BioC 3.0: CHECK report for SNPRelate on zin1

Package: SNPRelate

Version: 1.0.1

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.0.1.tar.gz

StartedAt: 2015-04-10 04:30:25 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:31:41 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 75.4 seconds

RetCode: 0

Status:  OK

CheckDir: SNPRelate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/SNPRelate.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.0.1’
* 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 ... [15s/15s] OK
* checking installed package size ... OK
* 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 ... NOTE
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... [32s/33s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [3s/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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/SNPRelate.Rcheck/00check.log’
for details.

* installing *source* package ‘SNPRelate’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c R_SNPRelate.c -o R_SNPRelate.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c SNPRelate.cpp -o SNPRelate.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dGenGWAS.cpp -o dGenGWAS.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c dVect.cpp -o dVect.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBD.cpp -o genIBD.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genIBS.cpp -o genIBS.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genKING.cpp -o genKING.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genLD.cpp -o genLD.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -DUSING_R -I. -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/gdsfmt/include"   -fpic  -g -O2  -Wall -c genPCA.cpp -o genPCA.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o dGenGWAS.o dVect.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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	0.012	0.004	0.017
SNPRelate-package	1.848	0.088	1.995
snpgdsAdmixProp	1.684	0.008	1.733
snpgdsAlleleSwitch	0.128	0.000	0.128
snpgdsApartSelection	0.160	0.008	0.166
snpgdsBED2GDS	0.072	0.000	0.072
snpgdsClose	0.008	0.004	0.011
snpgdsCombineGeno	0.488	0.000	0.488
snpgdsCreateGeno	0.276	0.008	0.287
snpgdsCreateGenoSet	0.192	0.000	0.189
snpgdsCutTree	2.724	0.012	2.769
snpgdsDiss	2.024	0.004	2.031
snpgdsDrawTree	2.068	0.000	2.098
snpgdsEIGMIX	1.672	0.004	1.689
snpgdsErrMsg	0.000	0.000	0.001
snpgdsExampleFileName	0.004	0.000	0.003
snpgdsFst	0.060	0.000	0.059
snpgdsGDS2BED	0.096	0.004	0.100
snpgdsGDS2Eigen	0.216	0.008	0.249
snpgdsGDS2PED	0.448	0.016	0.463
snpgdsGEN2GDS	0.000	0.000	0.001
snpgdsGRM	1.232	0.000	1.240
snpgdsGetGeno	0.397	0.000	0.403
snpgdsHCluster	2.436	0.004	2.461
snpgdsIBDKING	0.308	0.020	0.329
snpgdsIBDMLE	1.640	0.012	1.659
snpgdsIBDMLELogLik	1.764	0.004	1.777
snpgdsIBDMoM	0.204	0.004	0.210
snpgdsIBDSelection	0.068	0.004	0.073
snpgdsIBS	0.320	0.004	0.326
snpgdsIBSNum	0.480	0.004	0.488
snpgdsIndInb	0.072	0.012	0.085
snpgdsIndInbCoef	0.028	0.000	0.025
snpgdsLDMat	1.284	0.012	1.298
snpgdsLDpair	0.008	0.000	0.007
snpgdsLDpruning	0.108	0.000	0.106
snpgdsOpen	0.012	0.000	0.011
snpgdsOption	0.004	0.000	0.004
snpgdsPCA	0.396	0.000	0.396
snpgdsPCACorr	0.412	0.004	0.419
snpgdsPCASNPLoading	0.460	0.000	0.463
snpgdsPCASampLoading	0.412	0.004	0.419
snpgdsPairIBD	1.244	0.012	1.255
snpgdsPairIBDMLELogLik	1.240	0.008	1.274
snpgdsSNPList	0.024	0.004	0.028
snpgdsSNPListIntersect	0.084	0.000	0.095
snpgdsSNPListStrand	0.092	0.000	0.093
snpgdsSNPRateFreq	0.040	0.008	0.048
snpgdsSampMissRate	0.008	0.004	0.013
snpgdsSelectSNP	0.024	0.000	0.020
snpgdsSlidingWindow	2.292	0.004	2.307
snpgdsSummary	0.088	0.000	0.089
snpgdsTranspose	0.172	0.008	0.195
snpgdsVCF2GDS	0.056	0.032	0.088
snpgdsVCF2GDS_R	0.036	0.004	0.040