BioC 3.3: CHECK report for SeqArray on zin2

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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_1.12.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SeqArray.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.12.9’
* 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  9.3Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   1.6Mb
    libs      3.7Mb
* 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 ... OK
* 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: 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  -Wall -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  -Wall -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  -Wall -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  -Wall -c FileMerge.cpp -o FileMerge.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  -Wall -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  -Wall -c Index.cpp -o Index.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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -c SeqArray.cpp -o 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  -Wall -c pkg_test.cpp -o pkg_test.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  -Wall -c vectorization.c -o vectorization.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 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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	0.695	0.020	0.784
SeqVarGDSClass-class	0.094	0.012	0.106
seqAlleleFreq	0.034	0.000	0.034
seqApply	0.118	0.008	0.125
seqBED2GDS	0.143	0.012	0.178
seqBlockApply	0.051	0.004	0.052
seqDelete	0.211	0.012	0.232
seqDigest	0.031	0.000	0.032
seqExampleFileName	0.003	0.000	0.002
seqExport	0.542	0.528	1.108
seqGDS2SNP	0.020	0.000	0.025
seqGDS2VCF	0.303	0.004	0.317
seqGetData	0.061	0.000	0.060
seqGetFilter	0.031	0.008	0.036
seqMerge	1.059	0.052	1.166
seqMissing	0.047	0.000	0.048
seqNumAllele	0.005	0.000	0.004
seqOpen	0.037	0.000	0.037
seqOptimize	0.291	0.004	0.307
seqParallel	0.109	0.162	0.178
seqParallelSetup	0.057	0.038	0.070
seqSNP2GDS	0.333	0.012	0.368
seqSetFilter	0.073	0.000	0.073
seqStorageOption	1.354	0.033	1.417
seqSummary	0.179	0.012	0.191
seqSystem	0	0	0
seqTranspose	0.260	0.004	0.270
seqVCF2GDS	0.739	0.099	0.948
seqVCF_Header	0.073	0.001	0.073
seqVCF_SampID	0.000	0.001	0.002

BioC 3.3: CHECK report for SeqArray on zin2

Summary

Command output