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: 2017-10-18 09:15:39 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:17:56 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 137.2 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_1.10.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SNPRelate.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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	0.056	0.003	0.061
SNPRelate-package	1.765	0.073	1.899
snpgdsAdmixPlot	0.359	0.016	0.386
snpgdsAdmixProp	0.505	0.016	0.537
snpgdsAlleleSwitch	0.097	0.006	0.114
snpgdsApartSelection	0.137	0.009	0.147
snpgdsBED2GDS	0.211	0.008	0.223
snpgdsClose	0.014	0.000	0.014
snpgdsCombineGeno	0.561	0.022	0.606
snpgdsCreateGeno	0.278	0.018	0.318
snpgdsCreateGenoSet	0.150	0.008	0.171
snpgdsCutTree	2.290	0.056	2.418
snpgdsDiss	1.630	0.013	1.689
snpgdsDrawTree	1.525	0.009	1.579
snpgdsEIGMIX	0.312	0.010	0.331
snpgdsErrMsg	0	0	0
snpgdsExampleFileName	0.001	0.001	0.002
snpgdsFst	0.076	0.003	0.080
snpgdsGDS2BED	0.074	0.009	0.084
snpgdsGDS2Eigen	0.656	0.053	0.729
snpgdsGDS2PED	0.444	0.035	0.493
snpgdsGEN2GDS	0.001	0.000	0.000
snpgdsGRM	0.378	0.006	0.393
snpgdsGetGeno	0.274	0.012	0.290
snpgdsHCluster	1.780	0.021	1.839
snpgdsHWE	0.015	0.002	0.020
snpgdsIBDKING	0.525	0.010	0.554
snpgdsIBDMLE	0.777	0.012	0.815
snpgdsIBDMLELogLik	0.617	0.014	0.649
snpgdsIBDMoM	0.222	0.015	0.245
snpgdsIBDSelection	0.065	0.004	0.073
snpgdsIBS	0.334	0.009	0.362
snpgdsIBSNum	0.425	0.016	0.449
snpgdsIndInb	0.052	0.006	0.061
snpgdsIndInbCoef	0.041	0.001	0.043
snpgdsIndivBeta	0.282	0.008	0.294
snpgdsLDMat	0.409	0.017	0.440
snpgdsLDpair	0.019	0.002	0.021
snpgdsLDpruning	0.103	0.006	0.111
snpgdsOpen	0.014	0.001	0.014
snpgdsOption	0.003	0.001	0.004
snpgdsPCA	0.416	0.016	0.443
snpgdsPCACorr	0.550	0.043	0.617
snpgdsPCASNPLoading	0.366	0.008	0.391
snpgdsPCASampLoading	0.374	0.007	0.389
snpgdsPED2GDS	3.208	0.097	3.404
snpgdsPairIBD	0.620	0.012	0.645
snpgdsPairIBDMLELogLik	0.544	0.011	0.582
snpgdsPairScore	0.180	0.012	0.200
snpgdsSNPList	0.012	0.002	0.015
snpgdsSNPListIntersect	0.058	0.001	0.061
snpgdsSNPListStrand	0.057	0.002	0.061
snpgdsSNPRateFreq	0.019	0.003	0.021
snpgdsSampMissRate	0.005	0.001	0.006
snpgdsSelectSNP	0.008	0.001	0.010
snpgdsSlidingWindow	1.402	0.025	1.458
snpgdsSummary	0.197	0.003	0.203
snpgdsTranspose	0.124	0.007	0.135
snpgdsVCF2GDS	0.214	0.021	0.239
snpgdsVCF2GDS_R	0.246	0.009	0.266