BioC 3.5: CHECK report for SNPRelate on malbec2

Package: SNPRelate

Version: 1.10.2

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.10.2.tar.gz

StartedAt: 2017-08-16 02:23:13 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:25:07 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 114.3 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.10.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘1.10.2’
* 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 ... 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-3.5-bioc/meat/SNPRelate.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPRelate’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SNPRelate.cpp -o SNPRelate.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ThreadPool.cpp -o ThreadPool.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c dGenGWAS.cpp -o dGenGWAS.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c dVect.cpp -o dVect.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genBeta.cpp -o genBeta.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genEIGMIX.cpp -o genEIGMIX.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genFst.cpp -o genFst.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genHWE.cpp -o genHWE.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genIBD.cpp -o genIBD.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genIBS.cpp -o genIBS.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genKING.cpp -o genKING.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genLD.cpp -o genLD.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c genPCA.cpp -o genPCA.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -DUSING_R -I. -I"/home/biocbuild/bbs-3.5-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-3.5-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-3.5-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.5-bioc/R/lib -lRlapack -lpthread -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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	0.048	0.000	0.047
SNPRelate-package	1.976	0.024	2.000
snpgdsAdmixPlot	0.520	0.004	0.523
snpgdsAdmixProp	0.648	0.000	0.648
snpgdsAlleleSwitch	0.088	0.000	0.088
snpgdsApartSelection	0.092	0.000	0.090
snpgdsBED2GDS	0.152	0.004	0.157
snpgdsClose	0.016	0.000	0.014
snpgdsCombineGeno	0.472	0.008	0.480
snpgdsCreateGeno	0.628	0.008	0.637
snpgdsCreateGenoSet	0.160	0.012	0.172
snpgdsCutTree	2.312	0.040	2.353
snpgdsDiss	1.756	0.000	1.757
snpgdsDrawTree	1.960	0.000	1.958
snpgdsEIGMIX	0.588	0.004	0.594
snpgdsErrMsg	0.000	0.000	0.001
snpgdsExampleFileName	0.000	0.000	0.002
snpgdsFst	0.096	0.000	0.097
snpgdsGDS2BED	0.092	0.008	0.100
snpgdsGDS2Eigen	0.264	0.024	0.291
snpgdsGDS2PED	0.356	0.008	0.367
snpgdsGEN2GDS	0.004	0.000	0.000
snpgdsGRM	0.476	0.000	0.477
snpgdsGetGeno	0.268	0.000	0.266
snpgdsHCluster	1.96	0.00	1.96
snpgdsHWE	0.012	0.000	0.011
snpgdsIBDKING	0.432	0.004	0.435
snpgdsIBDMLE	1.164	0.000	1.166
snpgdsIBDMLELogLik	1.180	0.008	1.191
snpgdsIBDMoM	0.256	0.000	0.256
snpgdsIBDSelection	0.072	0.000	0.070
snpgdsIBS	0.372	0.004	0.374
snpgdsIBSNum	0.460	0.000	0.461
snpgdsIndInb	0.028	0.008	0.034
snpgdsIndInbCoef	0.032	0.000	0.031
snpgdsIndivBeta	0.296	0.000	0.296
snpgdsLDMat	0.396	0.016	0.411
snpgdsLDpair	0.012	0.004	0.014
snpgdsLDpruning	0.040	0.000	0.042
snpgdsOpen	0.012	0.000	0.012
snpgdsOption	0.000	0.000	0.002
snpgdsPCA	0.484	0.008	0.494
snpgdsPCACorr	0.592	0.016	0.610
snpgdsPCASNPLoading	0.480	0.000	0.484
snpgdsPCASampLoading	0.500	0.000	0.501
snpgdsPED2GDS	1.484	0.036	1.523
snpgdsPairIBD	0.852	0.016	0.871
snpgdsPairIBDMLELogLik	0.800	0.004	0.804
snpgdsPairScore	0.148	0.000	0.150
snpgdsSNPList	0.004	0.004	0.008
snpgdsSNPListIntersect	0.048	0.000	0.048
snpgdsSNPListStrand	0.048	0.000	0.046
snpgdsSNPRateFreq	0.012	0.004	0.015
snpgdsSampMissRate	0.008	0.000	0.006
snpgdsSelectSNP	0.008	0.000	0.007
snpgdsSlidingWindow	0.892	0.000	0.893
snpgdsSummary	0.264	0.000	0.263
snpgdsTranspose	0.184	0.008	0.189
snpgdsVCF2GDS	0.312	0.004	0.316
snpgdsVCF2GDS_R	0.340	0.012	0.349