[ Started: 2023-11-08 17:17:45 CET ]
[ decoupleR v2.6.0 for BioC-3.17 from https://github.com/saezlab/decoupleR@RELEASE_3_17 ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/usr/lib/R/library"             
Bioconductor version '3.17' is out-of-date; the current release version '3.18'
  is available with R version '4.3'; see https://bioconductor.org/install
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 
rhdf5filters (1.14.0 -> 1.14.1) [CRAN]
Installing 1 packages: rhdf5filters
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/rhdf5filters_1.14.1.tar.gz'
Content type 'application/x-gzip' length 1179474 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘rhdf5filters’ ...
** 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... yes
checking for blosc_compress in -lblosc... yes
configure: Using system BLOSC library
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 11.4.0-1ubuntu1~22.04) 11.4.0’
make -C zstd
make[1]: Entering directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/zstd'
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -shared H5Zzstd.c -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" \
 -lzstd -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o libH5Zzstd.so
make[1]: Leaving directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/zstd'
make -C blosc
make[1]: Entering directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/blosc'
g++ -std=gnu++17 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -shared -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" H5Zblosc.cpp \
-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro   -lblosc -lzstd -lz -o libH5Zblosc.so 
make[1]: Leaving directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/bzip2'
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -shared H5Zbzip2.c -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" \
 -lbz2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o libH5Zbz2.so
make[1]: Leaving directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -c lzf_c.c
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -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/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -shared H5Zlzf.c -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o libH5Zlzf.so
make[1]: Leaving directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/lzf'
make -C vbz
make[1]: Entering directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/vbz'
make -C third_party/streamvbyte
make[2]: Entering directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/vbz/third_party/streamvbyte'
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbyte_decode.c
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbyte_encode.c
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbytedelta_decode.c
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbytedelta_encode.c
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbyte_0124_encode.c
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -Iinclude -std=c99 -mavx -c ./src/streamvbyte_0124_decode.c
gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -Iinclude -std=c99 -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/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/vbz/third_party/streamvbyte'
make -C vbz
make[2]: Entering directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/vbz/vbz'
g++ -std=gnu++17 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.3-3.17/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 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.3-3.17/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 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.3-3.17/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/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/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 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -shared vbz_plugin.cpp \
libvbz.a -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -lzstd third_party/streamvbyte/libstreamvbyte.a -o libH5Zvbz.so
make[1]: Leaving directory '/tmp/RtmpL686Lv/R.INSTALL1ecfc419c39e1d/rhdf5filters/src/vbz'
mkdir -p "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so blosc/libH5Zblosc.so lzf/libH5Zlzf.so zstd/libH5Zzstd.so vbz/libH5Zvbz.so "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
gcc -I"/usr/share/R/include" -DNDEBUG -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include'    -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c rhdf5filters.c -o rhdf5filters.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o rhdf5filters.so rhdf5filters.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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)

The downloaded source packages are in
	‘/tmp/Rtmp747cwH/downloaded_packages’
[ Finished: 2023-11-08 17:18:02 CET ]