BioC 3.6: CHECK report for SNPRelate on malbec1

Package: SNPRelate

Version: 1.11.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.11.1.tar.gz

StartedAt: 2017-08-16 02:31:13 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:32:59 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 105.4 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.11.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SNPRelate.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.11.1’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.2Mb
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/SNPRelate.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPRelate’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_SNPRelate.c -o R_SNPRelate.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SNPRelate.cpp -o SNPRelate.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ThreadPool.cpp -o ThreadPool.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c dGenGWAS.cpp -o dGenGWAS.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c dVect.cpp -o dVect.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genBeta.cpp -o genBeta.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genEIGMIX.cpp -o genEIGMIX.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genFst.cpp -o genFst.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genHWE.cpp -o genHWE.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genIBD.cpp -o genIBD.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genIBS.cpp -o genIBS.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genKING.cpp -o genKING.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genLD.cpp -o genLD.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genPCA.cpp -o genPCA.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.6-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genSlideWin.cpp -o genSlideWin.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -lpthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.052	0.000	0.049
SNPRelate-package	1.900	0.028	1.930
snpgdsAdmixPlot	0.512	0.000	0.510
snpgdsAdmixProp	0.616	0.000	0.617
snpgdsAlleleSwitch	0.088	0.000	0.089
snpgdsApartSelection	0.088	0.000	0.089
snpgdsBED2GDS	0.152	0.004	0.156
snpgdsClose	0.012	0.000	0.015
snpgdsCombineGeno	0.432	0.004	0.436
snpgdsCreateGeno	0.544	0.008	0.553
snpgdsCreateGenoSet	0.132	0.004	0.137
snpgdsCutTree	2.324	0.036	2.364
snpgdsDiss	1.740	0.000	1.744
snpgdsDrawTree	1.760	0.000	1.762
snpgdsEIGMIX	0.504	0.000	0.506
snpgdsErrMsg	0	0	0
snpgdsExampleFileName	0.000	0.000	0.001
snpgdsFst	0.064	0.000	0.062
snpgdsGDS2BED	0.056	0.000	0.057
snpgdsGDS2Eigen	0.140	0.012	0.151
snpgdsGDS2PED	0.320	0.020	0.337
snpgdsGEN2GDS	0	0	0
snpgdsGRM	0.528	0.000	0.527
snpgdsGetGeno	0.272	0.000	0.272
snpgdsHCluster	2.036	0.000	2.035
snpgdsHWE	0.012	0.000	0.012
snpgdsIBDKING	0.444	0.000	0.447
snpgdsIBDMLE	1.136	0.004	1.143
snpgdsIBDMLELogLik	1.028	0.000	1.029
snpgdsIBDMoM	0.212	0.000	0.213
snpgdsIBDSelection	0.064	0.000	0.064
snpgdsIBS	0.332	0.004	0.337
snpgdsIBSNum	0.424	0.008	0.434
snpgdsIndInb	0.024	0.008	0.032
snpgdsIndInbCoef	0.032	0.000	0.031
snpgdsIndivBeta	0.280	0.000	0.281
snpgdsLDMat	0.408	0.000	0.408
snpgdsLDpair	0.012	0.000	0.013
snpgdsLDpruning	0.044	0.000	0.041
snpgdsOpen	0.012	0.000	0.012
snpgdsOption	0.004	0.000	0.002
snpgdsPCA	0.540	0.008	0.550
snpgdsPCACorr	0.640	0.020	0.663
snpgdsPCASNPLoading	0.664	0.000	0.664
snpgdsPCASampLoading	0.680	0.004	0.685
snpgdsPED2GDS	1.608	0.040	1.649
snpgdsPairIBD	0.868	0.000	0.865
snpgdsPairIBDMLELogLik	0.812	0.004	0.817
snpgdsPairScore	0.152	0.004	0.157
snpgdsSNPList	0.008	0.000	0.008
snpgdsSNPListIntersect	0.048	0.000	0.051
snpgdsSNPListStrand	0.048	0.000	0.049
snpgdsSNPRateFreq	0.016	0.000	0.016
snpgdsSampMissRate	0.008	0.000	0.007
snpgdsSelectSNP	0.008	0.000	0.006
snpgdsSlidingWindow	0.944	0.000	0.944
snpgdsSummary	0.144	0.004	0.149
snpgdsTranspose	0.092	0.008	0.102
snpgdsVCF2GDS	0.176	0.008	0.182
snpgdsVCF2GDS_R	0.200	0.004	0.204