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This page was generated on 2022-10-19 13:20:46 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for rhdf5filters on nebbiolo1


To the developers/maintainers of the rhdf5filters package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1644/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5filters 1.8.0  (landing page)
Mike Smith
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/rhdf5filters
git_branch: RELEASE_3_15
git_last_commit: b0b588b
git_last_commit_date: 2022-04-26 12:03:17 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rhdf5filters
Version: 1.8.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:rhdf5filters.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings rhdf5filters_1.8.0.tar.gz
StartedAt: 2022-10-18 21:28:28 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:28:45 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 17.0 seconds
RetCode: 0
Status:   OK  
CheckDir: rhdf5filters.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 for sufficient/correct file permissions ... 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 is not available
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters.Rcheck/00check.log’
for details.



Installation output

rhdf5filters.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL rhdf5filters
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* 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
make -C blosc
make[1]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++14 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/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++14 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++14 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++14 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.2
make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.2'
gcc -g -O2 -Wall -fpic -c lz4.c
gcc -g -O2 -Wall -fpic -c lz4hc.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.2'
make -C lib/zstd-1.4.5
make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/zstd-1.4.5'
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/zstd-1.4.5'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/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 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/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 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/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 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/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 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/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 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/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 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/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
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-3.15-bioc/R/library/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 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/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 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/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 '/home/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/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 -Wall -fpic -c -o H5Zblosc.o H5Zblosc.c \
-I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I./lib/blosc-1.20.1
H5Zblosc.c: In function ‘H5Z_filter_blosc’:
H5Zblosc.c:96:10: warning: unused variable ‘errmsg’ [-Wunused-variable]
   96 |     char errmsg[256];
      |          ^~~~~~
g++ -std=gnu++14 -g -O2 -Wall -fpic -L/usr/local/lib -shared -o libH5Zblosc.so H5Zblosc.o \
libblosc.a -lz
make[1]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/bzip2'
make -C bzip2-1.0.8
make[2]: Entering directory '/home/biocbuild/bbs-3.15-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-3.15-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-3.15-bioc/R/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-3.15-bioc/meat/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/home/biocbuild/bbs-3.15-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
make[2]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -Wall -fpic -shared H5Zlzf.c -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.15-bioc/meat/rhdf5filters/src/lzf'
mkdir -p "/home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so "/home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp blosc/libH5Zblosc.so "/home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp lzf/libH5Zlzf.so "/home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include" -I'/home/biocbuild/bbs-3.15-bioc/R/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-3.15-bioc/R/lib -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/libs
** 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
** 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/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  3.017   0.122   3.128 

Example timings

rhdf5filters.Rcheck/rhdf5filters-Ex.timings

nameusersystemelapsed
hdf5_plugin_path0.0010.0000.001