BioC 3.2: CHECK report for SeqArray on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SeqArray_1.9.12.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SeqArray.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.9.12’
* 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 ... [29s/29s] OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   1.9Mb
    libs      2.5Mb
* 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 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/34s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SeqArray-package 1.064   0.07   9.264
seqParallel      0.082   0.04   8.245
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [18s/34s]
 [18s/34s] 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/SeqArray.Rcheck/00check.log’
for details.

* installing *source* package ‘SeqArray’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c GetData.cpp -o GetData.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c Methods.cpp -o Methods.o
Methods.cpp: In function ‘SEXPREC* FC_IBD_Div(SEXP, SEXP)’:
Methods.cpp:242:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (XLENGTH(NumeratorDenominator) != 2*size)
                                         ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c R_SeqArray.c -o R_SeqArray.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ReadBySample.cpp -o ReadBySample.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ReadByVariant.cpp -o ReadByVariant.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c SeqArray.cpp -o SeqArray.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o SeqArray.so ConvGDS2VCF.o ConvVCF2GDS.o GetData.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/SeqArray.Rcheck/SeqArray/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SeqArray)

name	user	system	elapsed
SeqArray-package	1.064	0.070	9.264
SeqVarGDSClass-class	0.298	0.016	0.323
seqAlleleFreq	0.02	0.00	0.02
seqApply	0.082	0.008	0.090
seqCompress.Option	1.594	0.019	1.625
seqDelete	0.850	0.004	0.859
seqExampleFileName	0.003	0.000	0.003
seqExport	0.107	0.005	0.123
seqGDS2SNP	0.086	0.000	0.085
seqGDS2VCF	0.454	0.000	0.464
seqGetData	0.046	0.000	0.045
seqGetFilter	0.039	0.000	0.040
seqInfoNewVar	0.354	0.020	0.374
seqMissing	0.045	0.000	0.045
seqNumAllele	0.006	0.000	0.006
seqOpen	0.029	0.008	0.038
seqOptimize	1.462	0.016	1.495
seqParallel	0.082	0.040	8.245
seqParallelSetup	0.065	0.012	0.094
seqSetFilter	0.053	0.004	0.057
seqSetFilterChrom	0.029	0.004	0.032
seqSlidingWindow	0.045	0.016	0.060
seqSummary	0.021	0.004	0.026
seqTranspose	1.001	0.020	1.036
seqVCF.Header	0.034	0.000	0.034
seqVCF.SampID	0.002	0.000	0.002
seqVCF2GDS	1.785	0.020	1.842

BioC 3.2: CHECK report for SeqArray on zin1

Summary

Command output