BioC 3.4: CHECK report for SNPRelate on morelia

Package: SNPRelate

Version: 1.7.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.7.3.tar.gz

StartedAt: 2016-09-20 13:17:25 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:19:07 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 101.7 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_1.7.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SNPRelate.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.7.3’
* 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 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 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	0.021	0.001	0.021
SNPRelate-package	1.386	0.053	1.475
snpgdsAdmixProp	1.297	0.011	1.323
snpgdsAlleleSwitch	0.078	0.009	0.090
snpgdsApartSelection	0.092	0.006	0.099
snpgdsBED2GDS	0.068	0.006	0.076
snpgdsClose	0.019	0.001	0.020
snpgdsCombineGeno	0.376	0.021	0.402
snpgdsCreateGeno	0.112	0.013	0.125
snpgdsCreateGenoSet	0.167	0.011	0.179
snpgdsCutTree	2.077	0.037	2.126
snpgdsDiss	1.611	0.011	1.623
snpgdsDrawTree	1.505	0.006	1.512
snpgdsEIGMIX	1.231	0.005	1.236
snpgdsErrMsg	0.001	0.000	0.000
snpgdsExampleFileName	0.002	0.000	0.002
snpgdsFst	0.026	0.002	0.028
snpgdsGDS2BED	0.054	0.006	0.063
snpgdsGDS2Eigen	0.693	0.045	0.762
snpgdsGDS2PED	0.351	0.023	0.375
snpgdsGEN2GDS	0.000	0.000	0.001
snpgdsGRM	0.927	0.003	0.930
snpgdsGetGeno	0.278	0.007	0.285
snpgdsHCluster	1.936	0.012	1.952
snpgdsHWE	0.013	0.002	0.015
snpgdsIBDKING	0.403	0.012	0.415
snpgdsIBDMLE	0.495	0.009	0.517
snpgdsIBDMLELogLik	0.533	0.011	0.544
snpgdsIBDMoM	0.204	0.014	0.221
snpgdsIBDSelection	0.053	0.003	0.057
snpgdsIBS	0.351	0.007	0.358
snpgdsIBSNum	0.408	0.014	0.421
snpgdsIndInb	0.054	0.006	0.060
snpgdsIndInbCoef	0.009	0.002	0.010
snpgdsLDMat	0.360	0.021	0.400
snpgdsLDpair	0.006	0.001	0.007
snpgdsLDpruning	0.052	0.003	0.055
snpgdsOpen	0.015	0.001	0.016
snpgdsOption	0.002	0.000	0.003
snpgdsPCA	0.347	0.012	0.365
snpgdsPCACorr	0.355	0.006	0.375
snpgdsPCASNPLoading	0.371	0.006	0.379
snpgdsPCASampLoading	0.369	0.006	0.376
snpgdsPED2GDS	3.452	0.072	3.539
snpgdsPairIBD	0.392	0.011	0.402
snpgdsPairIBDMLELogLik	0.385	0.006	0.391
snpgdsPairScore	0.095	0.008	0.104
snpgdsSNPList	0.007	0.001	0.008
snpgdsSNPListIntersect	0.046	0.001	0.047
snpgdsSNPListStrand	0.066	0.003	0.069
snpgdsSNPRateFreq	0.016	0.002	0.021
snpgdsSampMissRate	0.006	0.001	0.006
snpgdsSelectSNP	0.007	0.001	0.007
snpgdsSlidingWindow	0.946	0.089	1.036
snpgdsSummary	0.088	0.001	0.089
snpgdsTranspose	0.193	0.008	0.207
snpgdsVCF2GDS	0.129	0.019	0.150
snpgdsVCF2GDS_R	0.046	0.008	0.055