BioC 3.2: CHECK report for SNPRelate on perceval

Package: SNPRelate

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.4.0.tar.gz

StartedAt: 2015-10-27 12:28:03 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 12:30:19 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 135.8 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SNPRelate.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.4.0’
* 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 ... [15s/15s] OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  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 ... [37s/37s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [47s/48s]
 [48s/48s] 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
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 genRec.cpp -o genRec.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 genRec.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-3.2-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	0.041	0.003	0.044
SNPRelate-package	2.219	0.124	2.433
snpgdsAdmixProp	2.072	0.022	2.105
snpgdsAlleleSwitch	0.133	0.015	0.153
snpgdsApartSelection	0.169	0.007	0.177
snpgdsBED2GDS	0.101	0.009	0.124
snpgdsClose	0.023	0.002	0.025
snpgdsCombineGeno	0.681	0.042	0.726
snpgdsCreateGeno	0.189	0.021	0.211
snpgdsCreateGenoSet	0.232	0.011	0.246
snpgdsCutTree	2.982	0.021	3.014
snpgdsDiss	2.293	0.008	2.301
snpgdsDrawTree	2.309	0.010	2.332
snpgdsEIGMIX	2.042	0.010	2.056
snpgdsErrMsg	0.001	0.000	0.001
snpgdsExampleFileName	0.001	0.000	0.002
snpgdsFst	0.073	0.006	0.078
snpgdsGDS2BED	0.099	0.014	0.114
snpgdsGDS2Eigen	0.320	0.041	0.362
snpgdsGDS2PED	0.797	0.072	0.928
snpgdsGEN2GDS	0.000	0.000	0.001
snpgdsGRM	1.384	0.004	1.388
snpgdsGetGeno	0.392	0.017	0.411
snpgdsHCluster	2.614	0.019	2.635
snpgdsHWE	0.022	0.002	0.025
snpgdsIBDKING	0.411	0.021	0.433
snpgdsIBDMLE	0.911	0.016	0.927
snpgdsIBDMLELogLik	0.914	0.017	0.931
snpgdsIBDMoM	0.380	0.089	0.472
snpgdsIBDSelection	0.116	0.007	0.125
snpgdsIBS	0.662	0.009	0.673
snpgdsIBSNum	0.706	0.015	0.722
snpgdsIndInb	0.081	0.009	0.089
snpgdsIndInbCoef	0.031	0.003	0.033
snpgdsLDMat	0.533	0.033	0.596
snpgdsLDpair	0.006	0.002	0.008
snpgdsLDpruning	0.076	0.009	0.086
snpgdsOpen	0.021	0.001	0.022
snpgdsOption	0.004	0.001	0.005
snpgdsPCA	0.555	0.016	0.576
snpgdsPCACorr	0.511	0.012	0.523
snpgdsPCASNPLoading	0.558	0.012	0.571
snpgdsPCASampLoading	0.538	0.010	0.547
snpgdsPED2GDS	2.590	0.128	2.781
snpgdsPairIBD	0.816	0.027	0.843
snpgdsPairIBDMLELogLik	0.753	0.010	0.764
snpgdsPairScore	0.185	0.016	0.202
snpgdsSNPList	0.047	0.002	0.049
snpgdsSNPListIntersect	0.120	0.004	0.124
snpgdsSNPListStrand	0.144	0.006	0.149
snpgdsSNPRateFreq	0.043	0.003	0.049
snpgdsSampMissRate	0.012	0.001	0.013
snpgdsSelectSNP	0.021	0.001	0.022
snpgdsSlidingWindow	1.784	0.113	1.897
snpgdsSummary	0.125	0.002	0.127
snpgdsTranspose	0.261	0.014	0.283
snpgdsVCF2GDS	0.148	0.027	0.194
snpgdsVCF2GDS_R	0.048	0.010	0.059