BioC 3.6: CHECK report for SNPRelate on veracruz1

Package: SNPRelate

Version: 1.11.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.11.1.tar.gz

StartedAt: 2017-08-16 08:44:37 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:46:43 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 125.2 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_1.11.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.11.1’
* 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-3.6-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-3.6-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	0.055	0.003	0.063
SNPRelate-package	1.593	0.060	1.700
snpgdsAdmixPlot	0.321	0.006	0.334
snpgdsAdmixProp	0.422	0.011	0.449
snpgdsAlleleSwitch	0.101	0.006	0.113
snpgdsApartSelection	0.144	0.013	0.167
snpgdsBED2GDS	0.196	0.007	0.208
snpgdsClose	0.014	0.001	0.016
snpgdsCombineGeno	0.498	0.015	0.519
snpgdsCreateGeno	0.260	0.014	0.288
snpgdsCreateGenoSet	0.157	0.010	0.178
snpgdsCutTree	2.236	0.041	2.339
snpgdsDiss	1.600	0.009	1.662
snpgdsDrawTree	1.487	0.005	1.530
snpgdsEIGMIX	0.348	0.008	0.373
snpgdsErrMsg	0.001	0.001	0.000
snpgdsExampleFileName	0.001	0.000	0.002
snpgdsFst	0.074	0.004	0.079
snpgdsGDS2BED	0.084	0.008	0.099
snpgdsGDS2Eigen	0.760	0.047	0.829
snpgdsGDS2PED	0.465	0.031	0.512
snpgdsGEN2GDS	0.001	0.000	0.000
snpgdsGRM	0.363	0.002	0.369
snpgdsGetGeno	0.268	0.009	0.281
snpgdsHCluster	1.781	0.021	1.841
snpgdsHWE	0.014	0.001	0.016
snpgdsIBDKING	0.534	0.009	0.569
snpgdsIBDMLE	0.794	0.009	0.822
snpgdsIBDMLELogLik	0.589	0.007	0.623
snpgdsIBDMoM	0.239	0.014	0.259
snpgdsIBDSelection	0.064	0.003	0.077
snpgdsIBS	0.337	0.008	0.354
snpgdsIBSNum	0.399	0.013	0.415
snpgdsIndInb	0.051	0.005	0.056
snpgdsIndInbCoef	0.044	0.002	0.047
snpgdsIndivBeta	0.277	0.007	0.295
snpgdsLDMat	0.469	0.023	0.505
snpgdsLDpair	0.020	0.001	0.025
snpgdsLDpruning	0.047	0.002	0.051
snpgdsOpen	0.015	0.001	0.019
snpgdsOption	0.003	0.001	0.005
snpgdsPCA	0.373	0.012	0.400
snpgdsPCACorr	0.489	0.029	0.538
snpgdsPCASNPLoading	0.344	0.011	0.362
snpgdsPCASampLoading	0.406	0.005	0.423
snpgdsPED2GDS	3.176	0.083	3.377
snpgdsPairIBD	0.603	0.008	0.635
snpgdsPairIBDMLELogLik	0.532	0.009	0.566
snpgdsPairScore	0.184	0.010	0.203
snpgdsSNPList	0.011	0.001	0.012
snpgdsSNPListIntersect	0.104	0.002	0.108
snpgdsSNPListStrand	0.047	0.001	0.049
snpgdsSNPRateFreq	0.018	0.002	0.021
snpgdsSampMissRate	0.008	0.001	0.009
snpgdsSelectSNP	0.009	0.001	0.009
snpgdsSlidingWindow	1.193	0.067	1.291
snpgdsSummary	0.193	0.001	0.203
snpgdsTranspose	0.142	0.007	0.163
snpgdsVCF2GDS	0.225	0.019	0.247
snpgdsVCF2GDS_R	0.246	0.008	0.269