BioC 3.2: CHECK report for SNPRelate on zin1

Package: SNPRelate

Version: 1.3.8

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.3.8.tar.gz

StartedAt: 2015-08-24 03:55:37 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:57:22 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 104.4 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.3.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘1.3.8’
* 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 ... [19s/19s] OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.9Mb
* 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 ... [30s/30s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [33s/33s]
 [33s/33s] 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	0.035	0.000	0.034
SNPRelate-package	1.641	0.052	1.719
snpgdsAdmixProp	1.601	0.020	1.621
snpgdsAlleleSwitch	0.097	0.000	0.106
snpgdsApartSelection	0.117	0.000	0.117
snpgdsBED2GDS	0.079	0.004	0.098
snpgdsClose	0.018	0.000	0.018
snpgdsCombineGeno	0.491	0.004	0.495
snpgdsCreateGeno	0.130	0.003	0.134
snpgdsCreateGenoSet	0.164	0.004	0.168
snpgdsCutTree	2.301	0.004	2.306
snpgdsDiss	1.946	0.007	1.959
snpgdsDrawTree	1.824	0.000	1.823
snpgdsEIGMIX	1.616	0.000	1.619
snpgdsErrMsg	0.001	0.000	0.001
snpgdsExampleFileName	0.000	0.004	0.001
snpgdsFst	0.046	0.000	0.049
snpgdsGDS2BED	0.078	0.004	0.081
snpgdsGDS2Eigen	0.178	0.028	0.206
snpgdsGDS2PED	0.479	0.008	0.495
snpgdsGEN2GDS	0	0	0
snpgdsGRM	1.207	0.000	1.208
snpgdsGetGeno	0.313	0.000	0.313
snpgdsHCluster	2.114	0.004	2.144
snpgdsHWE	0.016	0.000	0.015
snpgdsIBDKING	0.291	0.012	0.303
snpgdsIBDMLE	1.635	0.004	1.638
snpgdsIBDMLELogLik	1.497	0.000	1.495
snpgdsIBDMoM	0.186	0.016	0.202
snpgdsIBDSelection	0.077	0.000	0.076
snpgdsIBS	0.358	0.000	0.358
snpgdsIBSNum	0.432	0.004	0.436
snpgdsIndInb	0.076	0.000	0.076
snpgdsIndInbCoef	0.019	0.000	0.019
snpgdsLDMat	0.468	0.012	0.480
snpgdsLDpair	0.005	0.000	0.005
snpgdsLDpruning	0.058	0.000	0.058
snpgdsOpen	0.016	0.000	0.015
snpgdsOption	0.002	0.000	0.003
snpgdsPCA	0.338	0.004	0.341
snpgdsPCACorr	0.380	0.004	0.384
snpgdsPCASNPLoading	0.422	0.000	0.422
snpgdsPCASampLoading	0.408	0.008	0.416
snpgdsPED2GDS	1.849	0.024	1.896
snpgdsPairIBD	1.152	0.004	1.161
snpgdsPairIBDMLELogLik	1.216	0.008	1.241
snpgdsPairScore	0.117	0.008	0.126
snpgdsSNPList	0.029	0.000	0.029
snpgdsSNPListIntersect	0.086	0.000	0.085
snpgdsSNPListStrand	0.095	0.000	0.096
snpgdsSNPRateFreq	0.025	0.008	0.032
snpgdsSampMissRate	0.011	0.000	0.012
snpgdsSelectSNP	0.018	0.000	0.017
snpgdsSlidingWindow	1.385	0.000	1.387
snpgdsSummary	0.071	0.004	0.075
snpgdsTranspose	0.204	0.000	0.204
snpgdsVCF2GDS	0.143	0.020	0.198
snpgdsVCF2GDS_R	0.037	0.000	0.036