BioC 3.4: CHECK report for SNPRelate on morelia

Package: SNPRelate

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.8.0.tar.gz

StartedAt: 2017-04-15 08:20:29 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:22:32 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 122.8 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SNPRelate.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.0’
* 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  5.4Mb
  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-3.4-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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/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 -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_SNPRelate.c -o R_SNPRelate.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c SNPRelate.cpp -o SNPRelate.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ThreadPool.cpp -o ThreadPool.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c dGenGWAS.cpp -o dGenGWAS.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c dVect.cpp -o dVect.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c genBeta.cpp -o genBeta.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c genFst.cpp -o genFst.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c genHWE.cpp -o genHWE.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c genIBD.cpp -o genIBD.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c genIBS.cpp -o genIBS.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c genKING.cpp -o genKING.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c genLD.cpp -o genLD.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c genPCA.cpp -o genPCA.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c genRec.cpp -o genRec.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gdsfmt/include"   -fPIC  -Wall -mtune=core2 -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 genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genRec.o genSlideWin.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -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-3.4-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	0.032	0.002	0.034
SNPRelate-package	1.368	0.061	1.458
snpgdsAdmixProp	1.377	0.016	1.406
snpgdsAlleleSwitch	0.102	0.007	0.113
snpgdsApartSelection	0.160	0.011	0.170
snpgdsBED2GDS	0.099	0.009	0.109
snpgdsClose	0.024	0.002	0.026
snpgdsCombineGeno	0.403	0.020	0.428
snpgdsCreateGeno	0.207	0.012	0.219
snpgdsCreateGenoSet	0.157	0.011	0.169
snpgdsCutTree	2.347	0.040	2.390
snpgdsDiss	1.625	0.004	1.631
snpgdsDrawTree	1.751	0.007	1.762
snpgdsEIGMIX	1.306	0.009	1.318
snpgdsErrMsg	0.001	0.000	0.001
snpgdsExampleFileName	0.002	0.000	0.002
snpgdsFst	0.040	0.003	0.044
snpgdsGDS2BED	0.082	0.009	0.094
snpgdsGDS2Eigen	0.762	0.049	0.828
snpgdsGDS2PED	0.419	0.031	0.457
snpgdsGEN2GDS	0.001	0.000	0.001
snpgdsGRM	1.019	0.006	1.027
snpgdsGetGeno	0.305	0.012	0.318
snpgdsHCluster	1.990	0.017	2.016
snpgdsHWE	0.014	0.002	0.020
snpgdsIBDKING	0.470	0.012	0.483
snpgdsIBDMLE	0.673	0.009	0.682
snpgdsIBDMLELogLik	0.605	0.010	0.616
snpgdsIBDMoM	0.227	0.017	0.247
snpgdsIBDSelection	0.064	0.004	0.069
snpgdsIBS	0.359	0.008	0.373
snpgdsIBSNum	0.458	0.011	0.470
snpgdsIndInb	0.056	0.006	0.062
snpgdsIndInbCoef	0.006	0.000	0.006
snpgdsIndivBeta	2.356	0.014	2.373
snpgdsLDMat	0.403	0.019	0.449
snpgdsLDpair	0.005	0.002	0.006
snpgdsLDpruning	0.048	0.002	0.051
snpgdsOpen	0.013	0.000	0.014
snpgdsOption	0.004	0.001	0.005
snpgdsPCA	0.388	0.014	0.408
snpgdsPCACorr	0.379	0.009	0.389
snpgdsPCASNPLoading	0.353	0.006	0.364
snpgdsPCASampLoading	0.382	0.008	0.391
snpgdsPED2GDS	4.364	0.090	4.844
snpgdsPairIBD	0.431	0.007	0.438
snpgdsPairIBDMLELogLik	0.506	0.008	0.519
snpgdsPairScore	0.142	0.014	0.706
snpgdsSNPList	0.010	0.001	0.011
snpgdsSNPListIntersect	0.044	0.003	0.046
snpgdsSNPListStrand	0.054	0.002	0.056
snpgdsSNPRateFreq	0.016	0.002	0.022
snpgdsSampMissRate	0.010	0.001	0.010
snpgdsSelectSNP	0.006	0.000	0.007
snpgdsSlidingWindow	1.255	0.061	1.510
snpgdsSummary	0.112	0.001	0.114
snpgdsTranspose	0.241	0.010	0.377
snpgdsVCF2GDS	0.134	0.023	0.164
snpgdsVCF2GDS_R	0.048	0.009	0.058