kcdfvals.o kernel_estimation.o ks_test.o register_cmethods.o utils.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-GSVA/00new/GSVA/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 (GSVA) * installing *source* package ‘SparseArray’ ... ** this is package ‘SparseArray’ version ‘1.7.7’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c OPBufTree.c -o OPBufTree.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Rvector_summarization.c -o Rvector_summarization.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Rvector_utils.c -o Rvector_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SBT_utils.c -o SBT_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec.c -o SparseVec.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Math.c -o SparseVec_Math.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c argcheck_utils.c -o argcheck_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c coerceVector2.c -o coerceVector2.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c leaf_utils.c -o leaf_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c randomSparseArray.c -o randomSparseArray.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c readSparseCSV.c -o readSparseCSV.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c rowsum_methods.c -o rowsum_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c test.c -o test.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c thread_control.c -o thread_control.o gcc -shared -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Arith_methods.o SparseArray_Compare_methods.o SparseArray_Complex_methods.o SparseArray_Logic_methods.o SparseArray_Math_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_dim_tuning.o SparseArray_matrixStats.o SparseArray_misc_methods.o SparseArray_subassignment.o SparseArray_subassignment_OLD.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp installing to /home/omnipath/local/R/4.5-3.21/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray) * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.15.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2025-03-21 00:06:19] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-21 00:06:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:19] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-20 00:18:18 UTC; omnipath [2025-03-21 00:06:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-21 00:06:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-20 00:18:19 UTC; unix [2025-03-21 00:06:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-21 00:06:19] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-21 00:06:19] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-21 00:06:19] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-03-21 00:06:19] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-20); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.15.0(2024-10-29); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-21 00:06:19] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-03-21 00:06:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-21 00:06:19] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:19] [TRACE] [OmnipathR] Contains 1 files. [2025-03-21 00:06:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-21 00:06:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-21 00:06:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:19] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-21 00:06:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-21 00:06:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-21 00:06:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-21 00:06:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-21 00:06:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:19] [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 [2025-03-21 00:06:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-21 00:06:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:22] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-20 00:18:18 UTC; omnipath [2025-03-21 00:06:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-21 00:06:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-20 00:18:19 UTC; unix [2025-03-21 00:06:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-21 00:06:22] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-21 00:06:22] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-21 00:06:22] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-03-21 00:06:23] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-20); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.15.0(2024-10-29); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-21 00:06:23] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-03-21 00:06:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-21 00:06:23] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:23] [TRACE] [OmnipathR] Contains 1 files. [2025-03-21 00:06:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-21 00:06:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-21 00:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:23] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-21 00:06:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-21 00:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-21 00:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-21 00:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-21 00:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:23] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-21 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-21 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:25] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-20 00:18:18 UTC; omnipath [2025-03-21 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-21 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-20 00:18:19 UTC; unix [2025-03-21 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-21 00:06:25] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-21 00:06:25] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-21 00:06:25] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-03-21 00:06:25] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-20); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.15.0(2024-10-29); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-21 00:06:25] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-03-21 00:06:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-21 00:06:25] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:25] [TRACE] [OmnipathR] Contains 1 files. [2025-03-21 00:06:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-21 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-21 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-21 00:06:25] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-21 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-21 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-21 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-21 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-21 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-21 00:06:25] [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/RtmpP1lqUb/downloaded_packages’ Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2025-03-21 00:06:28 CET ]