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: 2017-10-18 02:36:23 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:38:22 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 118.4 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

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### Running command:
###
###   /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 3.4.2 (2017-09-28)
* 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	0.060	0.000	0.059
SNPRelate-package	1.920	0.028	1.948
snpgdsAdmixPlot	0.536	0.008	0.544
snpgdsAdmixProp	0.656	0.000	0.653
snpgdsAlleleSwitch	0.088	0.004	0.091
snpgdsApartSelection	0.092	0.000	0.093
snpgdsBED2GDS	0.160	0.000	0.159
snpgdsClose	0.012	0.000	0.012
snpgdsCombineGeno	0.448	0.000	0.448
snpgdsCreateGeno	0.596	0.000	0.599
snpgdsCreateGenoSet	0.132	0.004	0.135
snpgdsCutTree	2.296	0.032	2.330
snpgdsDiss	1.944	0.000	1.949
snpgdsDrawTree	1.824	0.004	1.830
snpgdsEIGMIX	0.480	0.000	0.483
snpgdsErrMsg	0.004	0.000	0.000
snpgdsExampleFileName	0.000	0.000	0.001
snpgdsFst	0.060	0.000	0.061
snpgdsGDS2BED	0.048	0.008	0.058
snpgdsGDS2Eigen	0.136	0.012	0.149
snpgdsGDS2PED	0.324	0.012	0.338
snpgdsGEN2GDS	0.004	0.000	0.000
snpgdsGRM	0.516	0.000	0.516
snpgdsGetGeno	0.284	0.000	0.285
snpgdsHCluster	2.076	0.008	2.085
snpgdsHWE	0.012	0.000	0.012
snpgdsIBDKING	0.448	0.000	0.445
snpgdsIBDMLE	1.232	0.004	1.236
snpgdsIBDMLELogLik	1.028	0.000	1.030
snpgdsIBDMoM	0.224	0.004	0.228
snpgdsIBDSelection	0.072	0.000	0.070
snpgdsIBS	0.400	0.000	0.399
snpgdsIBSNum	0.444	0.000	0.445
snpgdsIndInb	0.024	0.004	0.032
snpgdsIndInbCoef	0.028	0.000	0.029
snpgdsIndivBeta	0.288	0.000	0.287
snpgdsLDMat	0.400	0.004	0.404
snpgdsLDpair	0.012	0.000	0.013
snpgdsLDpruning	0.040	0.000	0.041
snpgdsOpen	0.012	0.000	0.011
snpgdsOption	0.004	0.000	0.002
snpgdsPCA	0.480	0.000	0.481
snpgdsPCACorr	0.612	0.020	0.632
snpgdsPCASNPLoading	0.524	0.008	0.532
snpgdsPCASampLoading	0.500	0.000	0.504
snpgdsPED2GDS	1.416	0.028	1.441
snpgdsPairIBD	0.840	0.004	0.846
snpgdsPairIBDMLELogLik	0.800	0.004	0.803
snpgdsPairScore	0.152	0.000	0.150
snpgdsSNPList	0.008	0.000	0.008
snpgdsSNPListIntersect	0.044	0.004	0.049
snpgdsSNPListStrand	0.044	0.000	0.044
snpgdsSNPRateFreq	0.016	0.000	0.017
snpgdsSampMissRate	0.008	0.000	0.007
snpgdsSelectSNP	0.008	0.000	0.006
snpgdsSlidingWindow	0.844	0.004	0.851
snpgdsSummary	0.148	0.000	0.145
snpgdsTranspose	0.104	0.000	0.105
snpgdsVCF2GDS	0.176	0.000	0.173
snpgdsVCF2GDS_R	0.196	0.000	0.196