##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:rhdf5filters.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings rhdf5filters_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rhdf5filters/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5filters’ version ‘1.23.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Hugo Gruson <hugo.gruson@embl.de>’

License components with restrictions and base license permitting such:
  BSD_2_clause + file LICENSE
File 'LICENSE':
  Copyright (c) 2020, Mike Smith <msmith@embl.de>
  
  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions are
  met:
  
      Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.
  
      Redistributions in binary form must reproduce the above copyright
      notice, this list of conditions and the following disclaimer in
      the documentation and/or other materials provided with the
      distribution.
  
  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
  LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
  A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
  HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
  LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
  DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
  THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘rhdf5filters’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is 17.0Mb
  sub-directories of 1Mb or more:
    lib  16.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... INFO
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 ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL rhdf5filters
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘rhdf5filters’ ...
** this is package ‘rhdf5filters’ version ‘1.23.0’
** using staged installation
checking for gcc... gcc -std=gnu2x
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 -std=gnu2x accepts -g... yes
checking for gcc -std=gnu2x option to enable C11 features... none needed
configure: is Bioc build machine
configure: configuring BZIP2 filter...
configure: compiling bundled bzip2 library
configure: configuring the Zstd filter...
configure: compiling bundled Zstd library
configure: configuring the BLOSC filter...
configure: compiling bundled BLOSC library
checking whether C compiler accepts -msse2... yes
configure: Bioc build machine; disabling MAVX2
checking for gcc __builtin_cpu_init function... (cached) true
checking for x86 sse2 instruction support... yes
configure: configuring the VBZ filter
machine=x86_64
CPU_ARCH=x86
checking whether C compiler accepts -mavx... yes
checking for x86 avx instruction support... yes
VBZ_FLAGS=-mssse3
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 '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/zstd'
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/pool.c -o common/pool.o -o common/pool.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -shared H5Zzstd.c -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" \
-I. -Icommon ../zstd/libzstd.a -L/usr/local/lib -o libH5Zzstd.so
make[1]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/zstd'
make -C blosc
make[1]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -c snappy.cc
snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::Append(const char*, size_t)’:
snappy.cc:1013:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
 1013 |         if (curr_iov_index_ + 1 >= output_iov_count_) {
      |             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::AppendFromSelf(size_t, size_t)’:
snappy.cc:1095:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
 1095 |           if (curr_iov_index_ + 1 >= output_iov_count_) {
      |               ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: At global scope:
snappy.cc:567:13: warning: ‘void snappy::ComputeTable()’ defined but not used [-Wunused-function]
  567 | static void ComputeTable() {
      |             ^~~~~~~~~~~~
g++ -std=gnu++17 -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.4
make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/blosc/lib/lz4-1.9.4'
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -c lz4.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -c lz4hc.c
make[2]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/blosc/lib/lz4-1.9.4'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c bitshuffle-sse2.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c shuffle-sse2.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c bitshuffle-generic.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c shuffle-generic.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -DSHUFFLE_SSE2_ENABLED  -c shuffle.c
In file included from shuffle.c:12:
shuffle-generic.h:61:13: warning: ‘unshuffle_generic_inline’ defined but not used [-Wunused-function]
   61 | static void unshuffle_generic_inline(const size_t type_size,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~
shuffle-generic.h:32:13: warning: ‘shuffle_generic_inline’ defined but not used [-Wunused-function]
   32 | static void shuffle_generic_inline(const size_t type_size,
      |             ^~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c blosclz.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c blosc.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c fastcopy.c
make[2]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/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/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 -Wall -Werror=format-security -fpic -shared -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" H5Zblosc.cpp \
-L/usr/local/lib -I./lib/blosc-1.20.1 ./libblosc.a ../zstd/libzstd.a -lz -o libH5Zblosc.so 
make[1]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/bzip2'
make -C bzip2-1.0.8
make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -D_FILE_OFFSET_BITS=64 -c huffman.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -D_FILE_OFFSET_BITS=64 -c compress.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -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 '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -shared H5Zbzip2.c -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" \
-Ibzip2-1.0.8 bzip2-1.0.8/libbz2.a -L/usr/local/lib -o libH5Zbz2.so
make[1]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/lzf/lzf'
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -c lzf_c.c
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/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 '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/lzf/lzf'
gcc -std=gnu2x -g -O2 -Wall -Werror=format-security -fpic -shared H5Zlzf.c -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so
make[1]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/lzf'
make -C vbz
make[1]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/vbz'
make -C third_party/streamvbyte
make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/vbz/third_party/streamvbyte'
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -mavx  -c ./src/streamvbyte_decode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -mavx  -c ./src/streamvbyte_encode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -mavx  -c ./src/streamvbytedelta_decode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -mavx  -c ./src/streamvbytedelta_encode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -mavx  -c ./src/streamvbyte_0124_encode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -mavx  -c ./src/streamvbyte_0124_decode.c
gcc -std=gnu99 -g -O2 -fpic -Iinclude -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/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 '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/vbz/third_party/streamvbyte'
make -C vbz
make[2]: Entering directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/vbz/vbz'
g++ -std=gnu++17 -g -O2 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/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 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/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 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/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 '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/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 -Wall -Werror=format-security -fpic -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -shared vbz_plugin.cpp \
libvbz.a -L/usr/local/lib ../zstd/libzstd.a third_party/streamvbyte/libstreamvbyte.a -o libH5Zvbz.so
make[1]: Leaving directory '/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5filters/src/vbz'
mkdir -p "/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so blosc/libH5Zblosc.so lzf/libH5Zlzf.so zstd/libH5Zzstd.so vbz/libH5Zvbz.so "/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I/usr/local/include -I"/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include" -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security -c rhdf5filters.c -o rhdf5filters.o
gcc -std=gnu2x -shared -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/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)

R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

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> if (requireNamespace("tinytest", quietly = TRUE)) {
+   tinytest::test_package("rhdf5filters")
+ }

test-filter-io.R..............    0 tests    
test-filter-io.R..............    0 tests    
test-filter-io.R..............    0 tests    
test-filter-io.R..............    0 tests    
test-filter-io.R..............    0 tests    
test-filter-io.R..............    0 tests    
test-filter-io.R..............    0 tests    
test-filter-io.R..............  252 tests OK 
test-filter-io.R..............  306 tests OK 
test-filter-io.R..............  312 tests OK 1.1s

test-filter-read.R............    0 tests    
test-filter-read.R............    0 tests    
test-filter-read.R............    0 tests    
test-filter-read.R............    0 tests    
test-filter-read.R............    0 tests    
test-filter-read.R............    0 tests    
test-filter-read.R............    5 tests OK 22ms

test-plugin-path.R............    0 tests    
test-plugin-path.R............    1 tests OK 
test-plugin-path.R............    2 tests OK 
test-plugin-path.R............    3 tests OK 2ms
All ok, 320 results (1.1s)
> 
> proc.time()
   user  system elapsed 
  1.174   0.088   1.253