BioC 3.2: CHECK report for SeqArray on perceval

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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_1.9.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SeqArray.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.9.12’
* 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 ... [35s/35s] OK
* checking installed package size ... OK
* 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 ... [27s/55s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SeqArray-package 1.378  0.110  15.560
seqParallel      0.138  0.011  14.206
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [26s/55s]
 [27s/55s] 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: OK

* installing *source* package ‘SeqArray’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GetData.cpp -o GetData.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c Methods.cpp -o Methods.o
Methods.cpp: In function ‘SEXPREC* FC_IBD_Div(SEXPREC*, SEXPREC*)’:
Methods.cpp:242: warning: comparison between signed and unsigned integer expressions
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_SeqArray.c -o R_SeqArray.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ReadBySample.cpp -o ReadBySample.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ReadByVariant.cpp -o ReadByVariant.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SeqArray.cpp -o SeqArray.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o SeqArray.so ConvGDS2VCF.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	1.378	0.110	15.560
SeqVarGDSClass-class	0.350	0.011	0.369
seqAlleleFreq	0.033	0.002	0.034
seqApply	0.117	0.014	0.130
seqCompress.Option	2.191	0.045	2.238
seqDelete	1.172	0.025	1.198
seqExampleFileName	0.004	0.001	0.004
seqExport	0.136	0.014	0.151
seqGDS2SNP	0.107	0.005	0.112
seqGDS2VCF	0.630	0.016	0.646
seqGetData	0.065	0.006	0.071
seqGetFilter	0.049	0.003	0.053
seqInfoNewVar	0.479	0.046	0.536
seqMissing	0.060	0.003	0.063
seqNumAllele	0.009	0.001	0.010
seqOpen	0.045	0.003	0.048
seqOptimize	2.000	0.030	2.032
seqParallel	0.138	0.011	14.206
seqParallelSetup	0.095	0.034	0.160
seqSetFilter	0.069	0.032	0.102
seqSetFilterChrom	0.059	0.026	0.085
seqSlidingWindow	0.080	0.026	0.106
seqSummary	0.036	0.010	0.046
seqTranspose	1.318	0.057	1.377
seqVCF.Header	0.061	0.011	0.071
seqVCF.SampID	0.005	0.001	0.006
seqVCF2GDS	2.536	0.053	2.595

BioC 3.2: CHECK report for SeqArray on perceval

Summary

Command output