BioC 3.4: CHECK report for PureCN on morelia

Package: PureCN

Version: 1.1.50

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.1.50.tar.gz

StartedAt: 2016-09-20 11:34:09 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:42:30 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 501.1 seconds

RetCode: 0

Status:  OK

CheckDir: PureCN.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.1.50.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/PureCN.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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   15.920  0.121  16.095
findFocal       13.387  0.079  13.471
runAbsoluteCN   12.742  0.089  12.848
segmentationCBS 11.383  0.098  11.523
* 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	0.723	0.031	0.754
bootstrapResults	0.881	0.022	0.904
calculateBamCoverageByInterval	0.080	0.005	0.086
calculateGCContentByInterval	0.036	0.002	0.038
calculateLogRatio	0.398	0.007	0.405
calculatePowerDetectSomatic	1.642	0.039	1.682
callAlterations	0.138	0.012	0.151
callLOH	0.191	0.007	0.199
centromeres	0.002	0.006	0.008
correctCoverageBias	0.331	0.005	0.335
createCurationFile	0.365	0.014	0.383
createNormalDatabase	1.653	0.015	1.670
createSNPBlacklist	0.001	0.000	0.000
createTargetWeights	0.861	0.008	0.871
filterTargets	15.920	0.121	16.095
filterVcfBasic	0.270	0.005	0.274
filterVcfMuTect	0.268	0.007	0.275
findBestNormal	1.325	0.009	1.335
findFocal	13.387	0.079	13.471
getDiploid	0.100	0.007	0.106
getSexFromCoverage	0.161	0.001	0.162
getSexFromVcf	0.292	0.011	0.304
plotAbs	0.202	0.014	0.216
plotBestNormal	1.839	0.011	1.851
poolCoverage	1.569	0.007	1.575
predictSomatic	0.341	0.012	0.352
readCoverageGatk	0.174	0.002	0.176
readCurationFile	0.194	0.011	0.204
runAbsoluteCN	12.742	0.089	12.848
segmentationCBS	11.383	0.098	11.523
segmentationPSCBS	0.003	0.000	0.004
setMappingBiasVcf	0.181	0.003	0.186
setPriorVcf	0.168	0.003	0.171