BioC 3.3: CHECK report for SNPRelate on zin2

Package: SNPRelate

Version: 1.6.6

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.6.6.tar.gz

StartedAt: 2016-10-13 06:58:28 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:00:27 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 118.4 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.6.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SNPRelate.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.6.6’
* 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-3.3-bioc/meat/SNPRelate.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPRelate’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c R_SNPRelate.c -o R_SNPRelate.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c SNPRelate.cpp -o SNPRelate.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ThreadPool.cpp -o ThreadPool.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dGenGWAS.cpp -o dGenGWAS.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dVect.cpp -o dVect.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genFst.cpp -o genFst.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genHWE.cpp -o genHWE.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBD.cpp -o genIBD.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBS.cpp -o genIBS.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genKING.cpp -o genKING.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genLD.cpp -o genLD.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genPCA.cpp -o genPCA.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genRec.cpp -o genRec.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genSlideWin.cpp -o genSlideWin.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.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-3.3-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.3-bioc/R/lib -lRlapack -lpthread -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/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	0.023	0.000	0.022
SNPRelate-package	1.853	0.013	1.881
snpgdsAdmixProp	1.644	0.008	1.653
snpgdsAlleleSwitch	0.097	0.000	0.098
snpgdsApartSelection	0.115	0.000	0.115
snpgdsBED2GDS	0.071	0.003	0.084
snpgdsClose	0.012	0.004	0.015
snpgdsCombineGeno	0.370	0.008	0.379
snpgdsCreateGeno	0.249	0.004	0.262
snpgdsCreateGenoSet	0.138	0.000	0.142
snpgdsCutTree	2.355	0.016	2.373
snpgdsDiss	1.915	0.008	1.925
snpgdsDrawTree	1.858	0.000	1.860
snpgdsEIGMIX	1.657	0.000	1.657
snpgdsErrMsg	0	0	0
snpgdsExampleFileName	0.001	0.000	0.001
snpgdsFst	0.066	0.000	0.066
snpgdsGDS2BED	0.070	0.004	0.075
snpgdsGDS2Eigen	0.174	0.024	0.197
snpgdsGDS2PED	0.453	0.016	0.470
snpgdsGEN2GDS	0.001	0.000	0.001
snpgdsGRM	1.261	0.004	1.289
snpgdsGetGeno	0.303	0.000	0.303
snpgdsHCluster	2.171	0.004	2.178
snpgdsHWE	0.014	0.000	0.014
snpgdsIBDKING	0.511	0.000	0.512
snpgdsIBDMLE	1.553	0.000	1.554
snpgdsIBDMLELogLik	1.551	0.012	1.566
snpgdsIBDMoM	0.208	0.012	0.219
snpgdsIBDSelection	0.071	0.004	0.076
snpgdsIBS	0.384	0.008	0.393
snpgdsIBSNum	0.472	0.028	0.501
snpgdsIndInb	0.064	0.000	0.064
snpgdsIndInbCoef	0.008	0.000	0.008
snpgdsLDMat	0.435	0.008	0.444
snpgdsLDpair	0.004	0.000	0.004
snpgdsLDpruning	0.038	0.000	0.037
snpgdsOpen	0.014	0.000	0.014
snpgdsOption	0.003	0.000	0.003
snpgdsPCA	0.511	0.000	0.512
snpgdsPCACorr	0.492	0.000	0.493
snpgdsPCASNPLoading	0.501	0.008	0.510
snpgdsPCASampLoading	0.488	0.000	0.488
snpgdsPED2GDS	1.740	0.040	1.838
snpgdsPairIBD	1.214	0.004	1.218
snpgdsPairIBDMLELogLik	1.193	0.004	1.196
snpgdsPairScore	0.109	0.008	0.123
snpgdsSNPList	0.013	0.000	0.014
snpgdsSNPListIntersect	0.053	0.000	0.052
snpgdsSNPListStrand	0.06	0.00	0.06
snpgdsSNPRateFreq	0.018	0.000	0.018
snpgdsSampMissRate	0.007	0.000	0.007
snpgdsSelectSNP	0.007	0.000	0.007
snpgdsSlidingWindow	1.060	0.000	1.059
snpgdsSummary	0.072	0.000	0.072
snpgdsTranspose	0.170	0.004	0.173
snpgdsVCF2GDS	0.097	0.004	0.125
snpgdsVCF2GDS_R	0.026	0.008	0.035