BioC 3.1: CHECK report for GWASTools on zin2

Package: GWASTools

Version: 1.14.2

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GWASTools_1.14.2.tar.gz

StartedAt: 2015-10-09 02:23:54 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:30:17 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 383.5 seconds

RetCode: 0

Status:  OK

CheckDir: GWASTools.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 GWASTools_1.14.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/GWASTools.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 ‘GWASTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GWASTools’ version ‘1.14.2’
* 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 ‘GWASTools’ can be installed ... [7s/12s] 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 ‘snpStats’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/50s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
vcfWrite 7.686  0.241  12.759
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [122s/192s]
 [122s/193s] 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/GWASTools.Rcheck/00check.log’
for details.

* installing *source* package ‘GWASTools’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘open’ from package ‘base’ in package ‘GWASTools’
Creating a generic function for ‘close’ from package ‘base’ in package ‘GWASTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GWASTools)

name	user	system	elapsed
BAFfromClusterMeans	1.192	0.020	1.602
BAFfromGenotypes	0.001	0.000	0.017
GdsGenotypeReader-class	0.033	0.000	0.053
GdsIntensityReader-class	0.012	0.004	0.046
GdsReader-class	0.047	0.000	0.119
GenotypeData-class	0.161	0.000	0.403
HLA	0.002	0.000	0.002
IntensityData-class	0.039	0.000	0.083
MatrixGenotypeReader-class	0.003	0.000	0.015
NcdfGenotypeReader-class	0.011	0.000	0.028
NcdfIntensityReader-class	0.018	0.000	0.047
NcdfReader-class	0.005	0.000	0.015
ScanAnnotationDataFrame-class	0.066	0.000	0.126
ScanAnnotationSQLite-class	0.050	0.001	0.101
SnpAnnotationDataFrame-class	0.081	0.003	0.184
SnpAnnotationSQLite-class	0.070	0.000	0.139
alleleFrequency	0.190	0.001	0.243
allequal	0.001	0.000	0.001
anomDetectBAF	1.495	0.004	2.286
anomDetectLOH	0.910	0.004	1.408
anomIdentifyLowQuality	0.934	0.000	1.333
anomSegStats	0.266	0.004	0.276
apartSnpSelection	0.063	0.000	0.109
assocCoxPH	0.375	0.007	0.734
assocRegression	0.620	0.004	0.740
assocTestCPH	0.002	0.000	0.001
assocTestFisherExact	0.000	0.004	0.001
assocTestRegression	0.000	0.000	0.003
batchTest	1.163	0.058	1.620
centromeres	0.003	0.000	0.002
chromIntensityPlot	0.079	0.004	0.083
convertNcdfGds	0.214	0.011	0.582
convertVcfGds	0.028	0.000	0.073
createDataFile	0.412	0.000	0.904
duplicateDiscordance	0.485	0.000	0.636
duplicateDiscordanceAcrossDatasets	0.117	0.004	0.126
duplicateDiscordanceProbability	0.001	0.000	0.001
exactHWE	0.046	0.000	0.047
findBAFvariance	0.384	0.000	0.416
gdsSubset	0.026	0.000	0.037
genoClusterPlot	1.526	0.031	2.218
genotypeToCharacter	0.001	0.000	0.001
getobj	0.001	0.000	0.001
gwasExactHW	0.000	0.000	0.001
hetByScanChrom	0.144	0.000	0.165
hetBySnpSex	0.136	0.000	0.188
ibdPlot	0.043	0.000	0.105
imputedDosageFile	0.855	0.008	1.535
intensityOutliersPlot	0.404	0.000	0.800
manhattanPlot	0.017	0.000	0.018
meanIntensityByScanChrom	0.359	0.000	0.369
mendelErr	1.112	0.004	1.554
mendelList	0.010	0.000	0.009
missingGenotypeByScanChrom	0.136	0.000	0.216
missingGenotypeBySnpSex	0.129	0.000	0.263
ncdfSubset	0.040	0.000	0.152
pasteSorted	0.001	0.000	0.001
pcaSnpFilters	0.002	0.000	0.002
pedigreeCheck	0.038	0.000	0.043
pedigreeDeleteDuplicates	0.005	0.000	0.006
pedigreeMaxUnrelated	0.079	0.000	0.145
pedigreePairwiseRelatedness	0.033	0.000	0.033
plinkToNcdf	1.862	0.016	3.262
plinkUtils	2.706	0.011	4.330
pseudoautoIntensityPlot	0.048	0.000	0.091
pseudoautosomal	0.002	0.000	0.003
qqPlot	0.097	0.016	0.218
qualityScoreByScan	0.237	0.000	0.254
qualityScoreBySnp	0.036	0.007	0.082
readWriteFirst	0.003	0.000	0.013
relationsMeanVar	0.002	0.000	0.002
saveas	0.001	0.000	0.001
setMissingGenotypes	0.070	0.001	0.152
simulateGenotypeMatrix	0.493	0.004	1.113
simulateIntensityMatrix	0.254	0.003	0.561
snpCorrelationPlot	0.013	0.000	0.014
snpStats	0.447	0.004	0.627
vcfWrite	7.686	0.241	12.759