BioC 3.1: CHECK report for SNPRelate on petty

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 02:06:49 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:08:51 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 122.5 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 Patched (2015-08-14 r69078)
* 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 ‘1.2.0’
* 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 ... [20s/20s] OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  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 ... [49s/50s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/4s]
 [4s/4s] 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
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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genFst.cpp -o genFst.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/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genHWE.cpp -o genHWE.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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genPCA.cpp -o genPCA.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/3.2/Resources/library/gdsfmt/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c genSlideWin.cpp -o genSlideWin.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 genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.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-3.1-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	0.020	0.003	0.022
SNPRelate-package	2.960	0.213	3.273
snpgdsAdmixProp	2.486	0.034	2.537
snpgdsAlleleSwitch	0.187	0.019	0.211
snpgdsApartSelection	0.243	0.009	0.252
snpgdsBED2GDS	0.150	0.012	0.163
snpgdsClose	0.017	0.002	0.020
snpgdsCombineGeno	0.925	0.062	1.083
snpgdsCreateGeno	0.265	0.026	0.293
snpgdsCreateGenoSet	0.298	0.017	0.317
snpgdsCutTree	3.685	0.021	3.717
snpgdsDiss	2.819	0.012	2.834
snpgdsDrawTree	2.901	0.012	2.920
snpgdsEIGMIX	2.300	0.015	2.329
snpgdsErrMsg	0.002	0.000	0.001
snpgdsExampleFileName	0.002	0.000	0.003
snpgdsFst	0.092	0.006	0.099
snpgdsGDS2BED	0.132	0.019	0.151
snpgdsGDS2Eigen	0.483	0.070	0.554
snpgdsGDS2PED	1.230	0.166	1.468
snpgdsGEN2GDS	0.001	0.000	0.001
snpgdsGRM	1.672	0.007	1.685
snpgdsGetGeno	0.550	0.028	0.579
snpgdsHCluster	3.327	0.030	3.374
snpgdsHWE	0.021	0.002	0.024
snpgdsIBDKING	0.546	0.029	0.576
snpgdsIBDMLE	1.337	0.024	1.362
snpgdsIBDMLELogLik	1.288	0.021	1.311
snpgdsIBDMoM	0.483	0.117	0.603
snpgdsIBDSelection	0.152	0.010	0.163
snpgdsIBS	0.837	0.013	0.852
snpgdsIBSNum	0.878	0.021	0.899
snpgdsIndInb	0.107	0.015	0.123
snpgdsIndInbCoef	0.040	0.003	0.044
snpgdsLDMat	0.676	0.048	0.796
snpgdsLDpair	0.009	0.002	0.011
snpgdsLDpruning	0.085	0.014	0.098
snpgdsOpen	0.018	0.002	0.020
snpgdsOption	0.006	0.001	0.007
snpgdsPCA	0.752	0.015	0.773
snpgdsPCACorr	0.698	0.012	0.711
snpgdsPCASNPLoading	0.848	0.016	0.868
snpgdsPCASampLoading	0.686	0.013	0.700
snpgdsPED2GDS	3.797	0.249	4.132
snpgdsPairIBD	1.134	0.032	1.167
snpgdsPairIBDMLELogLik	1.113	0.027	1.142
snpgdsSNPList	0.053	0.003	0.057
snpgdsSNPListIntersect	0.138	0.007	0.145
snpgdsSNPListStrand	0.171	0.009	0.179
snpgdsSNPRateFreq	0.077	0.005	0.083
snpgdsSampMissRate	0.019	0.002	0.022
snpgdsSelectSNP	0.028	0.002	0.031
snpgdsSlidingWindow	2.892	0.177	3.074
snpgdsSummary	0.160	0.002	0.162
snpgdsTranspose	0.413	0.018	0.437
snpgdsVCF2GDS	0.155	0.044	0.214
snpgdsVCF2GDS_R	0.066	0.012	0.078