BioC 3.3: CHECK report for SNPRelate on morelia

Package: SNPRelate

Version: 1.5.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SNPRelate_1.5.2.tar.gz

StartedAt: 2016-04-21 07:44:56 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:46:50 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 113.3 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_1.5.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SNPRelate.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.5.2’
* 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 ... [15s/15s] 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 ... [30s/30s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [36s/37s]
 [36s/37s] 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-3.3-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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/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-3.3-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	0.038	0.003	0.040
SNPRelate-package	1.577	0.085	1.694
snpgdsAdmixProp	1.375	0.015	1.404
snpgdsAlleleSwitch	0.088	0.009	0.100
snpgdsApartSelection	0.107	0.009	0.115
snpgdsBED2GDS	0.088	0.007	0.096
snpgdsClose	0.021	0.001	0.022
snpgdsCombineGeno	0.468	0.027	0.500
snpgdsCreateGeno	0.130	0.012	0.143
snpgdsCreateGenoSet	0.173	0.010	0.185
snpgdsCutTree	2.413	0.019	2.439
snpgdsDiss	1.762	0.008	1.789
snpgdsDrawTree	1.635	0.006	1.642
snpgdsEIGMIX	1.301	0.007	1.309
snpgdsErrMsg	0.001	0.000	0.001
snpgdsExampleFileName	0.001	0.000	0.002
snpgdsFst	0.054	0.004	0.057
snpgdsGDS2BED	0.097	0.009	0.108
snpgdsGDS2Eigen	0.732	0.045	0.785
snpgdsGDS2PED	0.493	0.041	0.534
snpgdsGEN2GDS	0	0	0
snpgdsGRM	1.014	0.006	1.021
snpgdsGetGeno	0.317	0.015	0.333
snpgdsHCluster	2.009	0.017	2.028
snpgdsHWE	0.015	0.001	0.016
snpgdsIBDKING	0.284	0.013	0.297
snpgdsIBDMLE	0.549	0.009	0.558
snpgdsIBDMLELogLik	0.643	0.008	0.652
snpgdsIBDMoM	0.234	0.042	0.278
snpgdsIBDSelection	0.084	0.005	0.091
snpgdsIBS	0.380	0.004	0.385
snpgdsIBSNum	0.474	0.015	0.491
snpgdsIndInb	0.061	0.005	0.066
snpgdsIndInbCoef	0.020	0.001	0.021
snpgdsLDMat	0.477	0.028	0.527
snpgdsLDpair	0.005	0.001	0.006
snpgdsLDpruning	0.054	0.006	0.060
snpgdsOpen	0.018	0.001	0.019
snpgdsOption	0.004	0.001	0.005
snpgdsPCA	0.330	0.008	0.343
snpgdsPCACorr	0.393	0.007	0.402
snpgdsPCASNPLoading	0.396	0.007	0.446
snpgdsPCASampLoading	0.377	0.008	0.386
snpgdsPED2GDS	4.547	0.099	4.661
snpgdsPairIBD	0.617	0.009	0.627
snpgdsPairIBDMLELogLik	0.465	0.009	0.474
snpgdsPairScore	0.118	0.013	0.134
snpgdsSNPList	0.026	0.002	0.028
snpgdsSNPListIntersect	0.086	0.007	0.093
snpgdsSNPListStrand	0.083	0.004	0.087
snpgdsSNPRateFreq	0.036	0.003	0.042
snpgdsSampMissRate	0.011	0.001	0.013
snpgdsSelectSNP	0.017	0.001	0.018
snpgdsSlidingWindow	1.258	0.055	1.317
snpgdsSummary	0.092	0.003	0.096
snpgdsTranspose	0.191	0.009	0.206
snpgdsVCF2GDS	0.136	0.021	0.156
snpgdsVCF2GDS_R	0.050	0.009	0.060