BioC 3.5: CHECK report for SNPRelate on veracruz2

Package: SNPRelate

Version: 1.10.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.10.2.tar.gz

StartedAt: 2017-08-16 08:26:22 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:28:36 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 133.6 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.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 SNPRelate_1.10.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SNPRelate.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPRelate/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SNPRelate’ version ‘1.10.2’
* 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 ‘SNPRelate’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
* 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 ‘runTests.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/SNPRelate.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPRelate’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ConvToGDS.cpp -o ConvToGDS.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_SNPRelate.c -o R_SNPRelate.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SNPRelate.cpp -o SNPRelate.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ThreadPool.cpp -o ThreadPool.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c dGenGWAS.cpp -o dGenGWAS.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c dVect.cpp -o dVect.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genBeta.cpp -o genBeta.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genEIGMIX.cpp -o genEIGMIX.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genFst.cpp -o genFst.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genHWE.cpp -o genHWE.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genIBD.cpp -o genIBD.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genIBS.cpp -o genIBS.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genKING.cpp -o genKING.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genLD.cpp -o genLD.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genPCA.cpp -o genPCA.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c genSlideWin.cpp -o genSlideWin.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 SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/SNPRelate.Rcheck/SNPRelate/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SNPRelate)

name	user	system	elapsed
SNPGDSFileClass-class	0.065	0.003	0.067
SNPRelate-package	1.779	0.066	1.899
snpgdsAdmixPlot	0.376	0.007	0.388
snpgdsAdmixProp	0.481	0.012	0.503
snpgdsAlleleSwitch	0.099	0.005	0.111
snpgdsApartSelection	0.119	0.010	0.130
snpgdsBED2GDS	0.179	0.008	0.190
snpgdsClose	0.016	0.000	0.017
snpgdsCombineGeno	0.566	0.020	0.613
snpgdsCreateGeno	0.264	0.014	0.288
snpgdsCreateGenoSet	0.133	0.009	0.143
snpgdsCutTree	2.303	0.045	2.439
snpgdsDiss	1.589	0.009	1.649
snpgdsDrawTree	1.514	0.006	1.588
snpgdsEIGMIX	0.336	0.009	0.354
snpgdsErrMsg	0.000	0.000	0.001
snpgdsExampleFileName	0.001	0.000	0.002
snpgdsFst	0.076	0.004	0.081
snpgdsGDS2BED	0.075	0.008	0.082
snpgdsGDS2Eigen	0.696	0.045	0.774
snpgdsGDS2PED	0.412	0.032	0.461
snpgdsGEN2GDS	0.001	0.001	0.000
snpgdsGRM	0.396	0.003	0.400
snpgdsGetGeno	0.282	0.010	0.306
snpgdsHCluster	1.804	0.019	1.891
snpgdsHWE	0.013	0.002	0.015
snpgdsIBDKING	0.498	0.009	0.519
snpgdsIBDMLE	0.796	0.010	0.829
snpgdsIBDMLELogLik	0.630	0.009	0.664
snpgdsIBDMoM	0.218	0.013	0.243
snpgdsIBDSelection	0.072	0.005	0.081
snpgdsIBS	0.328	0.008	0.349
snpgdsIBSNum	0.400	0.011	0.431
snpgdsIndInb	0.051	0.004	0.056
snpgdsIndInbCoef	0.031	0.002	0.033
snpgdsIndivBeta	0.272	0.007	0.279
snpgdsLDMat	0.388	0.018	0.425
snpgdsLDpair	0.017	0.001	0.019
snpgdsLDpruning	0.055	0.004	0.059
snpgdsOpen	0.014	0.000	0.015
snpgdsOption	0.002	0.001	0.003
snpgdsPCA	0.387	0.015	0.416
snpgdsPCACorr	0.469	0.029	0.525
snpgdsPCASNPLoading	0.385	0.009	0.407
snpgdsPCASampLoading	0.347	0.004	0.362
snpgdsPED2GDS	3.109	0.080	3.311
snpgdsPairIBD	0.624	0.008	0.657
snpgdsPairIBDMLELogLik	0.532	0.008	0.548
snpgdsPairScore	0.173	0.010	0.194
snpgdsSNPList	0.011	0.001	0.013
snpgdsSNPListIntersect	0.094	0.001	0.099
snpgdsSNPListStrand	0.051	0.001	0.058
snpgdsSNPRateFreq	0.016	0.002	0.018
snpgdsSampMissRate	0.007	0.001	0.008
snpgdsSelectSNP	0.005	0.001	0.005
snpgdsSlidingWindow	1.191	0.065	1.299
snpgdsSummary	0.199	0.001	0.206
snpgdsTranspose	0.147	0.009	0.165
snpgdsVCF2GDS	0.244	0.021	0.277
snpgdsVCF2GDS_R	0.269	0.008	0.290