BioC 3.3: CHECK report for PureCN on morelia

Package: PureCN

Version: 0.99.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_0.99.9.tar.gz

StartedAt: 2016-04-21 06:19:13 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 06:24:02 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 289.5 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_0.99.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/PureCN.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘0.99.9’
* 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 ... [14s/14s] 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 ... [133s/141s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
segmentationPSCBS 67.751  0.423  76.510
runAbsoluteCN     17.330  0.152  17.485
findFocal         17.116  0.188  17.414
segmentationCBS   14.812  0.137  14.952
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [18s/18s]
 [18s/18s] 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
chr.hash	0.002	0.001	0.003
correctCoverageBias	0.593	0.008	0.600
createCurationFile	0.219	0.008	0.231
createExonWeightFile	0.796	0.018	0.815
createNormalDatabase	1.025	0.006	1.032
createSNPBlacklist	0.001	0.000	0.000
filterVcfBasic	0.704	0.012	0.716
filterVcfMuTect	0.321	0.011	0.331
findBestNormal	1.355	0.023	1.378
findFocal	17.116	0.188	17.414
getSexFromCoverage	0.132	0.002	0.134
plotAbs	0.096	0.006	0.103
plotBestNormal	1.260	0.008	1.269
poolCoverage	1.602	0.024	1.625
predictSomatic	0.096	0.004	0.100
readCoverageGatk	0.132	0.001	0.133
readCurationFile	0.137	0.004	0.142
runAbsoluteCN	17.330	0.152	17.485
segmentationCBS	14.812	0.137	14.952
segmentationPSCBS	67.751	0.423	76.510
setPriorVcf	0.130	0.006	0.135