[ Started: 2025-07-19 19:33:14 CEST ]
[ CellNOptR v1.49.1 for BioC-3.22 from https://github.com/saezlab/CellNOptR@master (7001050 2024-04-11 11:28:56) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.5-3.22"
[3] "/home/omnipath/local/R/4.5"      "/usr/lib/R/library"             
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.22 (BiocManager 1.30.26), R 4.5.1 (2025-06-13)
Old packages: 'GenomeInfoDb', 'rhdf5', 'SparseArray'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/GenomeInfoDb_1.45.8.tar.gz'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/rhdf5_2.53.3.tar.gz'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/SparseArray_1.9.1.tar.gz'
* installing *source* package ‘GenomeInfoDb’ ...
** this is package ‘GenomeInfoDb’ version ‘1.45.8’
** package ‘GenomeInfoDb’ 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
** 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 (GenomeInfoDb)
* installing *source* package ‘rhdf5’ ...
** this is package ‘rhdf5’ version ‘2.53.3’
** package ‘rhdf5’ successfully unpacked and MD5 sums checked
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5.c -o H5.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5A.c -o H5A.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5D.c -o H5D.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5E.c -o H5E.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5F.c -o H5F.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5G.c -o H5G.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5I.c -o H5I.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5L.c -o H5L.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5O.c -o H5O.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5P.c -o H5P.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5PL.c -o H5PL.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5R.c -o H5R.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5S.c -o H5S.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5S_extras.c -o H5S_extras.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5T.c -o H5T.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5T_extras.c -o H5T_extras.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5Z.c -o H5Z.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c H5constants.c -o H5constants.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c HandleList.cpp -o HandleList.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c HandleListWrap.c -o HandleListWrap.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c bit64conversion.c -o bit64conversion.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c external_filters.c -o external_filters.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c h5dump.c -o h5dump.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c h5ls.c -o h5ls.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c h5testLock.c -o h5testLock.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c printdatatype.c -o printdatatype.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c utils.c -o utils.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rhdf5lib/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c wrap.c -o wrap.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5PL.o H5R.o H5S.o H5S_extras.o H5T.o H5T_extras.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/omnipath/local/R/4.5-3.22/Rhdf5lib/lib/libhdf5.a -L/home/omnipath/local/R/4.5-3.22/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.5-3.22/00LOCK-rhdf5/00new/rhdf5/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 (rhdf5)
* installing *source* package ‘SparseArray’ ...
** this is package ‘SparseArray’ version ‘1.9.1’
** package ‘SparseArray’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c OPBufTree.c -o OPBufTree.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c Rvector_summarization.c -o Rvector_summarization.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c Rvector_utils.c -o Rvector_utils.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SBT_utils.c -o SBT_utils.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_abind.c -o SparseArray_abind.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_subsetting.c -o SparseArray_subsetting.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseMatrix_mult.c -o SparseMatrix_mult.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseVec.c -o SparseVec.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseVec_Arith.c -o SparseVec_Arith.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseVec_Compare.c -o SparseVec_Compare.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseVec_Logic.c -o SparseVec_Logic.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseVec_Math.c -o SparseVec_Math.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SparseVec_dotprod.c -o SparseVec_dotprod.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c argcheck_utils.c -o argcheck_utils.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c coerceVector2.c -o coerceVector2.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c leaf_utils.c -o leaf_utils.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c randomSparseArray.c -o randomSparseArray.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c readSparseCSV.c -o readSparseCSV.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c rowsum_methods.c -o rowsum_methods.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c test.c -o test.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.22/IRanges/include' -I'/home/omnipath/local/R/4.5-3.22/XVector/include'    -fopenmp -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c thread_control.c -o thread_control.o
gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -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 -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.5-3.22/00LOCK-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)

The downloaded source packages are in
	‘/tmp/RtmpDDLvB4/downloaded_packages’
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.22 (BiocManager 1.30.26), R 4.5.1 (2025-06-13)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 4 packages ahead of CRAN: BiocGenerics, graph, Rgraphviz, RBGL
[ Finished: 2025-07-19 19:34:04 CEST ]