BioC 3.4: CHECK report for PureCN on zin1

Package: PureCN

Version: 1.1.50

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.1.50.tar.gz

StartedAt: 2016-09-20 10:54:34 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:05:23 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 648.1 seconds

RetCode: 0

Status:  OK

CheckDir: PureCN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.1.50.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/PureCN.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PureCN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PureCN’ version ‘1.1.50’
* 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 ‘PureCN’ can be installed ... 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
filterTargets   23.696  0.032  23.812
runAbsoluteCN   23.376  0.004  23.414
findFocal       23.056  0.012  23.145
segmentationCBS 15.916  0.008  15.991
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: OK

* installing *source* package ‘PureCN’ ...
** 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 (PureCN)

name	user	system	elapsed
autoCurateResults	0.668	0.008	0.676
bootstrapResults	0.996	0.004	1.002
calculateBamCoverageByInterval	0.084	0.000	0.084
calculateGCContentByInterval	0.032	0.000	0.035
calculateLogRatio	0.212	0.004	0.215
calculatePowerDetectSomatic	1.896	0.036	1.940
callAlterations	0.128	0.004	0.134
callLOH	0.220	0.004	0.222
centromeres	0.004	0.000	0.002
correctCoverageBias	0.616	0.004	0.621
createCurationFile	0.336	0.000	0.339
createNormalDatabase	1.076	0.000	1.073
createSNPBlacklist	0	0	0
createTargetWeights	0.764	0.004	0.769
filterTargets	23.696	0.032	23.812
filterVcfBasic	0.300	0.004	0.302
filterVcfMuTect	0.300	0.004	0.302
findBestNormal	1.152	0.004	1.160
findFocal	23.056	0.012	23.145
getDiploid	0.108	0.000	0.111
getSexFromCoverage	0.100	0.000	0.102
getSexFromVcf	0.196	0.004	0.203
plotAbs	0.180	0.004	0.187
plotBestNormal	1.380	0.000	1.382
poolCoverage	1.396	0.000	1.400
predictSomatic	0.392	0.000	0.404
readCoverageGatk	0.120	0.000	0.121
readCurationFile	0.212	0.008	0.221
runAbsoluteCN	23.376	0.004	23.414
segmentationCBS	15.916	0.008	15.991
segmentationPSCBS	0.004	0.000	0.003
setMappingBiasVcf	0.144	0.008	0.152
setPriorVcf	0.156	0.008	0.167