BioC 3.1: CHECK report for SNPRelate on zin2

Package: SNPRelate

Version: 1.2.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.2.0.tar.gz

StartedAt: 2015-10-09 05:40:13 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:41:19 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 66.5 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/SNPRelate.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ... [16s/17s] OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.7Mb
* 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 ... [28s/28s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [2s/2s] 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-3.1-bioc/meat/SNPRelate.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPRelate’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c R_SNPRelate.c -o R_SNPRelate.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c SNPRelate.cpp -o SNPRelate.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dGenGWAS.cpp -o dGenGWAS.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dVect.cpp -o dVect.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genFst.cpp -o genFst.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genHWE.cpp -o genHWE.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBD.cpp -o genIBD.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBS.cpp -o genIBS.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genKING.cpp -o genKING.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genLD.cpp -o genLD.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genPCA.cpp -o genPCA.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genSlideWin.cpp -o genSlideWin.o
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o dGenGWAS.o dVect.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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	0.011	0.000	0.012
SNPRelate-package	1.577	0.048	1.661
snpgdsAdmixProp	1.570	0.004	1.572
snpgdsAlleleSwitch	0.083	0.008	0.091
snpgdsApartSelection	0.104	0.000	0.105
snpgdsBED2GDS	0.076	0.000	0.079
snpgdsClose	0.008	0.000	0.008
snpgdsCombineGeno	0.449	0.012	0.461
snpgdsCreateGeno	0.096	0.000	0.096
snpgdsCreateGenoSet	0.152	0.004	0.156
snpgdsCutTree	2.407	0.000	2.412
snpgdsDiss	1.739	0.000	1.737
snpgdsDrawTree	1.779	0.004	1.782
snpgdsEIGMIX	1.479	0.008	1.487
snpgdsErrMsg	0	0	0
snpgdsExampleFileName	0.001	0.000	0.001
snpgdsFst	0.048	0.000	0.048
snpgdsGDS2BED	0.076	0.000	0.077
snpgdsGDS2Eigen	0.154	0.028	0.181
snpgdsGDS2PED	0.414	0.004	0.419
snpgdsGEN2GDS	0.001	0.000	0.000
snpgdsGRM	1.079	0.000	1.079
snpgdsGetGeno	0.351	0.000	0.352
snpgdsHCluster	1.986	0.008	1.994
snpgdsHWE	0.013	0.000	0.014
snpgdsIBDKING	0.256	0.012	0.268
snpgdsIBDMLE	1.458	0.000	1.458
snpgdsIBDMLELogLik	1.533	0.004	1.538
snpgdsIBDMoM	0.197	0.004	0.200
snpgdsIBDSelection	0.060	0.008	0.068
snpgdsIBS	0.326	0.000	0.326
snpgdsIBSNum	0.436	0.000	0.437
snpgdsIndInb	0.073	0.000	0.073
snpgdsIndInbCoef	0.019	0.000	0.019
snpgdsLDMat	0.442	0.004	0.456
snpgdsLDpair	0.004	0.000	0.004
snpgdsLDpruning	0.05	0.00	0.05
snpgdsOpen	0.01	0.00	0.01
snpgdsOption	0.003	0.000	0.003
snpgdsPCA	0.320	0.004	0.324
snpgdsPCACorr	0.339	0.004	0.343
snpgdsPCASNPLoading	0.355	0.000	0.356
snpgdsPCASampLoading	0.358	0.000	0.358
snpgdsPED2GDS	1.591	0.032	1.639
snpgdsPairIBD	1.111	0.000	1.111
snpgdsPairIBDMLELogLik	1.107	0.004	1.111
snpgdsSNPList	0.023	0.000	0.023
snpgdsSNPListIntersect	0.065	0.000	0.065
snpgdsSNPListStrand	0.073	0.004	0.078
snpgdsSNPRateFreq	0.036	0.000	0.036
snpgdsSampMissRate	0.01	0.00	0.01
snpgdsSelectSNP	0.016	0.000	0.016
snpgdsSlidingWindow	1.362	0.000	1.362
snpgdsSummary	0.104	0.000	0.104
snpgdsTranspose	0.176	0.008	0.184
snpgdsVCF2GDS	0.066	0.016	0.097
snpgdsVCF2GDS_R	0.033	0.004	0.037