BioC 3.4: CHECK report for SNPRelate on malbec1

Package: SNPRelate

Version: 1.8.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.8.0.tar.gz

StartedAt: 2017-04-15 01:22:53 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:24:45 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 111.4 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SNPRelate.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   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 ... 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-3.4-bioc/meat/SNPRelate.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPRelate’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c R_SNPRelate.c -o R_SNPRelate.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c SNPRelate.cpp -o SNPRelate.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ThreadPool.cpp -o ThreadPool.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dGenGWAS.cpp -o dGenGWAS.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dVect.cpp -o dVect.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genBeta.cpp -o genBeta.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genFst.cpp -o genFst.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genHWE.cpp -o genHWE.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBD.cpp -o genIBD.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBS.cpp -o genIBS.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genKING.cpp -o genKING.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genLD.cpp -o genLD.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genPCA.cpp -o genPCA.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genRec.cpp -o genRec.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genSlideWin.cpp -o genSlideWin.o
g++ -shared -L/home/biocbuild/bbs-3.4-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 genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genRec.o genSlideWin.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -lpthread -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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	0.024	0.000	0.022
SNPRelate-package	1.756	0.032	1.792
snpgdsAdmixProp	1.784	0.012	1.798
snpgdsAlleleSwitch	0.088	0.000	0.088
snpgdsApartSelection	0.104	0.004	0.109
snpgdsBED2GDS	0.084	0.004	0.089
snpgdsClose	0.012	0.000	0.013
snpgdsCombineGeno	0.356	0.004	0.363
snpgdsCreateGeno	0.600	0.004	0.606
snpgdsCreateGenoSet	0.124	0.000	0.123
snpgdsCutTree	2.228	0.020	2.250
snpgdsDiss	1.816	0.000	1.818
snpgdsDrawTree	1.760	0.004	1.768
snpgdsEIGMIX	1.728	0.000	1.732
snpgdsErrMsg	0.000	0.000	0.001
snpgdsExampleFileName	0	0	0
snpgdsFst	0.064	0.000	0.064
snpgdsGDS2BED	0.052	0.008	0.057
snpgdsGDS2Eigen	0.128	0.020	0.149
snpgdsGDS2PED	0.392	0.004	0.394
snpgdsGEN2GDS	0	0	0
snpgdsGRM	1.324	0.000	1.326
snpgdsGetGeno	0.288	0.000	0.290
snpgdsHCluster	1.968	0.004	1.972
snpgdsHWE	0.008	0.004	0.012
snpgdsIBDKING	0.428	0.008	0.439
snpgdsIBDMLE	1.096	0.004	1.099
snpgdsIBDMLELogLik	1.020	0.012	1.031
snpgdsIBDMoM	0.200	0.004	0.203
snpgdsIBDSelection	0.068	0.000	0.070
snpgdsIBS	0.344	0.004	0.346
snpgdsIBSNum	0.492	0.004	0.496
snpgdsIndInb	0.032	0.000	0.032
snpgdsIndInbCoef	0.008	0.000	0.007
snpgdsIndivBeta	1.692	0.004	1.695
snpgdsLDMat	0.376	0.012	0.390
snpgdsLDpair	0.004	0.000	0.004
snpgdsLDpruning	0.032	0.000	0.033
snpgdsOpen	0.012	0.000	0.012
snpgdsOption	0.004	0.000	0.002
snpgdsPCA	0.572	0.012	0.585
snpgdsPCACorr	0.548	0.004	0.553
snpgdsPCASNPLoading	0.520	0.000	0.521
snpgdsPCASampLoading	0.508	0.000	0.508
snpgdsPED2GDS	1.460	0.028	1.487
snpgdsPairIBD	0.784	0.008	0.794
snpgdsPairIBDMLELogLik	0.788	0.004	0.792
snpgdsPairScore	0.088	0.016	0.108
snpgdsSNPList	0.008	0.000	0.008
snpgdsSNPListIntersect	0.040	0.000	0.039
snpgdsSNPListStrand	0.044	0.000	0.046
snpgdsSNPRateFreq	0.016	0.000	0.016
snpgdsSampMissRate	0.008	0.000	0.007
snpgdsSelectSNP	0.004	0.000	0.007
snpgdsSlidingWindow	0.892	0.000	0.894
snpgdsSummary	0.060	0.000	0.058
snpgdsTranspose	0.144	0.000	0.145
snpgdsVCF2GDS	0.080	0.008	0.086
snpgdsVCF2GDS_R	0.024	0.004	0.027