[ Started: 2025-02-21 00:05:09 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: 'BiocCheck', 'BiocParallel', 'HDF5Array', 'SparseArray', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/BiocCheck_1.43.10.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/BiocParallel_1.41.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/HDF5Array_1.35.15.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/SparseArray_1.7.6.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz' * installing *source* package ‘BiocCheck’ ... ** this is package ‘BiocCheck’ version ‘1.43.10’ ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocCheck) * installing *source* package ‘BiocParallel’ ... ** this is package ‘BiocParallel’ version ‘1.41.2’ ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking for library containing shm_open... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/mman.h... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I/usr/local/include -fpic -g -O2 -c ipcmutex.cpp -o ipcmutex.o g++ -std=gnu++11 -shared -L/usr/local/lib -o BiocParallel.so cpp11.o ipcmutex.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-BiocParallel/00new/BiocParallel/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 (BiocParallel) * installing *source* package ‘SparseArray’ ... ** this is package ‘SparseArray’ version ‘1.7.6’ ** 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 [2025-02-21 00:06:00] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-21 00:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:00] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-20 00:18:21 UTC; omnipath [2025-02-21 00:06:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-21 00:06:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-20 00:18:22 UTC; unix [2025-02-21 00:06:00] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-21 00:06:00] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-21 00:06:00] [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=2025-02-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-21 00:06:00] [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] [2025-02-21 00:06:00] [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 [2025-02-21 00:06:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-21 00:06:00] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:00] [TRACE] [OmnipathR] Contains 1 files. [2025-02-21 00:06:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-21 00:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-21 00:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:00] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-21 00:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-21 00:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-21 00:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-21 00:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-21 00:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:00] [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 [2025-02-21 00:06:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-21 00:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:03] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:03] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-20 00:18:21 UTC; omnipath [2025-02-21 00:06:03] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-21 00:06:03] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-20 00:18:22 UTC; unix [2025-02-21 00:06:03] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-21 00:06:03] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-21 00:06:03] [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=2025-02-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-21 00:06:03] [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] [2025-02-21 00:06:03] [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 [2025-02-21 00:06:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-21 00:06:03] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:03] [TRACE] [OmnipathR] Contains 1 files. [2025-02-21 00:06:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-21 00:06:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-21 00:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:03] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-21 00:06:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-21 00:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-21 00:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-21 00:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-21 00:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:03] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-21 00:06:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-21 00:06:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:05] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-20 00:18:21 UTC; omnipath [2025-02-21 00:06:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-21 00:06:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-20 00:18:22 UTC; unix [2025-02-21 00:06:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-21 00:06:05] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-21 00:06:05] [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=2025-02-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-21 00:06:05] [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] [2025-02-21 00:06:05] [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 [2025-02-21 00:06:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-21 00:06:05] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:05] [TRACE] [OmnipathR] Contains 1 files. [2025-02-21 00:06:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-21 00:06:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-21 00:06:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-21 00:06:05] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-21 00:06:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-21 00:06:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-21 00:06:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-21 00:06:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-21 00:06:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-21 00:06:06] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘HDF5Array’ ... ** this is package ‘HDF5Array’ version ‘1.35.15’ ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (HDF5Array) The downloaded source packages are in ‘/tmp/RtmpUbgi06/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: 2025-02-21 00:06:23 CET ]