Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-11-26 15:05:35 -0500 (Fri, 26 Nov 2021).

CHECK results for SeqArray on tokay2

To the developers/maintainers of the SeqArray package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqArray.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1762/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.34.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/SeqArray
git_branch: RELEASE_3_14
git_last_commit: b2f6a92
git_last_commit_date: 2021-10-26 12:07:16 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SeqArray
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SeqArray_1.34.0.tar.gz
StartedAt: 2021-11-26 05:20:14 -0500 (Fri, 26 Nov 2021)
EndedAt: 2021-11-26 05:23:51 -0500 (Fri, 26 Nov 2021)
EllapsedTime: 216.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqArray.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SeqArray_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SeqArray.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SeqArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqArray' version '1.34.0'
* 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 whether package 'SeqArray' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/SeqArray/libs/i386/SeqArray.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/SeqArray/libs/x64/SeqArray.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'SeqArray/libs/i386/SeqArray.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection', 'R_new_custom_connection'
File 'SeqArray/libs/x64/SeqArray.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection', 'R_new_custom_connection'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
seqVCF2GDS   0.69   0.07   10.23
seqUnitApply 0.22   0.05    5.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
seqVCF2GDS   0.52   0.05    9.81
seqUnitApply 0.28   0.01    6.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R'
 OK
** running tests for arch 'x64' ...
  Running 'test.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SeqArray.Rcheck/00check.log'
for details.



Installation output

SeqArray.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SeqArray_1.34.0.tar.gz && rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqArray.buildbin-libdir SeqArray_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SeqArray_1.34.0.zip && rm SeqArray_1.34.0.tar.gz SeqArray_1.34.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1930k    0  1135    0     0  13989      0  0:02:21 --:--:--  0:02:21 14012
100 1930k  100 1930k    0     0  5074k      0 --:--:-- --:--:-- --:--:-- 5067k

install for i386

* installing *source* package 'SeqArray' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ConvToGDS.cpp -o ConvToGDS.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FileMerge.cpp -o FileMerge.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GetData.cpp -o GetData.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Index.cpp -o Index.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Methods.cpp -o Methods.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_SeqArray.c -o R_SeqArray.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadBySample.cpp -o ReadBySample.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadByUnit.cpp -o ReadByUnit.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadByVariant.cpp -o ReadByVariant.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SeqArray.cpp -o SeqArray.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pkg_test.cpp -o pkg_test.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c samtools_ext.c -o samtools_ext.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c vectorization.c -o vectorization.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/SeqArray.buildbin-libdir/00LOCK-SeqArray/00new/SeqArray/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SeqArray'
    finding HTML links ... done
    KG_P1_SampData                          html  
    SeqArray-package                        html  
    SeqVarGDSClass-class                    html  
    finding level-2 HTML links ... done

    seqAddValue                             html  
    seqAlleleFreq                           html  
    seqApply                                html  
    seqAsVCF                                html  
    seqBED2GDS                              html  
    seqBlockApply                           html  
    seqCheck                                html  
    seqClose                                html  
    seqDelete                               html  
    seqDigest                               html  
    seqExampleFileName                      html  
    seqExport                               html  
    seqGDS2SNP                              html  
    seqGDS2VCF                              html  
    seqGetData                              html  
    seqGetFilter                            html  
    seqMerge                                html  
    seqMissing                              html  
    seqNewVarData                           html  
    seqNumAllele                            html  
    seqOpen                                 html  
    seqOptimize                             html  
    seqParallel                             html  
    seqParallelSetup                        html  
    seqRecompress                           html  
    seqResetVariantID                       html  
    seqSNP2GDS                              html  
    seqSetFilter                            html  
    seqSetFilterCond                        html  
    seqStorageOption                        html  
    seqSummary                              html  
    seqSystem                               html  
    seqTranspose                            html  
    seqUnitApply                            html  
    seqUnitFilterCond                       html  
    seqUnitSlidingWindows                   html  
    seqVCF2GDS                              html  
    seqVCF_Header                           html  
    seqVCF_SampID                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SeqArray' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ConvToGDS.cpp -o ConvToGDS.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FileMerge.cpp -o FileMerge.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GetData.cpp -o GetData.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Index.cpp -o Index.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Methods.cpp -o Methods.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_SeqArray.c -o R_SeqArray.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadBySample.cpp -o ReadBySample.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadByUnit.cpp -o ReadByUnit.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadByVariant.cpp -o ReadByVariant.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SeqArray.cpp -o SeqArray.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pkg_test.cpp -o pkg_test.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c samtools_ext.c -o samtools_ext.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DUSING_R -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c vectorization.c -o vectorization.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SeqArray.dll tmp.def ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/SeqArray.buildbin-libdir/SeqArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqArray' as SeqArray_1.34.0.zip
* DONE (SeqArray)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SeqArray' successfully unpacked and MD5 sums checked

Tests output

SeqArray.Rcheck/tests_i386/test.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> if (.Platform$OS.type != "windows")
+     BiocGenerics:::testPackage("SeqArray")
> 
> proc.time()
   user  system elapsed 
   0.31    0.01    0.29 

SeqArray.Rcheck/tests_x64/test.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> if (.Platform$OS.type != "windows")
+     BiocGenerics:::testPackage("SeqArray")
> 
> proc.time()
   user  system elapsed 
   0.28    0.03    0.29 

Example timings

SeqArray.Rcheck/examples_i386/SeqArray-Ex.timings

nameusersystemelapsed
SeqArray-package0.560.010.66
SeqVarGDSClass-class0.280.000.28
seqAddValue0.140.050.19
seqAlleleFreq0.050.030.08
seqApply0.140.020.15
seqAsVCF000
seqBED2GDS0.470.060.97
seqBlockApply0.090.020.11
seqCheck0.030.000.03
seqDelete0.130.000.12
seqDigest0.030.000.03
seqExampleFileName000
seqExport0.360.320.69
seqGDS2SNP0.040.030.08
seqGDS2VCF0.390.020.41
seqGetData0.100.000.09
seqGetFilter0.060.000.06
seqMerge0.730.090.83
seqMissing0.080.000.08
seqNewVarData0.020.000.01
seqNumAllele000
seqOpen0.060.000.07
seqOptimize0.200.020.21
seqParallel0.140.004.24
seqParallelSetup0.100.024.81
seqRecompress0.280.200.49
seqResetVariantID0.030.010.04
seqSNP2GDS2.090.182.67
seqSetFilter0.080.010.10
seqSetFilterCond0.080.000.08
seqStorageOption0.880.051.23
seqSummary0.170.010.19
seqSystem000
seqTranspose0.260.020.28
seqUnitApply0.220.055.05
seqUnitFilterCond0.090.000.10
seqUnitSlidingWindows0.060.000.06
seqVCF2GDS 0.69 0.0710.23
seqVCF_Header0.080.000.08
seqVCF_SampID000

SeqArray.Rcheck/examples_x64/SeqArray-Ex.timings

nameusersystemelapsed
SeqArray-package0.470.090.76
SeqVarGDSClass-class0.170.000.17
seqAddValue0.170.030.22
seqAlleleFreq0.060.000.06
seqApply0.190.000.19
seqAsVCF000
seqBED2GDS0.370.080.61
seqBlockApply0.110.020.13
seqCheck0.040.000.03
seqDelete0.150.000.15
seqDigest0.030.000.04
seqExampleFileName000
seqExport0.570.220.81
seqGDS2SNP0.060.010.08
seqGDS2VCF0.330.030.36
seqGetData0.090.000.09
seqGetFilter0.060.020.08
seqMerge0.740.080.81
seqMissing0.090.000.09
seqNewVarData000
seqNumAllele000
seqOpen0.080.000.08
seqOptimize0.190.030.22
seqParallel0.070.004.44
seqParallelSetup0.160.014.28
seqRecompress0.250.100.35
seqResetVariantID0.010.010.03
seqSNP2GDS1.540.071.60
seqSetFilter0.110.000.11
seqSetFilterCond0.080.000.08
seqStorageOption0.810.121.52
seqSummary0.160.020.17
seqSystem000
seqTranspose0.270.080.34
seqUnitApply0.280.016.08
seqUnitFilterCond0.060.000.06
seqUnitSlidingWindows0.030.000.04
seqVCF2GDS0.520.059.81
seqVCF_Header0.070.000.08
seqVCF_SampID000