[ Started: 2026-03-31 20:24:11 CEST ] [ CARNIVAL v2.5.1 for BioC-3.23 from https://github.com/saezlab/CARNIVAL@dev (81a0120 2022-03-17 09:59:10) ] [1] "Libraries: " "/home/omnipath/local/R/4.6-3.23" [3] "/home/omnipath/local/R/4.6" "/opt/R-devel/lib/R/library" Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-23 r89685) Old packages: 'furrr', 'progressr', 'ps', 'SparseArray', 'venn', 'vroom', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/furrr_0.4.0.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/progressr_0.19.0.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/ps_1.9.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.12.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/venn_1.13.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/vroom_1.7.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/wppi_1.19.0.tar.gz' * installing *source* package ‘furrr’ ... ** this is package ‘furrr’ version ‘0.4.0’ ** package ‘furrr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (furrr) * installing *source* package ‘progressr’ ... ** this is package ‘progressr’ version ‘0.19.0’ ** package ‘progressr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (progressr) * installing *source* package ‘ps’ ... ** this is package ‘ps’ version ‘1.9.2’ ** package ‘ps’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -g -O2 -L/usr/local/lib -Wall px.c -o px In file included from /usr/include/features.h:502, from /usr/include/unistd.h:25, from px.c:6: In function ‘read’, inlined from ‘echo_from_fd’ at px.c:83:9: /usr/include/x86_64-linux-gnu/bits/unistd.h:28:10: warning: ‘__read_alias’ specified size 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 28 | return __glibc_fortify (read, __nbytes, sizeof (char), | ^~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/unistd-decl.h: In function ‘echo_from_fd’: /usr/include/x86_64-linux-gnu/bits/unistd-decl.h:29:16: note: in a call to function ‘__read_alias’ declared with attribute ‘access (write_only, 2, 3)’ 29 | extern ssize_t __REDIRECT_FORTIFY (__read_alias, (int __fd, void *__buf, | ^~~~~~~~~~~~~~~~~~ gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-common.c -o api-common.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c common.c -o common.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c extra.c -o extra.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dummy.c -o dummy.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c error-codes.c -o error-codes.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cleancall.c -o cleancall.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c posix.c -o posix.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-posix.c -o api-posix.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c linux.c -o linux.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-linux.c -o api-linux.o gcc -std=gnu2x -shared -L/usr/local/lib -o ps.so init.o api-common.o common.o extra.o dummy.o error-codes.o cleancall.o posix.o api-posix.o linux.o api-linux.o installing via 'install.libs.R' to /home/omnipath/local/R/4.6-3.23/00LOCK-ps/00new/ps ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (ps) * installing *source* package ‘SparseArray’ ... ** this is package ‘SparseArray’ version ‘1.11.12’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c OPBufTree.c -o OPBufTree.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Rvector_summarization.c -o Rvector_summarization.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Rvector_utils.c -o Rvector_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SBT_utils.c -o SBT_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_abind.c -o SparseArray_abind.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_subsetting.c -o SparseArray_subsetting.o SparseArray_subsetting.c: In function ‘REC_subset_SVT_as_SVT’: SparseArray_subsetting.c:843:26: warning: comparison between pointer and integer 843 | if (offs != i2 || ans_elt != subSVT) | ^~ gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec.c -o SparseVec.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Math.c -o SparseVec_Math.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_subassignment.c -o SparseVec_subassignment.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_subsetting.c -o SparseVec_subsetting.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c argcheck_utils.c -o argcheck_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c coerceVector2.c -o coerceVector2.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c leaf_utils.c -o leaf_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c misc_utils.c -o misc_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c randomSparseArray.c -o randomSparseArray.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c readSparseCSV.c -o readSparseCSV.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c rowsum_methods.c -o rowsum_methods.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c test.c -o test.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/S4Vectors/include' -I'/home/omnipath/local/R/4.6-3.23/IRanges/include' -I'/home/omnipath/local/R/4.6-3.23/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c thread_control.c -o thread_control.o gcc -std=gnu2x -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_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 SparseVec_subassignment.o SparseVec_subsetting.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o misc_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp installing to /home/omnipath/local/R/4.6-3.23/00LOCK-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 ‘venn’ ... ** this is package ‘venn’ version ‘1.13’ ** package ‘venn’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (venn) * installing *source* package ‘vroom’ ... ** this is package ‘vroom’ version ‘1.7.1’ ** package ‘vroom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c Iconv.cpp -o Iconv.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c LocaleInfo.cpp -o LocaleInfo.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c altrep.cc -o altrep.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c delimited_index.cc -o delimited_index.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c delimited_index_connection.cc -o delimited_index_connection.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c fixed_width_index_connection.cc -o fixed_width_index_connection.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c gen.cc -o gen.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c grisu3.c -o grisu3.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c guess_type.cc -o guess_type.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c iconv_file.cc -o iconv_file.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c index_collection.cc -o index_collection.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom.cc -o vroom.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_big_int.cc -o vroom_big_int.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_chr.cc -o vroom_chr.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_date.cc -o vroom_date.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_dbl.cc -o vroom_dbl.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_dttm.cc -o vroom_dttm.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_errors.cpp -o vroom_errors.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_fct.cc -o vroom_fct.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_fwf.cc -o vroom_fwf.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_int.cc -o vroom_int.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_num.cc -o vroom_num.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_rle.cc -o vroom_rle.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_time.cc -o vroom_time.o g++ -std=gnu++20 -I"/opt/R-devel/lib/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.6-3.23/cpp11/include' -I'/home/omnipath/local/R/4.6-3.23/progress/include' -I'/home/omnipath/local/R/4.6-3.23/tzdb/include' -I/usr/local/include -fpic -g -O2 -c vroom_write.cc -o vroom_write.o g++ -std=gnu++20 -shared -L/usr/local/lib -o vroom.so Iconv.o LocaleInfo.o altrep.o cpp11.o delimited_index.o delimited_index_connection.o fixed_width_index_connection.o gen.o grisu3.o guess_type.o iconv_file.o index_collection.o vroom.o vroom_big_int.o vroom_chr.o vroom_date.o vroom_dbl.o vroom_dttm.o vroom_errors.o vroom_fct.o vroom_fwf.o vroom_int.o vroom_num.o vroom_rle.o vroom_time.o vroom_write.o installing to /home/omnipath/local/R/4.6-3.23/00LOCK-vroom/00new/vroom/libs ** R ** 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 ** 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 (vroom) * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.19.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2026-03-31 20:26:25] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 20:26:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:25] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:25] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-30 19:46:53 UTC; omnipath [2026-03-31 20:26:25] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-31 20:26:25] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-30 19:46:55 UTC; unix [2026-03-31 20:26:25] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.11 [2026-03-31 20:26:25] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-31 20:26:25] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-31; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-31 20:26:25] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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] [2026-03-31 20:26:26] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-03-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); wppi 1.19.0(2025-11-18); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-31 20:26:26] [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 [2026-03-31 20:26:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-31 20:26:26] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:26] [TRACE] [OmnipathR] Contains 1 files. [2026-03-31 20:26:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-31 20:26:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 20:26:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:26] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-31 20:26:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-31 20:26:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-31 20:26:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-31 20:26:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-31 20:26:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:26] [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 [2026-03-31 20:26:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 20:26:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:28] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:28] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-30 19:46:53 UTC; omnipath [2026-03-31 20:26:28] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-31 20:26:28] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-30 19:46:55 UTC; unix [2026-03-31 20:26:28] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.11 [2026-03-31 20:26:28] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-31 20:26:29] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-31; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-31 20:26:29] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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] [2026-03-31 20:26:29] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-03-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); wppi 1.19.0(2025-11-18); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-31 20:26:29] [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 [2026-03-31 20:26:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-31 20:26:29] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:29] [TRACE] [OmnipathR] Contains 1 files. [2026-03-31 20:26:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-31 20:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 20:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:29] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-31 20:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-31 20:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-31 20:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-31 20:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-31 20:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:29] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-03-31 20:26:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 20:26:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:31] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-30 19:46:53 UTC; omnipath [2026-03-31 20:26:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-31 20:26:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-30 19:46:55 UTC; unix [2026-03-31 20:26:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.11 [2026-03-31 20:26:31] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-31 20:26:31] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-31; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-31 20:26:31] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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] [2026-03-31 20:26:31] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-03-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); wppi 1.19.0(2025-11-18); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-31 20:26:31] [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 [2026-03-31 20:26:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-31 20:26:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:31] [TRACE] [OmnipathR] Contains 1 files. [2026-03-31 20:26:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-31 20:26:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 20:26:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-31 20:26:31] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-31 20:26:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-31 20:26:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-31 20:26:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-31 20:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-31 20:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 20:26:32] [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/RtmpiycaF0/downloaded_packages’ Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-23 r89685) 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: ps, vroom [ Finished: 2026-03-31 20:26:35 CEST ]