Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:05 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 gdsfmt on nebbiolo2


To the developers/maintainers of the gdsfmt package:
- Please 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 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 745/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.34.1  (landing page)
Xiuwen Zheng
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/gdsfmt
git_branch: RELEASE_3_16
git_last_commit: d5fa465
git_last_commit_date: 2023-03-31 04:54:01 -0400 (Fri, 31 Mar 2023)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: gdsfmt
Version: 1.34.1
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gdsfmt_1.34.1.tar.gz
StartedAt: 2023-04-10 20:50:14 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:52:17 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 123.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gdsfmt.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings gdsfmt_1.34.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/gdsfmt.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘gdsfmt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gdsfmt’ version ‘1.34.1’
* 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
* checking installed package size ... NOTE
  installed size is 43.6Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
* 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 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘gdsfmt.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.



Installation output

gdsfmt.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL gdsfmt
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘gdsfmt’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c R_CoreArray.cpp -o R_CoreArray.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c gdsfmt.cpp -o gdsfmt.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c digest.cpp -o digest.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dAny.cpp -o CoreArray/dAny.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dBase.cpp -o CoreArray/dBase.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dFile.cpp -o CoreArray/dFile.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dStream.cpp -o CoreArray/dStream.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/compress.c -o ZLIB/compress.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/infback.c -o ZLIB/infback.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/trees.c -o ZLIB/trees.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c LZ4/lz4.c -o LZ4/lz4.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c LZ4/lz4hc.c -o LZ4/lz4hc.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c LZ4/lz4frame.c -o LZ4/lz4frame.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fpic  -g -O2  -Wall -c LZ4/xxhash.c -o LZ4/xxhash.o
cd XZ && tar -xzf xz-5.2.5.tar.gz
cd XZ/xz-5.2.5 && \
	./configure CC="gcc" CPP="gcc -E" CXX="g++ -std=gnu++14" CXXCPP="" --build="" \
	--with-pic --enable-silent-rules --quiet --disable-xz > /dev/null
cd XZ/xz-5.2.5/src/liblzma && make
make[1]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/gdsfmt/src/XZ/xz-5.2.5/src/liblzma'
Making all in api
make[2]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/gdsfmt/src/XZ/xz-5.2.5/src/liblzma/api'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/gdsfmt/src/XZ/xz-5.2.5/src/liblzma/api'
make[2]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/gdsfmt/src/XZ/xz-5.2.5/src/liblzma'
  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
make[2]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/gdsfmt/src/XZ/xz-5.2.5/src/liblzma'
make[1]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/gdsfmt/src/XZ/xz-5.2.5/src/liblzma'
cp XZ/xz-5.2.5/src/liblzma/.libs/liblzma.a  .
rm -rf XZ/xz-5.2.5/dos
rm -rf XZ/xz-5.2.5/po
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/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 -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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.

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


RUNIT TEST PROTOCOL -- Mon Apr 10 20:52:10 2023 
*********************************************** 
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 
 91.091   4.738  95.977 

Example timings

gdsfmt.Rcheck/gdsfmt-Ex.timings

nameusersystemelapsed
add.gdsn0.0860.0040.090
addfile.gdsn0.0060.0000.006
addfolder.gdsn0.0260.0000.026
append.gdsn0.0110.0040.015
apply.gdsn0.0250.0040.028
assign.gdsn0.0190.0040.023
cache.gdsn0.0020.0000.002
cleanup.gds0.0110.0000.011
closefn.gds000
clusterApply.gdsn0.0520.0180.466
cnt.gdsn0.0010.0000.001
compression.gdsn0.0050.0000.005
copyto.gdsn0.0260.0000.026
createfn.gds0.0000.0060.006
delete.attr.gdsn0.0020.0020.003
delete.gdsn0.0060.0000.006
diagnosis.gds0.0040.0070.011
digest.gdsn0.0490.0000.050
exist.gdsn0.0010.0000.001
gdsfmt-package0.0290.0000.030
get.attr.gdsn0.0000.0020.003
getfile.gdsn0.0040.0050.009
getfolder.gdsn0.0270.0000.027
index.gdsn0.0100.0030.013
is.element.gdsn0.0010.0000.002
is.sparse.gdsn1.1960.1121.308
lasterr.gds000
ls.gdsn0.0000.0020.002
moveto.gdsn0.0290.0060.034
name.gdsn0.0010.0000.001
objdesp.gdsn0.0040.0040.009
openfn.gds0.0020.0040.006
permdim.gdsn0.0020.0080.009
print.gds.class0.0160.0000.016
put.attr.gdsn0.0000.0030.004
read.gdsn0.0080.0050.014
readex.gdsn0.0050.0010.007
readmode.gdsn0.0000.0020.003
rename.gdsn0.0040.0010.004
setdim.gdsn0.0060.0040.009
showfile.gds0.0030.0000.003
summarize.gdsn0.0010.0000.001
sync.gds0.0030.0000.003
system.gds0.0050.0000.005
unload.gdsn0.0040.0000.003
write.gdsn0.0020.0000.001