BioC 3.4: CHECK report for PureCN on morelia

Package: PureCN

Version: 1.2.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.2.3.tar.gz

StartedAt: 2017-04-15 06:35:39 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 06:47:38 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 718.4 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_1.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/PureCN.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.3’
* 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
segmentationPSCBS 69.449  0.374  80.769
runAbsoluteCN     27.544  0.222  27.794
filterTargets     16.927  0.165  17.184
findFocal         16.690  0.146  16.853
segmentationCBS   13.572  0.115  13.705
* 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	1.299	0.044	1.344
bootstrapResults	0.893	0.026	0.919
calculateBamCoverageByInterval	0.103	0.001	0.104
calculateGCContentByInterval	0.046	0.003	0.049
calculateLogRatio	0.483	0.005	0.488
calculatePowerDetectSomatic	1.848	0.028	1.879
callAlterations	0.167	0.011	0.179
callAlterationsFromSegmentation	1.112	0.011	1.123
callLOH	0.191	0.007	0.198
centromeres	0.002	0.005	0.008
correctCoverageBias	0.468	0.008	0.476
createCurationFile	0.386	0.017	0.407
createNormalDatabase	1.574	0.045	1.622
createSNPBlacklist	0.000	0.000	0.001
createTargetWeights	1.321	0.015	1.338
filterTargets	16.927	0.165	17.184
filterVcfBasic	0.384	0.008	0.392
filterVcfMuTect	0.400	0.004	0.404
findBestNormal	1.850	0.012	1.863
findFocal	16.690	0.146	16.853
getDiploid	0.126	0.006	0.133
getSexFromCoverage	0.263	0.002	0.267
getSexFromVcf	0.260	0.009	0.269
plotAbs	0.242	0.015	0.257
plotBestNormal	2.320	0.012	2.335
poolCoverage	2.308	0.025	2.334
predictSomatic	0.545	0.009	0.555
readCoverageGatk	0.242	0.001	0.244
readCurationFile	0.281	0.009	0.291
runAbsoluteCN	27.544	0.222	27.794
segmentationCBS	13.572	0.115	13.705
segmentationPSCBS	69.449	0.374	80.769
setMappingBiasVcf	0.239	0.010	0.249
setPriorVcf	0.195	0.002	0.198