##############################################################################
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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqArray.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SeqArray_1.48.1.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SeqArray.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SeqArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqArray' version '1.48.1'
* 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 whether package 'SeqArray' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 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 ... NOTE
Namespace in Imports field not imported from: 'digest'
  All declared Imports should be used.
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'seqGDS2VCF.Rd':
  '[Rsamtools:zip]{bgzip}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SeqVarGDSClass-class.Rd: gds.class, DNAStringSet, DNAStringSetList,
    DataFrameList
  seqAddValue.Rd: add.gdsn
  seqApply.Rd: gdsn.class
  seqBED2GDS.Rd: cleanup.gds
  seqBlockApply.Rd: gdsn.class
  seqClose.Rd: gds.class
  seqExport.Rd: cleanup.gds
  seqGDS2SNP.Rd: add.gdsn, cleanup.gds
  seqMerge.Rd: cleanup.gds
  seqNewVarData.Rd: IntegerList
  seqOpen.Rd: openfn.gds, gds.class
  seqRecompress.Rd: cleanup.gds
  seqResetVariantID.Rd: cleanup.gds
  seqSNP2GDS.Rd: add.gdsn, cleanup.gds
  seqSetFilter.Rd: GRanges, GRangesList, IRanges
  seqStorageOption.Rd: add.gdsn, compression.gdsn
  seqTranspose.Rd: add.gdsn
  seqUnitApply.Rd: gdsn.class
  seqVCF2GDS.Rd: cleanup.gds
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 LazyData ... 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 x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/SeqArray/libs/x64/SeqArray.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
seqVCF2GDS 1.13   0.11    5.52
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test.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: 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/SeqArray.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SeqArray
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'SeqArray' ...
** this is package 'SeqArray' version '1.48.1'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c ConvToGDS.cpp -o ConvToGDS.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c FileMerge.cpp -o FileMerge.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c GetData.cpp -o GetData.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c Index.cpp -o Index.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c Methods.cpp -o Methods.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c R_SeqArray.c -o R_SeqArray.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c ReadBySample.cpp -o ReadBySample.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c ReadByUnit.cpp -o ReadByUnit.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c ReadByVariant.cpp -o ReadByVariant.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c SeqArray.cpp -o SeqArray.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c pkg_test.cpp -o pkg_test.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c samtools_ext.c -o samtools_ext.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'E:/biocbuild/bbs-3.21-bioc/R/library/gdsfmt/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c vectorization.cpp -o vectorization.o
g++ -std=gnu++17 -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:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-SeqArray/00new/SeqArray/libs/x64
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SeqArray)

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   0.20    0.06    0.25