BioC 3.5: CHECK report for SeqArray on toluca2

Package: SeqArray

Version: 1.15.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqArray_1.15.6.tar.gz

StartedAt: 2017-04-23 09:43:03 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:50:23 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 440.0 seconds

RetCode: 0

Status:  OK

CheckDir: SeqArray.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqArray_1.15.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SeqArray.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.15.6’
* 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  6.4Mb
  sub-directories of 1Mb or more:
    doc       3.9Mb
    extdata   1.6Mb
* 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
Examples with CPU or elapsed time > 5s
          user system elapsed
seqMerge 3.245  2.691   6.346
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/SeqArray.Rcheck/00check.log’
for details.

* installing *source* package ‘SeqArray’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ConvToGDS.cpp -o ConvToGDS.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c FileMerge.cpp -o FileMerge.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c GetData.cpp -o GetData.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Index.cpp -o Index.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Methods.cpp -o Methods.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c R_SeqArray.c -o R_SeqArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ReadBySample.cpp -o ReadBySample.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ReadByVariant.cpp -o ReadByVariant.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c SeqArray.cpp -o SeqArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c pkg_test.cpp -o pkg_test.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c vectorization.c -o vectorization.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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	0.760	0.433	1.220
SeqVarGDSClass-class	0.221	0.007	0.229
seqAlleleFreq	0.034	0.005	0.040
seqApply	0.126	0.012	0.140
seqBED2GDS	0.340	0.166	0.512
seqBlockApply	0.057	0.007	0.065
seqDelete	0.394	0.379	0.776
seqDigest	0.033	0.003	0.035
seqExampleFileName	0.003	0.001	0.003
seqExport	0.797	1.557	2.376
seqGDS2SNP	0.018	0.005	0.023
seqGDS2VCF	0.410	0.012	0.426
seqGetData	0.116	0.007	0.124
seqGetFilter	0.051	0.004	0.055
seqMerge	3.245	2.691	6.346
seqMissing	0.057	0.003	0.061
seqNumAllele	0.004	0.001	0.006
seqOpen	0.047	0.002	0.053
seqOptimize	0.531	0.452	1.072
seqParallel	0.169	0.155	0.256
seqParallelSetup	0.078	0.046	0.115
seqSNP2GDS	1.506	0.243	1.820
seqSetFilter	0.080	0.011	0.090
seqSetFilterCond	0.054	0.008	0.060
seqStorageOption	0.788	0.111	0.912
seqSummary	0.213	0.014	0.228
seqSystem	0.001	0.000	0.001
seqTranspose	0.483	0.446	0.946
seqVCF2GDS	1.574	1.817	3.455
seqVCF_Header	0.097	0.010	0.108
seqVCF_SampID	0.003	0.000	0.004