BioC 3.1: CHECK report for SNPRelate on morelia

Package: SNPRelate

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.2.0.tar.gz

StartedAt: 2015-10-09 06:29:58 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:31:12 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 73.9 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/SNPRelate.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ... [13s/13s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
* 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 ... [28s/28s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [2s/2s] 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-3.1-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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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 dGenGWAS.o dVect.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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-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	0.014	0.001	0.035
SNPRelate-package	1.256	0.112	1.408
snpgdsAdmixProp	1.316	0.041	1.372
snpgdsAlleleSwitch	0.134	0.047	0.183
snpgdsApartSelection	0.088	0.004	0.093
snpgdsBED2GDS	0.071	0.007	0.077
snpgdsClose	0.012	0.002	0.014
snpgdsCombineGeno	0.455	0.046	0.506
snpgdsCreateGeno	0.136	0.030	0.166
snpgdsCreateGenoSet	0.140	0.009	0.150
snpgdsCutTree	2.105	0.155	2.280
snpgdsDiss	1.542	0.071	1.614
snpgdsDrawTree	1.791	0.186	1.978
snpgdsEIGMIX	1.266	0.077	1.345
snpgdsErrMsg	0.001	0.000	0.000
snpgdsExampleFileName	0.001	0.000	0.001
snpgdsFst	0.042	0.002	0.044
snpgdsGDS2BED	0.079	0.008	0.087
snpgdsGDS2Eigen	0.501	0.143	0.646
snpgdsGDS2PED	0.388	0.048	0.436
snpgdsGEN2GDS	0	0	0
snpgdsGRM	0.891	0.004	0.895
snpgdsGetGeno	0.277	0.007	0.285
snpgdsHCluster	2.048	0.283	2.354
snpgdsHWE	0.015	0.002	0.016
snpgdsIBDKING	0.267	0.024	0.573
snpgdsIBDMLE	0.633	0.012	0.645
snpgdsIBDMLELogLik	0.511	0.014	0.526
snpgdsIBDMoM	0.203	0.063	0.268
snpgdsIBDSelection	0.073	0.009	0.083
snpgdsIBS	0.309	0.006	0.316
snpgdsIBSNum	0.439	0.014	0.453
snpgdsIndInb	0.054	0.006	0.060
snpgdsIndInbCoef	0.020	0.006	0.025
snpgdsLDMat	0.452	0.113	0.587
snpgdsLDpair	0.004	0.001	0.004
snpgdsLDpruning	0.048	0.005	0.054
snpgdsOpen	0.007	0.001	0.007
snpgdsOption	0.003	0.001	0.003
snpgdsPCA	0.283	0.008	0.295
snpgdsPCACorr	0.325	0.006	0.330
snpgdsPCASNPLoading	0.306	0.043	0.352
snpgdsPCASampLoading	0.354	0.007	0.363
snpgdsPED2GDS	3.714	0.122	3.845
snpgdsPairIBD	0.450	0.013	0.463
snpgdsPairIBDMLELogLik	0.389	0.008	0.396
snpgdsSNPList	0.020	0.001	0.021
snpgdsSNPListIntersect	0.057	0.001	0.059
snpgdsSNPListStrand	0.063	0.002	0.065
snpgdsSNPRateFreq	0.035	0.001	0.038
snpgdsSampMissRate	0.007	0.001	0.008
snpgdsSelectSNP	0.013	0.001	0.014
snpgdsSlidingWindow	1.137	0.131	1.589
snpgdsSummary	0.062	0.001	0.062
snpgdsTranspose	0.309	0.008	0.406
snpgdsVCF2GDS	0.086	0.024	0.110
snpgdsVCF2GDS_R	0.051	0.013	0.064