BioC 3.5: CHECK report for SNPRelate on toluca2

Package: SNPRelate

Version: 1.9.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.9.8.tar.gz

StartedAt: 2017-04-23 10:09:53 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 10:12:11 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 137.9 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_1.9.8.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SNPRelate.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.9.8’
* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
snpgdsPED2GDS 4.843  0.141   5.162
* 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 -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/gdsfmt/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/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 genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.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-3.5-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	0.076	0.004	0.080
SNPRelate-package	1.963	0.176	2.158
snpgdsAdmixPlot	0.340	0.007	0.357
snpgdsAdmixProp	0.513	0.015	0.536
snpgdsAlleleSwitch	0.111	0.005	0.117
snpgdsApartSelection	0.157	0.009	0.167
snpgdsBED2GDS	0.270	0.008	0.279
snpgdsClose	0.020	0.000	0.022
snpgdsCombineGeno	0.666	0.022	0.704
snpgdsCreateGeno	0.263	0.020	0.290
snpgdsCreateGenoSet	0.162	0.010	0.177
snpgdsCutTree	2.641	0.054	2.745
snpgdsDiss	1.749	0.009	1.768
snpgdsDrawTree	1.654	0.007	1.673
snpgdsEIGMIX	0.352	0.012	0.371
snpgdsErrMsg	0.001	0.000	0.001
snpgdsExampleFileName	0.001	0.001	0.001
snpgdsFst	0.088	0.003	0.091
snpgdsGDS2BED	0.087	0.009	0.095
snpgdsGDS2Eigen	0.878	0.051	0.938
snpgdsGDS2PED	0.461	0.097	0.567
snpgdsGEN2GDS	0.001	0.000	0.001
snpgdsGRM	0.385	0.005	0.393
snpgdsGetGeno	0.327	0.012	0.339
snpgdsHCluster	1.968	0.022	2.072
snpgdsHWE	0.015	0.001	0.017
snpgdsIBDKING	0.561	0.010	0.593
snpgdsIBDMLE	0.850	0.011	0.865
snpgdsIBDMLELogLik	0.663	0.009	0.673
snpgdsIBDMoM	0.250	0.015	0.270
snpgdsIBDSelection	0.074	0.005	0.081
snpgdsIBS	0.393	0.009	0.405
snpgdsIBSNum	0.490	0.015	0.507
snpgdsIndInb	0.052	0.006	0.058
snpgdsIndInbCoef	0.055	0.003	0.059
snpgdsIndivBeta	0.299	0.007	0.308
snpgdsLDMat	0.518	0.024	0.553
snpgdsLDpair	0.021	0.001	0.023
snpgdsLDpruning	0.048	0.004	0.052
snpgdsOpen	0.019	0.001	0.019
snpgdsOption	0.004	0.001	0.004
snpgdsPCA	0.398	0.015	0.417
snpgdsPCACorr	0.509	0.067	0.584
snpgdsPCASNPLoading	0.367	0.005	0.378
snpgdsPCASampLoading	0.387	0.006	0.394
snpgdsPED2GDS	4.843	0.141	5.162
snpgdsPairIBD	0.695	0.008	0.709
snpgdsPairIBDMLELogLik	0.573	0.009	0.584
snpgdsPairScore	0.198	0.011	0.213
snpgdsSNPList	0.012	0.001	0.013
snpgdsSNPListIntersect	0.071	0.003	0.074
snpgdsSNPListStrand	0.060	0.002	0.064
snpgdsSNPRateFreq	0.017	0.002	0.018
snpgdsSampMissRate	0.008	0.001	0.009
snpgdsSelectSNP	0.008	0.001	0.008
snpgdsSlidingWindow	1.174	0.086	1.264
snpgdsSummary	0.235	0.002	0.238
snpgdsTranspose	0.159	0.008	0.169
snpgdsVCF2GDS	0.271	0.020	0.293
snpgdsVCF2GDS_R	0.308	0.007	0.316