BioC 3.5: CHECK report for PureCN on oaxaca

Package: PureCN

Version: 1.5.47

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.5.47.tar.gz

StartedAt: 2017-03-04 07:25:49 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:42:08 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 978.8 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_1.5.47.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PureCN.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.5.47’
* 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 ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   2.3Mb
* 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   146.503  0.725 156.226
runAbsoluteCN        32.564  0.260  32.842
filterTargets        31.517  0.243  31.847
findFocal            20.616  0.177  20.805
segmentationCBS      16.501  0.145  16.656
correctCoverageBias  14.956  0.136  15.097
findBestNormal       10.706  0.044  10.752
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/PureCN.Rcheck/00check.log’
for details.

* installing *source* package ‘PureCN’ ...
** R
** data
** inst
** byte-compile and prepare 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
bootstrapResults	1.161	0.040	1.201
calculateBamCoverageByInterval	0.281	0.013	0.294
calculateGCContentByInterval	0.463	0.031	0.495
calculateLogRatio	1.198	0.013	1.213
calculatePowerDetectSomatic	1.852	0.006	1.896
callAlterations	0.140	0.008	0.150
callAlterationsFromSegmentation	0.788	0.013	0.802
callLOH	0.187	0.005	0.192
centromeres	0.001	0.003	0.005
correctCoverageBias	14.956	0.136	15.097
createCurationFile	0.346	0.012	0.362
createNormalDatabase	1.609	0.004	1.614
createSNPBlacklist	0.001	0.000	0.001
createTargetWeights	1.305	0.009	1.315
filterTargets	31.517	0.243	31.847
filterVcfBasic	0.947	0.015	0.962
filterVcfMuTect	0.558	0.007	0.565
findBestNormal	10.706	0.044	10.752
findFocal	20.616	0.177	20.805
getSexFromCoverage	0.202	0.001	0.204
getSexFromVcf	0.172	0.006	0.177
plotAbs	0.878	0.010	0.890
plotBestNormal	2.164	0.011	2.175
poolCoverage	2.498	0.009	2.507
predictSomatic	0.353	0.009	0.362
readCoverageGatk	0.288	0.002	0.291
readCurationFile	0.293	0.014	0.308
runAbsoluteCN	32.564	0.260	32.842
segmentationCBS	16.501	0.145	16.656
segmentationPSCBS	146.503	0.725	156.226
setMappingBiasVcf	0.195	0.008	0.202
setPriorVcf	0.213	0.003	0.216