BioC 3.2: CHECK report for SNPRelate on zin1

Package: SNPRelate

Version: 1.4.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.4.2.tar.gz

StartedAt: 2016-04-23 05:36:44 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:38:40 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 116.1 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.4.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SNPRelate.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.4.2’
* 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 ... [20s/20s] OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.0Mb
* 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 ... [31s/31s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [41s/41s]
 [41s/42s] 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-3.2-bioc/meat/SNPRelate.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPRelate’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c R_SNPRelate.c -o R_SNPRelate.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c SNPRelate.cpp -o SNPRelate.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dGenGWAS.cpp -o dGenGWAS.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dVect.cpp -o dVect.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genFst.cpp -o genFst.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genHWE.cpp -o genHWE.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBD.cpp -o genIBD.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBS.cpp -o genIBS.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genKING.cpp -o genKING.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genLD.cpp -o genLD.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genPCA.cpp -o genPCA.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genRec.cpp -o genRec.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genSlideWin.cpp -o genSlideWin.o
g++ -shared -L/home/biocbuild/bbs-3.2-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 genRec.o genSlideWin.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.2-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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	0.032	0.003	0.036
SNPRelate-package	1.669	0.052	1.766
snpgdsAdmixProp	1.632	0.004	1.638
snpgdsAlleleSwitch	0.092	0.008	0.108
snpgdsApartSelection	0.117	0.004	0.120
snpgdsBED2GDS	0.076	0.008	0.097
snpgdsClose	0.017	0.000	0.016
snpgdsCombineGeno	0.473	0.004	0.477
snpgdsCreateGeno	0.137	0.008	0.145
snpgdsCreateGenoSet	0.178	0.004	0.182
snpgdsCutTree	2.334	0.000	2.366
snpgdsDiss	1.911	0.000	1.913
snpgdsDrawTree	1.900	0.000	1.902
snpgdsEIGMIX	1.685	0.000	1.687
snpgdsErrMsg	0.001	0.000	0.001
snpgdsExampleFileName	0.001	0.000	0.001
snpgdsFst	0.055	0.000	0.055
snpgdsGDS2BED	0.091	0.000	0.091
snpgdsGDS2Eigen	0.179	0.032	0.210
snpgdsGDS2PED	0.442	0.020	0.462
snpgdsGEN2GDS	0.000	0.000	0.001
snpgdsGRM	1.187	0.000	1.210
snpgdsGetGeno	0.354	0.000	0.357
snpgdsHCluster	2.110	0.008	2.123
snpgdsHWE	0.014	0.000	0.015
snpgdsIBDKING	0.291	0.004	0.294
snpgdsIBDMLE	1.662	0.000	1.681
snpgdsIBDMLELogLik	1.623	0.004	1.628
snpgdsIBDMoM	0.217	0.008	0.224
snpgdsIBDSelection	0.077	0.000	0.077
snpgdsIBS	0.343	0.000	0.343
snpgdsIBSNum	0.440	0.008	0.464
snpgdsIndInb	0.086	0.000	0.086
snpgdsIndInbCoef	0.024	0.000	0.028
snpgdsLDMat	0.468	0.015	0.510
snpgdsLDpair	0.005	0.000	0.005
snpgdsLDpruning	0.061	0.000	0.065
snpgdsOpen	0.014	0.000	0.017
snpgdsOption	0.004	0.000	0.003
snpgdsPCA	0.383	0.008	0.393
snpgdsPCACorr	0.408	0.000	0.413
snpgdsPCASNPLoading	0.430	0.000	0.429
snpgdsPCASampLoading	0.427	0.000	0.427
snpgdsPED2GDS	1.827	0.036	1.950
snpgdsPairIBD	1.302	0.000	1.340
snpgdsPairIBDMLELogLik	1.225	0.000	1.227
snpgdsPairScore	0.108	0.004	0.116
snpgdsSNPList	0.028	0.000	0.027
snpgdsSNPListIntersect	0.079	0.000	0.079
snpgdsSNPListStrand	0.089	0.000	0.089
snpgdsSNPRateFreq	0.029	0.000	0.029
snpgdsSampMissRate	0.009	0.000	0.009
snpgdsSelectSNP	0.016	0.000	0.016
snpgdsSlidingWindow	1.451	0.000	1.494
snpgdsSummary	0.085	0.000	0.086
snpgdsTranspose	0.224	0.004	0.228
snpgdsVCF2GDS	0.125	0.012	0.180
snpgdsVCF2GDS_R	0.027	0.008	0.042