##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rhdf5filters.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rhdf5filters_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/rhdf5filters.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rhdf5filters/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rhdf5filters' version '1.8.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 whether package 'rhdf5filters' can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/rhdf5filters/libs/x64/rhdf5filters.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/rhdf5filters.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rhdf5filters
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'rhdf5filters' ...
** using staged installation
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

`R CMD config MAKE` -C blosc
make[1]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc'
`R CMD config MAKE` -C lib/snappy-1.1.1
make[2]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++11    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -c snappy.cc
g++ -std=gnu++11    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++11    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++11    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
`R CMD config MAKE` -C lib/lz4-1.9.2
make[2]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.2'
gcc    -c lz4.c
gcc    -c lz4hc.c
make[2]: Leaving directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.2'
`R CMD config MAKE` -C lib/zstd-1.4.5
make[2]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/zstd-1.4.5'
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc    -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/zstd-1.4.5'
`R CMD config MAKE` -C lib/blosc-1.20.1 all
make[2]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c bitshuffle-generic.c
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_remainder':
bitshuffle-generic.c:40:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   40 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_scal':
bitshuffle-generic.c:48:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   48 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_byte_remainder':
bitshuffle-generic.c:85:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   85 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_elem':
bitshuffle-generic.c:109:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  109 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bitrow_eight':
bitshuffle-generic.c:121:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  121 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_elem_scal':
bitshuffle-generic.c:139:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  139 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_shuffle_bit_eightelem_scal':
bitshuffle-generic.c:204:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  204 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_untrans_bit_elem_scal':
bitshuffle-generic.c:220:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  220 | }
      | ^
gcc    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c shuffle-generic.c
shuffle-generic.c: In function 'blosc_internal_shuffle_generic':
shuffle-generic.c:17:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   17 | }
      | ^
shuffle-generic.c: In function 'blosc_internal_unshuffle_generic':
shuffle-generic.c:25:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   25 | }
      | ^
gcc    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5     -c shuffle.c
shuffle.c: In function 'blosc_internal_shuffle':
shuffle.c:390:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  390 | }
      | ^
shuffle.c: In function 'blosc_internal_unshuffle':
shuffle.c:403:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  403 | }
      | ^
shuffle.c: In function 'blosc_internal_bitshuffle':
shuffle.c:430:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  430 | }
      | ^
shuffle.c: In function 'blosc_internal_bitunshuffle':
shuffle.c:457:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  457 | }
      | ^
gcc    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c blosclz.c
gcc    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c blosc.c
gcc    -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c fastcopy.c
make[2]: Leaving directory '/f/biocbuild/bbs-3.15-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/lz4-1.9.2/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    -c -o H5Zblosc.o H5Zblosc.c \
-lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I./lib/blosc-1.20.1
g++ -std=gnu++11     -shared -o libH5Zblosc.so H5Zblosc.o \
libblosc.a -lz
make[1]: Leaving directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc'
`R CMD config MAKE` -C bzip2
make[1]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/bzip2'
`R CMD config MAKE` -C bzip2-1.0.8
make[2]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc    -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc    -D_FILE_OFFSET_BITS=64 -c huffman.c
gcc    -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc    -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc    -D_FILE_OFFSET_BITS=64 -c compress.c
gcc    -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc    -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
make[2]: Leaving directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc    -shared H5Zbzip2.c -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" \
-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a  -o libH5Zbz2.so
make[1]: Leaving directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/bzip2'
`R CMD config MAKE` -C lzf
make[1]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/lzf'
`R CMD config MAKE` -C lzf
make[2]: Entering directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/lzf/lzf'
gcc    -c lzf_c.c
gcc    -c lzf_d.c
rm -f liblzf.a
ar cq liblzf.a lzf_c.o lzf_d.o
make[2]: Leaving directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/lzf/lzf'
gcc    -shared H5Zlzf.c -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a  -o libH5Zlzf.so
make[1]: Leaving directory '/f/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/lzf'
mkdir -p "F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64/"
cp blosc/libH5Zblosc.so "F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zblosc.dll"
cp bzip2/libH5Zbz2.so "F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zbz2.dll"
cp lzf/libH5Zlzf.so "F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zlzf.dll"
gcc  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -lpthread -I"F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rhdf5filters.c -o rhdf5filters.o
gcc -shared -s -static-libgcc -o rhdf5filters.dll tmp.def rhdf5filters.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/libs/x64
** 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 (rhdf5filters)

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(rhdf5filters)
> 
> test_check("rhdf5filters")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 315 ]
> 
> proc.time()
   user  system elapsed 
   3.62    0.71   11.11