BioC 3.6: CHECK report for SeqArray on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SeqArray_1.17.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.17.3’
* 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
* checking installed package size ... NOTE
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc       3.9Mb
    extdata   1.6Mb
    libs      3.9Mb
* 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 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 compiled code ... NOTE
File ‘SeqArray/libs/SeqArray.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* 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 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck/00check.log’
for details.

* installing *source* package ‘SeqArray’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c FileMerge.cpp -o FileMerge.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c GetData.cpp -o GetData.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Index.cpp -o Index.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Methods.cpp -o Methods.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_SeqArray.c -o R_SeqArray.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ReadBySample.cpp -o ReadBySample.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ReadByVariant.cpp -o ReadByVariant.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SeqArray.cpp -o SeqArray.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c pkg_test.cpp -o pkg_test.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c vectorization.c -o vectorization.o
g++ -shared -L/home/biocbuild/bbs-3.6-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 ReadByVariant.o SeqArray.o pkg_test.o vectorization.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck/SeqArray/libs
** R
** data
** 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
* DONE (SeqArray)

name	user	system	elapsed
SeqArray-package	0.540	0.012	0.607
SeqVarGDSClass-class	0.228	0.004	0.233
seqAlleleFreq	0.028	0.000	0.025
seqApply	0.100	0.004	0.104
seqAsVCF	0.004	0.000	0.003
seqBED2GDS	0.268	0.088	0.407
seqBlockApply	0.048	0.000	0.050
seqDelete	0.124	0.012	0.133
seqDigest	0.028	0.000	0.027
seqExampleFileName	0.000	0.000	0.002
seqExport	0.400	0.488	0.898
seqGDS2SNP	0.012	0.004	0.017
seqGDS2VCF	0.276	0.004	0.282
seqGetData	0.048	0.000	0.051
seqGetFilter	0.028	0.000	0.030
seqMerge	0.704	0.032	0.736
seqMissing	0.040	0.004	0.041
seqNumAllele	0.004	0.000	0.003
seqOpen	0.028	0.000	0.029
seqOptimize	0.128	0.012	0.140
seqParallel	0.108	0.140	0.180
seqParallelSetup	0.076	0.036	0.103
seqSNP2GDS	1.308	0.080	1.408
seqSetFilter	0.048	0.016	0.062
seqSetFilterCond	0.040	0.000	0.041
seqStorageOption	0.468	0.008	0.478
seqSummary	0.112	0.000	0.115
seqSystem	0	0	0
seqTranspose	0.148	0.004	0.154
seqVCF2GDS	0.424	0.096	0.516
seqVCF_Header	0.040	0.004	0.046
seqVCF_SampID	0.004	0.000	0.001

BioC 3.6: CHECK report for SeqArray on malbec1

Summary

Command output