[ Started: 2025-03-07 00:05:10 CET ]
[ CARNIVAL v2.7.2 for BioC-3.21 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.5-3.21"
[3] "/home/omnipath/local/R/4.5"      "/opt/R-devel/lib/R/library"     
Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable)
  (2025-02-12 r87715)
Old packages: 'BiocNeighbors', 'bit', 'DESeq2', 'rhdf5filters', 'wppi'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/BiocNeighbors_2.1.3.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/bit_4.6.0.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/DESeq2_1.47.5.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/rhdf5filters_1.19.2.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz'
* installing *source* package ‘BiocNeighbors’ ...
** this is package ‘BiocNeighbors’ version ‘2.1.3’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/assorthead/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/assorthead/include' -I/usr/local/include    -fpic  -g -O2   -c annoy.cpp -o annoy.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/assorthead/include' -I/usr/local/include    -fpic  -g -O2   -c exhaustive.cpp -o exhaustive.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/assorthead/include' -I/usr/local/include    -fpic  -g -O2   -c find_mutual_nns.cpp -o find_mutual_nns.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/assorthead/include' -I/usr/local/include    -fpic  -g -O2   -c generics.cpp -o generics.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/assorthead/include' -I/usr/local/include    -fpic  -g -O2   -c hnsw.cpp -o hnsw.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/assorthead/include' -I/usr/local/include    -fpic  -g -O2   -c kmknn.cpp -o kmknn.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/assorthead/include' -I/usr/local/include    -fpic  -g -O2   -c vptree.cpp -o vptree.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o BiocNeighbors.so RcppExports.o annoy.o exhaustive.o find_mutual_nns.o generics.o hnsw.o kmknn.o vptree.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-BiocNeighbors/00new/BiocNeighbors/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 (BiocNeighbors)
* installing *source* package ‘bit’ ...
** this is package ‘bit’ version ‘4.6.0’
** package ‘bit’ 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 -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c attrutil.c -o attrutil.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c bit.c -o bit.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c chunkutil.c -o chunkutil.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c clone.c -o clone.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c integerutil.c -o integerutil.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c merge.c -o merge.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c rle.c -o rle.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c sort.c -o sort.o
gcc -shared -L/usr/local/lib -o bit.so attrutil.o bit.o chunkutil.o clone.o init.o integerutil.o merge.o rle.o sort.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-bit/00new/bit/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 (bit)
* installing *source* package ‘DESeq2’ ...
** this is package ‘DESeq2’ version ‘1.47.5’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2   -c DESeq2.cpp -o DESeq2.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-DESeq2/00new/DESeq2/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 (DESeq2)
* installing *source* package ‘rhdf5filters’ ...
** this is package ‘rhdf5filters’ version ‘1.19.2’
** using staged installation
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
configure: is NOT Bioc build machine
configure: configuring BZIP2 filter...
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 bzlib.h... yes
checking for BZ2_bzDecompressInit in -lbz2... yes
configure: Using system bzip2 library
configure: configuring the Zstd filter...
checking for zstd.h... yes
checking for ZSTD_decompress in -lzstd... yes
configure: Using system Zstd library
configure: configuring the BLOSC filter...
checking for blosc.h... no
configure: compiling bundled BLOSC library
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -mavx2... yes
checking for gcc __builtin_cpu_init function... (cached) true
checking for x86 sse2 instruction support... yes
checking for x86 avx2 instruction support... yes
configure: configuring the VBZ filter
checking whether C compiler accepts -mavx... yes
checking for x86 avx instruction support... yes
configure: creating ./config.status
config.status: creating src/bzip2/Makefile
config.status: creating src/zstd/Makefile
config.status: creating src/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/blosc/Makefile
config.status: creating src/vbz/Makefile
config.status: creating src/vbz/vbz/Makefile
config.status: creating src/vbz/third_party/streamvbyte/Makefile
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make -C zstd
make[1]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/zstd'
gcc -g -O2 -fpic -shared H5Zzstd.c -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" \
 -lzstd -L/usr/local/lib -o libH5Zzstd.so
make[1]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/zstd'
make -C blosc
make[1]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -c snappy.cc
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.4
make[2]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/blosc/lib/lz4-1.9.4'
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -c lz4.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -c lz4hc.c
make[2]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/blosc/lib/lz4-1.9.4'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-avx2.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-avx2.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-sse2.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-sse2.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-generic.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-generic.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c blosclz.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c blosc.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c fastcopy.c
make[2]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/blosc/lib/blosc-1.20.1'
rm -f libblosc.a
ar cq libblosc.a lib/blosc-1.20.1/bitshuffle-avx2.o lib/blosc-1.20.1/blosc.o lib/blosc-1.20.1/shuffle-avx2.o lib/blosc-1.20.1/shuffle-sse2.o lib/blosc-1.20.1/bitshuffle-generic.o lib/blosc-1.20.1/blosclz.o lib/blosc-1.20.1/shuffle.o lib/blosc-1.20.1/bitshuffle-sse2.o lib/blosc-1.20.1/fastcopy.o lib/blosc-1.20.1/shuffle-generic.o lib/snappy-1.1.1/snappy.o lib/snappy-1.1.1/snappy-c.o lib/snappy-1.1.1/snappy-sinksource.o lib/snappy-1.1.1/snappy-stubs-internal.o lib/lz4-1.9.4/lz4.o lib/lz4-1.9.4/lz4hc.o 
ranlib libblosc.a
g++ -std=gnu++17 -g -O2 -fpic -shared -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" H5Zblosc.cpp \
-L/usr/local/lib -I./lib/blosc-1.20.1 ./libblosc.a -lzstd -lz -o libH5Zblosc.so 
make[1]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/bzip2'
gcc -g -O2 -fpic -shared H5Zbzip2.c -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" \
 -lbz2 -L/usr/local/lib -o libH5Zbz2.so
make[1]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -c lzf_c.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -c lzf_d.c
rm -f liblzf.a
ar cq liblzf.a lzf_c.o lzf_d.o
ranlib liblzf.a
make[2]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -fpic -shared H5Zlzf.c -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so
make[1]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/lzf'
make -C vbz
make[1]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/vbz'
make -C third_party/streamvbyte
make[2]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/vbz/third_party/streamvbyte'
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -mavx  -c ./src/streamvbyte_decode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -mavx  -c ./src/streamvbyte_encode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -mavx  -c ./src/streamvbytedelta_decode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -mavx  -c ./src/streamvbytedelta_encode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -mavx  -c ./src/streamvbyte_0124_encode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -mavx  -c ./src/streamvbyte_0124_decode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -mavx  -c ./src/streamvbyte_zigzag.c
rm -f libstreamvbyte.a
ar cq libstreamvbyte.a streamvbyte_decode.o streamvbyte_encode.o streamvbytedelta_decode.o streamvbytedelta_encode.o streamvbyte_0124_encode.o streamvbyte_0124_decode.o streamvbyte_zigzag.o
ranlib libstreamvbyte.a 
make[2]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/vbz/third_party/streamvbyte'
make -C vbz
make[2]: Entering directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/vbz/vbz'
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -mssse3 -c vbz.cpp -o vbz.o
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -mssse3 -c v0/vbz_streamvbyte.cpp -o v0/vbz_streamvbyte.o
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -mssse3 -c v1/vbz_streamvbyte.cpp -o v1/vbz_streamvbyte.o
make[2]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/vbz/vbz'
rm -f libvbz.a
ar cq libvbz.a vbz/vbz.o vbz/v0/vbz_streamvbyte.o vbz/v1/vbz_streamvbyte.o
ranlib libvbz.a
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -shared vbz_plugin.cpp \
libvbz.a -L/usr/local/lib -lzstd third_party/streamvbyte/libstreamvbyte.a -o libH5Zvbz.so
make[1]: Leaving directory '/tmp/RtmpM6V1TZ/R.INSTALL1564648daf249/rhdf5filters/src/vbz'
mkdir -p "/home/omnipath/local/R/4.5-3.21/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so blosc/libH5Zblosc.so lzf/libH5Zlzf.so zstd/libH5Zzstd.so vbz/libH5Zvbz.so "/home/omnipath/local/R/4.5-3.21/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -I"/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include" -I'/home/omnipath/local/R/4.5-3.21/Rhdf5lib/include' -I/usr/local/include   -g -O2 -fpic  -g -O2  -c rhdf5filters.c -o rhdf5filters.o
gcc -shared -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-rhdf5filters/00new/rhdf5filters/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 (rhdf5filters)
* installing *source* package ‘wppi’ ...
** this is package ‘wppi’ version ‘1.15.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2025-03-07 00:06:55] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:55] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-06 00:08:26 UTC; omnipath
[2025-03-07 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-07 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-06 00:08:27 UTC; unix
[2025-03-07 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-07 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-07 00:06:55] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-07 00:06:55] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-07 00:06:55] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-06); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.4(2025-02-27); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.15.0(2024-10-29); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-07 00:06:55] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:55] [TRACE]   [OmnipathR] Cache locked: FALSE
Note: wrong number of arguments to '/' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:58] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:06:58] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-06 00:08:26 UTC; omnipath
[2025-03-07 00:06:58] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-07 00:06:58] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-06 00:08:27 UTC; unix
[2025-03-07 00:06:58] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-07 00:06:58] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-07 00:06:58] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-07 00:06:58] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-07 00:06:58] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-06); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.4(2025-02-27); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.15.0(2024-10-29); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-07 00:06:58] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:06:58] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-07 00:07:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 00:07:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:07:00] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:07:00] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-06 00:08:26 UTC; omnipath
[2025-03-07 00:07:00] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-07 00:07:00] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-06 00:08:27 UTC; unix
[2025-03-07 00:07:00] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-07 00:07:00] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-07 00:07:01] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-07 00:07:01] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-07 00:07:01] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-06); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.4(2025-02-27); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.15.0(2024-10-29); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-07 00:07:01] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:07:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-07 00:07:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 00:07:01] [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/RtmpKjdXKg/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' 

Skipping 1 packages ahead of CRAN: bit
[ Finished: 2025-03-07 00:07:04 CET ]