BioC 3.0: CHECK report for SNPRelate on perceval

Package: SNPRelate

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SNPRelate_1.0.1.tar.gz

StartedAt: 2015-04-10 06:33:23 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 06:35:03 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 99.6 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 --no-multiarch SNPRelate_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SNPRelate.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.1’
* 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 ... [14s/16s] OK
* checking installed package size ... OK
* 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 ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [38s/40s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/4s]
 [5s/5s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/SNPRelate.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPRelate’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ConvToGDS.cpp -o ConvToGDS.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_SNPRelate.c -o R_SNPRelate.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c SNPRelate.cpp -o SNPRelate.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c dGenGWAS.cpp -o dGenGWAS.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c dVect.cpp -o dVect.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genIBD.cpp -o genIBD.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genIBS.cpp -o genIBS.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genKING.cpp -o genKING.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genLD.cpp -o genLD.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genPCA.cpp -o genPCA.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o dGenGWAS.o dVect.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -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-3.0-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	0.015	0.003	0.029
SNPRelate-package	2.593	0.163	3.004
snpgdsAdmixProp	2.070	0.025	2.159
snpgdsAlleleSwitch	0.135	0.022	0.242
snpgdsApartSelection	0.249	0.014	0.263
snpgdsBED2GDS	0.081	0.014	0.139
snpgdsClose	0.014	0.003	0.017
snpgdsCombineGeno	0.713	0.044	0.802
snpgdsCreateGeno	0.389	0.027	0.433
snpgdsCreateGenoSet	0.238	0.025	0.281
snpgdsCutTree	2.836	0.030	2.914
snpgdsDiss	2.039	0.015	2.070
snpgdsDrawTree	2.062	0.013	2.096
snpgdsEIGMIX	2.156	0.020	2.244
snpgdsErrMsg	0.000	0.000	0.001
snpgdsExampleFileName	0.002	0.001	0.004
snpgdsFst	0.064	0.008	0.072
snpgdsGDS2BED	0.094	0.014	0.108
snpgdsGDS2Eigen	0.290	0.046	0.336
snpgdsGDS2PED	0.703	0.092	0.900
snpgdsGEN2GDS	0.000	0.000	0.001
snpgdsGRM	1.504	0.010	1.519
snpgdsGetGeno	0.596	0.036	0.631
snpgdsHCluster	2.421	0.031	2.479
snpgdsIBDKING	0.425	0.027	0.474
snpgdsIBDMLE	0.891	0.029	0.928
snpgdsIBDMLELogLik	0.888	0.021	0.916
snpgdsIBDMoM	0.429	0.126	0.590
snpgdsIBDSelection	0.123	0.009	0.142
snpgdsIBS	0.644	0.010	0.664
snpgdsIBSNum	0.701	0.022	0.726
snpgdsIndInb	0.081	0.022	0.103
snpgdsIndInbCoef	0.027	0.004	0.031
snpgdsLDMat	1.657	0.094	1.880
snpgdsLDpair	0.009	0.004	0.013
snpgdsLDpruning	0.193	0.011	0.203
snpgdsOpen	0.014	0.002	0.016
snpgdsOption	0.007	0.001	0.007
snpgdsPCA	0.747	0.020	0.809
snpgdsPCACorr	0.830	0.015	0.857
snpgdsPCASNPLoading	0.951	0.013	0.978
snpgdsPCASampLoading	0.972	0.016	0.989
snpgdsPairIBD	0.753	0.017	0.771
snpgdsPairIBDMLELogLik	0.751	0.023	0.774
snpgdsSNPList	0.034	0.003	0.037
snpgdsSNPListIntersect	0.094	0.005	0.099
snpgdsSNPListStrand	0.107	0.006	0.113
snpgdsSNPRateFreq	0.062	0.006	0.081
snpgdsSampMissRate	0.011	0.003	0.014
snpgdsSelectSNP	0.019	0.003	0.023
snpgdsSlidingWindow	2.955	0.021	2.986
snpgdsSummary	0.129	0.001	0.130
snpgdsTranspose	0.253	0.011	0.319
snpgdsVCF2GDS	0.131	0.053	0.297
snpgdsVCF2GDS_R	0.053	0.013	0.095