Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1762/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5filters 1.16.0  (landing page)
Mike Smith
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/rhdf5filters
git_branch: RELEASE_3_19
git_last_commit: 1d29c0e
git_last_commit_date: 2024-04-30 11:21:38 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for rhdf5filters on nebbiolo1

To the developers/maintainers of the rhdf5filters package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5filters.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: rhdf5filters
Version: 1.16.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:rhdf5filters.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings rhdf5filters_1.16.0.tar.gz
StartedAt: 2024-06-17 03:05:11 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 03:05:30 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 19.0 seconds
RetCode: 0
Status:   OK  
CheckDir: rhdf5filters.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:rhdf5filters.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings rhdf5filters_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘rhdf5filters/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5filters’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘rhdf5filters’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    lib   9.1Mb
* 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 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 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters.Rcheck/00check.log’
for details.


Installation output

rhdf5filters.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL rhdf5filters
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* 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 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 11.4.0-1ubuntu1~22.04) 11.4.0’
make -C zstd
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/zstd'
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -Wall -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 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -Wall -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 -Wall -fpic -shared H5Zzstd.c -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" \
-I. -Icommon ../zstd/libzstd.a -L/usr/local/lib -o libH5Zzstd.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/zstd'
make -C blosc
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/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 -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.4
make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.4'
gcc -g -O2 -Wall -fpic -c lz4.c
gcc -g -O2 -Wall -fpic -c lz4hc.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.19-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-3.19-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c bitshuffle-sse2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c shuffle-sse2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c bitshuffle-generic.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c shuffle-generic.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/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 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c blosclz.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2  -c blosc.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/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 '/home/biocbuild/bbs-3.19-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/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 -fpic -shared -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/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 '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/bzip2'
make -C bzip2-1.0.8
make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c blocksort.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c huffman.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c crctable.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c randtable.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c compress.c
gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c decompress.c
gcc -g -O2 -Wall -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-3.19-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -g -O2 -Wall -fpic -shared H5Zbzip2.c -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/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 '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -Wall -fpic -c lzf_c.c
gcc -g -O2 -Wall -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-3.19-bioc/meat/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -Wall -fpic -shared H5Zlzf.c -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/lzf'
make -C vbz
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/vbz'
make -C third_party/streamvbyte
make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/vbz/third_party/streamvbyte'
gcc -std=gnu99  -fpic -Iinclude -c ./src/streamvbyte_decode.c
gcc -std=gnu99  -fpic -Iinclude -c ./src/streamvbyte_encode.c
gcc -std=gnu99  -fpic -Iinclude -c ./src/streamvbytedelta_decode.c
gcc -std=gnu99  -fpic -Iinclude -c ./src/streamvbytedelta_encode.c
gcc -std=gnu99  -fpic -Iinclude -c ./src/streamvbyte_0124_encode.c
gcc -std=gnu99  -fpic -Iinclude -c ./src/streamvbyte_0124_decode.c
gcc -std=gnu99  -fpic -Iinclude -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 '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/vbz/third_party/streamvbyte'
make -C vbz
make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/vbz/vbz'
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/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 -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/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 -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/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 '/home/biocbuild/bbs-3.19-bioc/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 -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/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 '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/vbz'
mkdir -p "/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so blosc/libH5Zblosc.so lzf/libH5Zlzf.so zstd/libH5Zzstd.so vbz/libH5Zvbz.so "/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include" -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include   -g -O2 -Wall -fpic  -g -O2  -Wall -c rhdf5filters.c -o rhdf5filters.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/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)

Tests output

rhdf5filters.Rcheck/tests/tinytest.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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.

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.

> 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 1.7s

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 41ms

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 3ms
All ok, 320 results (1.7s)
> 
> proc.time()
   user  system elapsed 
  1.823   0.097   1.909 

Example timings

rhdf5filters.Rcheck/rhdf5filters-Ex.timings

nameusersystemelapsed
available_filters0.0090.0040.013
hdf5_plugin_path0.0010.0000.000