Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 767/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.41.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/gdsfmt
git_branch: devel
git_last_commit: d505de2
git_last_commit_date: 2024-04-30 10:41:13 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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 gdsfmt on merida1

To the developers/maintainers of the gdsfmt package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gdsfmt.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: gdsfmt
Version: 1.41.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gdsfmt_1.41.0.tar.gz
StartedAt: 2024-06-10 03:53:36 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 03:58:51 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 315.2 seconds
RetCode: 0
Status:   OK  
CheckDir: gdsfmt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gdsfmt_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gdsfmt.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gdsfmt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gdsfmt’ version ‘1.41.0’
* 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 ‘gdsfmt’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
* 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 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 whether startup messages can be suppressed ... 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS 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 ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.


Installation output

gdsfmt.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gdsfmt
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘gdsfmt’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c R_CoreArray.cpp -o R_CoreArray.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gdsfmt.cpp -o gdsfmt.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c digest.cpp -o digest.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dAny.cpp -o CoreArray/dAny.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dBase.cpp -o CoreArray/dBase.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dFile.cpp -o CoreArray/dFile.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dStream.cpp -o CoreArray/dStream.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/compress.c -o ZLIB/compress.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/infback.c -o ZLIB/infback.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/trees.c -o ZLIB/trees.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c LZ4/lz4.c -o LZ4/lz4.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c LZ4/lz4frame.c -o LZ4/lz4frame.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c LZ4/xxhash.c -o LZ4/xxhash.o
cd XZ && tar -xzf xz-5.2.9.tar.gz
cd XZ/xz-5.2.9 && \
		./configure CC="clang -arch x86_64" CPP="clang -arch x86_64 -E" CXX="clang++ -arch x86_64 -std=gnu++17" CXXCPP="" --build="" \
		--with-pic --enable-silent-rules --quiet --disable-xz --disable-shared > /dev/null
cd XZ/xz-5.2.9/src/liblzma && make
Making all in api
make[2]: Nothing to be done for `all'.
  CC       liblzma_la-tuklib_physmem.lo
  CC       liblzma_la-tuklib_cpucores.lo
  CC       liblzma_la-common.lo
  CC       liblzma_la-block_util.lo
  CC       liblzma_la-easy_preset.lo
  CC       liblzma_la-filter_common.lo
  CC       liblzma_la-hardware_physmem.lo
  CC       liblzma_la-index.lo
  CC       liblzma_la-stream_flags_common.lo
  CC       liblzma_la-vli_size.lo
  CC       liblzma_la-hardware_cputhreads.lo
  CC       liblzma_la-alone_encoder.lo
  CC       liblzma_la-block_buffer_encoder.lo
  CC       liblzma_la-block_encoder.lo
  CC       liblzma_la-block_header_encoder.lo
  CC       liblzma_la-easy_buffer_encoder.lo
  CC       liblzma_la-easy_encoder.lo
  CC       liblzma_la-easy_encoder_memusage.lo
  CC       liblzma_la-filter_buffer_encoder.lo
  CC       liblzma_la-filter_encoder.lo
  CC       liblzma_la-filter_flags_encoder.lo
  CC       liblzma_la-index_encoder.lo
  CC       liblzma_la-stream_buffer_encoder.lo
  CC       liblzma_la-stream_encoder.lo
  CC       liblzma_la-stream_flags_encoder.lo
  CC       liblzma_la-vli_encoder.lo
  CC       liblzma_la-outqueue.lo
  CC       liblzma_la-stream_encoder_mt.lo
  CC       liblzma_la-alone_decoder.lo
  CC       liblzma_la-auto_decoder.lo
  CC       liblzma_la-block_buffer_decoder.lo
  CC       liblzma_la-block_decoder.lo
  CC       liblzma_la-block_header_decoder.lo
  CC       liblzma_la-easy_decoder_memusage.lo
  CC       liblzma_la-filter_buffer_decoder.lo
  CC       liblzma_la-filter_decoder.lo
  CC       liblzma_la-filter_flags_decoder.lo
  CC       liblzma_la-index_decoder.lo
  CC       liblzma_la-index_hash.lo
  CC       liblzma_la-stream_buffer_decoder.lo
  CC       liblzma_la-stream_decoder.lo
  CC       liblzma_la-stream_flags_decoder.lo
  CC       liblzma_la-vli_decoder.lo
  CC       liblzma_la-check.lo
  CC       liblzma_la-crc32_table.lo
  CC       liblzma_la-crc32_fast.lo
  CC       liblzma_la-crc64_table.lo
  CC       liblzma_la-crc64_fast.lo
  CC       liblzma_la-sha256.lo
  CC       liblzma_la-lz_encoder.lo
  CC       liblzma_la-lz_encoder_mf.lo
  CC       liblzma_la-lz_decoder.lo
  CC       liblzma_la-lzma_encoder_presets.lo
  CC       liblzma_la-lzma_encoder.lo
  CC       liblzma_la-lzma_encoder_optimum_fast.lo
  CC       liblzma_la-lzma_encoder_optimum_normal.lo
  CC       liblzma_la-fastpos_table.lo
  CC       liblzma_la-lzma_decoder.lo
  CC       liblzma_la-lzma2_encoder.lo
  CC       liblzma_la-lzma2_decoder.lo
  CC       liblzma_la-price_table.lo
  CC       liblzma_la-delta_common.lo
  CC       liblzma_la-delta_encoder.lo
  CC       liblzma_la-delta_decoder.lo
  CC       liblzma_la-simple_coder.lo
  CC       liblzma_la-simple_encoder.lo
  CC       liblzma_la-simple_decoder.lo
  CC       liblzma_la-x86.lo
  CC       liblzma_la-powerpc.lo
  CC       liblzma_la-ia64.lo
  CC       liblzma_la-arm.lo
  CC       liblzma_la-armthumb.lo
  CC       liblzma_la-sparc.lo
  CCLD     liblzma.la
  PC       liblzma.pc
cp XZ/xz-5.2.9/src/liblzma/.libs/liblzma.a  .
rm -rf XZ/xz-5.2.9/dos
rm -rf XZ/xz-5.2.9/po
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o gdsfmt.so R_CoreArray.o gdsfmt.o digest.o CoreArray/CoreArray.o CoreArray/dAllocator.o CoreArray/dAny.o CoreArray/dBase.o CoreArray/dBitGDS.o CoreArray/dEndian.o CoreArray/dFile.o CoreArray/dParallel.o CoreArray/dParallel_Ext.o CoreArray/dPlatform.o CoreArray/dRealGDS.o CoreArray/dSerial.o CoreArray/dStrGDS.o CoreArray/dStream.o CoreArray/dStruct.o CoreArray/dSparse.o CoreArray/dVLIntGDS.o ZLIB/adler32.o ZLIB/compress.o ZLIB/crc32.o ZLIB/deflate.o ZLIB/infback.o ZLIB/inffast.o ZLIB/inflate.o ZLIB/inftrees.o ZLIB/trees.o ZLIB/uncompr.o ZLIB/zutil.o LZ4/lz4.o LZ4/lz4hc.o LZ4/lz4frame.o LZ4/xxhash.o ./liblzma.a -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-gdsfmt/00new/gdsfmt/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 (gdsfmt)

Tests output

gdsfmt.Rcheck/tests/runTests.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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Type 'license()' or 'licence()' for distribution details.

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> options(test.verbose=FALSE)
> BiocGenerics:::testPackage("gdsfmt")


RUNIT TEST PROTOCOL -- Mon Jun 10 03:58:33 2024 
*********************************************** 
Number of test functions: 25 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gdsfmt RUnit Tests - 25 test functions, 0 errors, 0 failures
Number of test functions: 25 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
180.528  37.774 249.789 

Example timings

gdsfmt.Rcheck/gdsfmt-Ex.timings

nameusersystemelapsed
add.gdsn0.2310.0410.285
addfile.gdsn0.0210.0080.031
addfolder.gdsn0.0580.0140.073
append.gdsn0.0370.0090.054
apply.gdsn0.0660.0480.123
assign.gdsn0.0480.0240.075
cache.gdsn0.0040.0030.008
cleanup.gds0.0310.0080.042
closefn.gds0.0010.0030.004
clusterApply.gdsn0.0770.0350.776
cnt.gdsn0.0020.0030.005
compression.gdsn0.0090.0030.013
copyto.gdsn0.0590.0080.070
createfn.gds0.0160.0040.021
delete.attr.gdsn0.0080.0040.011
delete.gdsn0.0180.0040.024
diagnosis.gds0.0250.0100.036
digest.gdsn0.0740.0200.141
exist.gdsn0.0020.0040.006
gdsfmt-package0.0830.0190.106
get.attr.gdsn0.0070.0040.012
getfile.gdsn0.0130.0070.022
getfolder.gdsn0.0860.0090.099
index.gdsn0.0300.0060.038
is.element.gdsn0.0040.0080.012
is.sparse.gdsn2.1930.1132.499
lasterr.gds0.0010.0010.000
ls.gdsn0.0020.0040.008
moveto.gdsn0.0810.0170.107
name.gdsn0.0020.0040.009
objdesp.gdsn0.0130.0090.026
openfn.gds0.0150.0070.025
permdim.gdsn0.0200.0150.037
print.gds.class0.0420.0100.094
put.attr.gdsn0.0080.0060.016
read.gdsn0.0340.0140.054
readex.gdsn0.0160.0130.030
readmode.gdsn0.0060.0040.011
rename.gdsn0.0130.0060.021
setdim.gdsn0.0270.0130.046
showfile.gds0.0080.0040.015
summarize.gdsn0.0030.0050.011
sync.gds0.0070.0040.014
system.gds0.0100.0060.018
unload.gdsn0.0080.0040.015
write.gdsn0.0040.0060.014