BioC 3.2: CHECK report for SNPRelate on oaxaca

Package: SNPRelate

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.4.2.tar.gz

StartedAt: 2016-04-23 04:34:53 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:37:15 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 141.9 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SNPRelate.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.4.2’
* 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 ... [16s/19s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
* 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 ... [33s/38s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
snpgdsPED2GDS 5.231  0.117   5.447
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [39s/44s]
 [39s/44s] 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-3.2-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 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/3.2/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 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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	0.050	0.008	0.427
SNPRelate-package	1.694	0.085	2.005
snpgdsAdmixProp	1.425	0.016	1.497
snpgdsAlleleSwitch	0.109	0.009	0.137
snpgdsApartSelection	0.163	0.012	0.175
snpgdsBED2GDS	0.099	0.008	0.107
snpgdsClose	0.022	0.002	0.024
snpgdsCombineGeno	0.523	0.027	0.554
snpgdsCreateGeno	0.139	0.017	0.158
snpgdsCreateGenoSet	0.192	0.009	0.203
snpgdsCutTree	2.510	0.015	2.547
snpgdsDiss	1.818	0.007	1.828
snpgdsDrawTree	1.783	0.011	1.795
snpgdsEIGMIX	1.374	0.009	1.430
snpgdsErrMsg	0.001	0.000	0.001
snpgdsExampleFileName	0.001	0.000	0.002
snpgdsFst	0.058	0.004	0.077
snpgdsGDS2BED	0.094	0.009	0.103
snpgdsGDS2Eigen	0.839	0.052	0.931
snpgdsGDS2PED	0.491	0.038	0.585
snpgdsGEN2GDS	0.000	0.000	0.001
snpgdsGRM	1.020	0.004	1.052
snpgdsGetGeno	0.377	0.013	0.396
snpgdsHCluster	2.171	0.016	2.242
snpgdsHWE	0.015	0.002	0.048
snpgdsIBDKING	0.270	0.013	0.304
snpgdsIBDMLE	0.700	0.011	0.712
snpgdsIBDMLELogLik	0.712	0.014	0.727
snpgdsIBDMoM	0.269	0.045	3.514
snpgdsIBDSelection	0.085	0.004	0.238
snpgdsIBS	0.461	0.004	0.534
snpgdsIBSNum	0.503	0.014	0.552
snpgdsIndInb	0.068	0.007	0.074
snpgdsIndInbCoef	0.024	0.002	0.026
snpgdsLDMat	0.457	0.033	1.299
snpgdsLDpair	0.006	0.002	0.008
snpgdsLDpruning	0.068	0.005	0.073
snpgdsOpen	0.019	0.001	0.021
snpgdsOption	0.004	0.001	0.005
snpgdsPCA	0.384	0.010	0.400
snpgdsPCACorr	0.383	0.006	0.390
snpgdsPCASNPLoading	0.404	0.008	0.413
snpgdsPCASampLoading	0.404	0.009	0.413
snpgdsPED2GDS	5.231	0.117	5.447
snpgdsPairIBD	0.717	0.014	0.740
snpgdsPairIBDMLELogLik	0.588	0.014	0.602
snpgdsPairScore	0.120	0.012	0.134
snpgdsSNPList	0.028	0.002	0.030
snpgdsSNPListIntersect	0.076	0.003	0.079
snpgdsSNPListStrand	0.104	0.005	0.109
snpgdsSNPRateFreq	0.035	0.004	0.040
snpgdsSampMissRate	0.011	0.001	0.013
snpgdsSelectSNP	0.016	0.001	0.018
snpgdsSlidingWindow	1.713	0.076	1.806
snpgdsSummary	0.097	0.000	0.097
snpgdsTranspose	0.254	0.010	0.272
snpgdsVCF2GDS	0.138	0.020	0.176
snpgdsVCF2GDS_R	0.045	0.008	0.053