##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SeqArray_1.48.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SeqArray.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.48.3’
* 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 ‘SeqArray’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      2.8Mb
* 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 loading without being on the library search path ... 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 ... 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 is not available
File ‘SeqArray/libs/SeqArray.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’, ‘R_new_custom_connection’

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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/SeqArray.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SeqArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘SeqArray’ ...
** this is package ‘SeqArray’ version ‘1.48.3’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ConvToGDS.cpp -o ConvToGDS.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileMerge.cpp -o FileMerge.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c GetData.cpp -o GetData.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Index.cpp -o Index.o
Index.cpp: In member function ‘void SeqArray::CProgress::ShowProgress()’:
Index.cpp:1273:66: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1273 |                                 if (R_Process_StatusFName.size() < *R_Process_Count) return;
      |                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Methods.cpp -o Methods.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_SeqArray.c -o R_SeqArray.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ReadBySample.cpp -o ReadBySample.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ReadByUnit.cpp -o ReadByUnit.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ReadByVariant.cpp -o ReadByVariant.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c SeqArray.cpp -o SeqArray.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pkg_test.cpp -o pkg_test.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c samtools_ext.c -o samtools_ext.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -DUSING_R -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c vectorization.cpp -o vectorization.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o SeqArray.so 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 -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-SeqArray/00new/SeqArray/libs
** 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
** 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 (SeqArray)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following object is masked from 'package:SeqArray':

    rowRanges


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:SeqArray':

    rowRanges

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'SummarizedExperiment'

The following object is masked from 'package:SeqArray':

    colData

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following objects are masked from 'package:SeqArray':

    alt, filt, fixed, geno, header, info, qual, ref

The following object is masked from 'package:base':

    tabulate

[W::bcf_hdr_check_sanity] GL should be declared as Number=G
# of selected variants: 898

[..................................................]  0%, ETC: ---    
[======================================>...........] 76%, ETC: 4s    
[==================================================] 100%, used 12s    

[..................................................]  0%, ETC: ---    
[==================================================] 100%, used 10s    

[..................................................]  0%, ETC: ---    
[==================================================] 100%, used 9s    

[..................................................]  0%, ETC: ---    
[==================================================] 100%, used 6s    
# of selected variants: 655

[..................................................]  0%, ETC: ---    
[==================================================] 100%, used 5s    

[..................................................]  0%, ETC: ---    
[==================================================] 100%, used 5s    

[..................................................]  0%, ETC: ---    
[==================================================] 100%, used 6s    

[..................................................]  0%, ETC: ---    
[==================================================] 100%, used 2s    

Attaching package: 'Matrix'

The following object is masked from 'package:VariantAnnotation':

    expand

The following object is masked from 'package:S4Vectors':

    expand

# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348


RUNIT TEST PROTOCOL -- Thu Oct 16 03:36:41 2025 
*********************************************** 
Number of test functions: 28 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SeqArray RUnit Tests - 28 test functions, 0 errors, 0 failures
Number of test functions: 28 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 61.416  68.488 118.368