[ Started: 2023-03-25 21:32:32 CET ]
[ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/opt/R-devel/lib/R/library"     
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
  (2023-03-16 r83996)
Old packages: 'covr', 'rhdf5filters'
trying URL 'https://cloud.r-project.org/src/contrib/covr_3.6.2.tar.gz'
Content type 'application/x-gzip' length 162879 bytes (159 KB)
==================================================
downloaded 159 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/rhdf5filters_1.11.2.tar.gz'
Content type 'application/x-gzip' length 1006834 bytes (983 KB)
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downloaded 983 KB

* installing *source* package ‘covr’ ...
** package ‘covr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c reassign.c -o reassign.o
gcc -shared -L/usr/local/lib -o covr.so reassign.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-covr/00new/covr/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 (covr)
* installing *source* package ‘rhdf5filters’ ...
** using staged installation
configuring the BLOSC filter...
x86_CPU=true
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
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: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/blosc/Makefile
configure:    BZIP2_LIB=bzip2/libH5Zbz2.so
configure:    BLOSC_LIB=blosc/libH5Zblosc.so
configure:    LZF_LIB=lzf/libH5Zlzf.so
configure: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/blosc/Makefile
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
make -C blosc
make[1]: Entering directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -c snappy.cc
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.2
make[2]: Entering directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/blosc/lib/lz4-1.9.2'
gcc -g -O2 -fpic -c lz4.c
gcc -g -O2 -fpic -c lz4hc.c
make[2]: Leaving directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/blosc/lib/lz4-1.9.2'
make -C lib/zstd-1.4.5
make[2]: Entering directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/blosc/lib/zstd-1.4.5'
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/blosc/lib/zstd-1.4.5'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-avx2.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-avx2.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-sse2.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-sse2.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-generic.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-generic.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c blosclz.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c blosc.c
gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c fastcopy.c
make[2]: Leaving directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/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/lz4-1.9.2/lz4.o lib/lz4-1.9.2/lz4hc.o lib/zstd-1.4.5/common/debug.o lib/zstd-1.4.5/common/entropy_common.o lib/zstd-1.4.5/common/error_private.o lib/zstd-1.4.5/common/fse_decompress.o lib/zstd-1.4.5/common/pool.o lib/zstd-1.4.5/common/threading.o lib/zstd-1.4.5/common/xxhash.o lib/zstd-1.4.5/common/zstd_common.o lib/zstd-1.4.5/compress/fse_compress.o lib/zstd-1.4.5/compress/hist.o lib/zstd-1.4.5/compress/huf_compress.o lib/zstd-1.4.5/compress/zstd_compress.o lib/zstd-1.4.5/compress/zstd_compress_literals.o lib/zstd-1.4.5/compress/zstd_compress_sequences.o lib/zstd-1.4.5/compress/zstd_compress_superblock.o lib/zstd-1.4.5/compress/zstd_double_fast.o lib/zstd-1.4.5/compress/zstd_fast.o lib/zstd-1.4.5/compress/zstd_lazy.o lib/zstd-1.4.5/compress/zstd_ldm.o lib/zstd-1.4.5/compress/zstd_opt.o lib/zstd-1.4.5/compress/zstdmt_compress.o lib/zstd-1.4.5/decompress/huf_decompress.o lib/zstd-1.4.5/decompress/zstd_ddict.o lib/zstd-1.4.5/decompress/zstd_decompress.o lib/zstd-1.4.5/decompress/zstd_decompress_block.o
ranlib libblosc.a
gcc -g -O2 -fpic -c -o H5Zblosc.o H5Zblosc.c \
-I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I./lib/blosc-1.20.1
g++ -std=gnu++17 -g -O2 -fpic -L/usr/local/lib -shared -o libH5Zblosc.so H5Zblosc.o \
libblosc.a -lz
make[1]: Leaving directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/bzip2'
make -C bzip2-1.0.8
make[2]: Entering directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c huffman.c
gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c compress.c
gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c bzlib.c
rm -f libbz2.a
ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
ranlib libbz2.a
make[2]: Leaving directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -g -O2 -fpic -shared H5Zbzip2.c -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" \
-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -L/usr/local/lib -o libH5Zbz2.so
make[1]: Leaving directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -fpic -c lzf_c.c
gcc -g -O2 -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/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -fpic -shared H5Zlzf.c -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so
make[1]: Leaving directory '/tmp/Rtmpz0JZz1/R.INSTALL30c9b62445e93d/rhdf5filters/src/lzf'
mkdir -p "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp blosc/libH5Zblosc.so "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp lzf/libH5Zlzf.so "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I'/home/omnipath/local/R/4.3-3.17/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/4.3-3.17/00LOCK-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/RtmpUAn5TI/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
  (2023-03-16 r83996)
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: covr
[ Finished: 2023-03-25 21:33:16 CET ]