##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:rhdf5filters.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings rhdf5filters_1.13.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘rhdf5filters/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5filters’ version ‘1.13.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rhdf5filters’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 16.8Mb
  sub-directories of 1Mb or more:
    lib  16.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘rhdf5filters.Rmd’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘rhdf5filters.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.187   0.019   0.200 

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
* checking PDF version of manual without index ... ERROR
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL rhdf5filters
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘rhdf5filters’ ...
** using staged installation
configuring the BLOSC filter...
x86_CPU=false
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
checking whether C compiler accepts -msse2... no
checking whether C compiler accepts -mavx2... no
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:    ZSTD_LIB=zstd/libH5Zzstd.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 (GCC) 10.3.1’
make -C zstd
make[1]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/zstd'
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/pool.c -o common/pool.o -o common/pool.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
rm -f libzstd.a
ar cq libzstd.a common/debug.o common/entropy_common.o common/error_private.o common/fse_decompress.o common/pool.o common/threading.o common/xxhash.o common/zstd_common.o compress/fse_compress.o compress/hist.o compress/huf_compress.o compress/zstd_compress.o compress/zstd_compress_literals.o compress/zstd_compress_sequences.o compress/zstd_compress_superblock.o compress/zstd_double_fast.o compress/zstd_fast.o compress/zstd_lazy.o compress/zstd_ldm.o compress/zstd_opt.o compress/zstdmt_compress.o decompress/huf_decompress.o decompress/zstd_ddict.o decompress/zstd_decompress.o decompress/zstd_decompress_block.o
ranlib libzstd.a
gcc -g -O2 -fPIC -shared H5Zzstd.c -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" \
libzstd.a -L/usr/local/lib -o libH5Zzstd.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/zstd'
make -C blosc
make[1]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -c snappy.cc
g++ -std=gnu++17 -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.4
make[2]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.4'
gcc -g -O2 -fPIC -c lz4.c
gcc -g -O2 -fPIC -c lz4hc.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.4'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c bitshuffle-generic.c
gcc -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c shuffle-generic.c
gcc -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd     -c shuffle.c
gcc -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c blosclz.c
gcc -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c blosc.c
gcc -g -O2 -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c fastcopy.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1'
rm -f libblosc.a
ar cq libblosc.a lib/blosc-1.20.1/blosc.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/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
gcc -g -O2 -fPIC -c -o H5Zblosc.o H5Zblosc.c \
-I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/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 ../zstd/libzstd.a -lz
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/bzip2'
make -C bzip2-1.0.8
make[2]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/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 '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -g -O2 -fPIC -shared H5Zbzip2.c -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" \
-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -L/usr/local/lib -o libH5Zbz2.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/home/biocbuild/bbs-3.18-bioc/meat/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 '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -fPIC -shared H5Zlzf.c -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-bioc/meat/rhdf5filters/src/lzf'
mkdir -p "/home/biocbuild/R/R-4.3.0/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so "/home/biocbuild/R/R-4.3.0/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp blosc/libH5Zblosc.so "/home/biocbuild/R/R-4.3.0/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp lzf/libH5Zlzf.so "/home/biocbuild/R/R-4.3.0/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp zstd/libH5Zzstd.so "/home/biocbuild/R/R-4.3.0/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
gcc -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I/usr/local/include -I"/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include" -I'/home/biocbuild/R/R-4.3.0/site-library/Rhdf5lib/include' -I/usr/local/include   -g -O2 -fPIC  -g -O2  -c rhdf5filters.c -o rhdf5filters.o
gcc -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/site-library/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)