BioC 3.3: CHECK report for SeqArray on linux2.bioconductor.org

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SeqArray_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SeqArray.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.11.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SeqArray’ can be installed ... [25s/25s] OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    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 ... [22s/28s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SeqArray-package 1.645   0.07   7.504
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [18s/24s]
 [18s/24s] 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-3.3-bioc/meat/SeqArray.Rcheck/00check.log’
for details.

* installing *source* package ‘SeqArray’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c ConvToGDS.cpp -o ConvToGDS.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c GetData.cpp -o GetData.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c Methods.cpp -o Methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c R_SeqArray.c -o R_SeqArray.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c ReadBySample.cpp -o ReadBySample.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c ReadByVariant.cpp -o ReadByVariant.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -c SeqArray.cpp -o SeqArray.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o GetData.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	1.645	0.070	7.504
SeqVarGDSClass-class	0.243	0.008	0.253
seqAlleleCount	0.006	0.000	0.006
seqAlleleFreq	0.016	0.000	0.016
seqApply	0.069	0.004	0.071
seqBED2GDS	0.182	0.000	0.185
seqDelete	1.067	0.008	1.075
seqExampleFileName	0.004	0.000	0.004
seqExport	0.157	0.004	0.162
seqGDS2SNP	0.097	0.000	0.097
seqGDS2VCF	0.661	0.000	0.662
seqGetData	0.059	0.004	0.063
seqGetFilter	0.056	0.000	0.055
seqMissing	0.059	0.004	0.063
seqNumAllele	0.008	0.000	0.009
seqOpen	0.053	0.000	0.053
seqOptimize	1.806	0.000	1.807
seqParallel	0.136	0.102	0.170
seqParallelSetup	0.056	0.042	0.090
seqSNP2GDS	0.521	0.028	0.549
seqSetFilter	0.066	0.000	0.066
seqSetFilterChrom	0.033	0.000	0.033
seqStorage.Option	2.038	0.040	2.077
seqSummary	0.032	0.000	0.032
seqTranspose	1.139	0.012	1.151
seqVCF.Header	0.050	0.000	0.051
seqVCF.SampID	0.003	0.000	0.004
seqVCF2GDS	2.299	0.020	2.319

BioC 3.3: CHECK report for SeqArray on linux2.bioconductor.org

Summary

Command output