BioC 3.2: CHECK report for SeqArray on oaxaca

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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_1.10.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SeqArray.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.10.6’
* 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 ... [33s/33s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   1.9Mb
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/29s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
SeqArray-package 0.81  0.054   7.161
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [221s/222s]
 [221s/222s] 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-3.2-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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c SeqArray.cpp -o SeqArray.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 GetData.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.810	0.054	7.161
SeqVarGDSClass-class	0.213	0.007	0.220
seqAlleleCount	0.009	0.001	0.010
seqAlleleFreq	0.027	0.001	0.028
seqApply	0.106	0.011	0.117
seqBED2GDS	0.188	0.018	0.671
seqDelete	0.498	0.017	0.593
seqExampleFileName	0.003	0.000	0.005
seqExport	0.150	0.010	0.182
seqGDS2SNP	0.078	0.004	0.083
seqGDS2VCF	0.550	0.010	0.591
seqGetData	0.056	0.003	0.060
seqGetFilter	0.058	0.003	0.063
seqMerge	1.968	0.067	2.056
seqMissing	0.055	0.002	0.058
seqNumAllele	0.008	0.000	0.009
seqOpen	0.045	0.002	0.047
seqOptimize	0.498	0.017	0.578
seqParallel	0.181	0.135	0.227
seqParallelSetup	0.058	0.031	0.088
seqSNP2GDS	0.443	0.050	0.584
seqSetFilter	0.064	0.010	0.075
seqSetFilterChrom	0.034	0.005	0.038
seqStorage.Option	2.340	0.069	2.591
seqSummary	0.040	0.005	0.044
seqTranspose	0.532	0.015	0.549
seqVCF.Header	0.168	0.001	0.170
seqVCF.SampID	0.003	0.001	0.004
seqVCF2GDS	1.223	0.029	1.270

BioC 3.2: CHECK report for SeqArray on oaxaca

Summary

Command output