BioC 3.2: CHECK report for SNPRelate on linux1.bioconductor.org

Package: SNPRelate

Version: 1.4.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SNPRelate_1.4.0.tar.gz

StartedAt: 2015-10-27 08:17:50 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:19:47 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 117.2 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_1.4.0.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 ‘1.4.0’
* 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 ... [21s/21s] OK
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    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 ... [32s/32s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [41s/41s]
 [42s/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	0.041	0.000	0.041
SNPRelate-package	2.235	0.099	2.342
snpgdsAdmixProp	1.744	0.020	1.770
snpgdsAlleleSwitch	0.134	0.004	0.140
snpgdsApartSelection	0.150	0.004	0.155
snpgdsBED2GDS	0.114	0.000	0.115
snpgdsClose	0.025	0.000	0.025
snpgdsCombineGeno	0.643	0.004	0.648
snpgdsCreateGeno	0.152	0.012	0.164
snpgdsCreateGenoSet	0.220	0.000	0.221
snpgdsCutTree	2.134	0.008	2.149
snpgdsDiss	1.938	0.000	1.939
snpgdsDrawTree	1.949	0.000	1.949
snpgdsEIGMIX	1.486	0.000	1.485
snpgdsErrMsg	0	0	0
snpgdsExampleFileName	0.001	0.000	0.001
snpgdsFst	0.045	0.000	0.044
snpgdsGDS2BED	0.062	0.008	0.071
snpgdsGDS2Eigen	0.153	0.000	0.153
snpgdsGDS2PED	0.551	0.020	0.571
snpgdsGEN2GDS	0.001	0.000	0.001
snpgdsGRM	1.261	0.000	1.261
snpgdsGetGeno	0.444	0.008	0.456
snpgdsHCluster	1.953	0.008	1.966
snpgdsHWE	0.016	0.000	0.015
snpgdsIBDKING	0.248	0.012	0.260
snpgdsIBDMLE	1.761	0.000	1.761
snpgdsIBDMLELogLik	1.752	0.008	1.761
snpgdsIBDMoM	0.214	0.044	0.262
snpgdsIBDSelection	0.057	0.000	0.057
snpgdsIBS	0.271	0.000	0.271
snpgdsIBSNum	0.469	0.008	0.479
snpgdsIndInb	0.086	0.000	0.086
snpgdsIndInbCoef	0.023	0.000	0.027
snpgdsLDMat	0.396	0.008	0.404
snpgdsLDpair	0.004	0.000	0.004
snpgdsLDpruning	0.048	0.000	0.047
snpgdsOpen	0.013	0.000	0.012
snpgdsOption	0.002	0.000	0.003
snpgdsPCA	0.301	0.004	0.305
snpgdsPCACorr	0.316	0.004	0.316
snpgdsPCASNPLoading	0.332	0.004	0.340
snpgdsPCASampLoading	0.331	0.000	0.330
snpgdsPED2GDS	1.392	0.032	1.426
snpgdsPairIBD	1.288	0.008	1.307
snpgdsPairIBDMLELogLik	1.468	0.008	1.481
snpgdsPairScore	0.157	0.004	0.161
snpgdsSNPList	0.038	0.000	0.039
snpgdsSNPListIntersect	0.117	0.000	0.116
snpgdsSNPListStrand	0.126	0.004	0.130
snpgdsSNPRateFreq	0.040	0.000	0.041
snpgdsSampMissRate	0.014	0.000	0.013
snpgdsSelectSNP	0.02	0.00	0.02
snpgdsSlidingWindow	1.838	0.000	1.851
snpgdsSummary	0.113	0.000	0.113
snpgdsTranspose	0.165	0.008	0.170
snpgdsVCF2GDS	0.128	0.012	0.143
snpgdsVCF2GDS_R	0.045	0.004	0.050