BioC 3.6: CHECK report for PureCN on veracruz1

Package: PureCN

Version: 1.7.44

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.7.44.tar.gz

StartedAt: 2017-08-16 07:07:31 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:25:31 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 1080.3 seconds

RetCode: 0

Status:  OK

CheckDir: PureCN.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.7.44.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PureCN.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.7.44’
* 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  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.9Mb
* 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   142.750  0.736 147.084
runAbsoluteCN        35.558  0.732  35.549
filterTargets        29.862  0.344  30.515
findFocal            22.429  0.304  22.837
correctCoverageBias  21.034  0.125  21.776
segmentationCBS      19.089  0.307  19.281
findBestNormal       12.157  0.048  12.490
annotateTargets       8.376  0.448   9.446
* 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-3.6-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
annotateTargets	8.376	0.448	9.446
bootstrapResults	0.636	0.039	0.698
calculateBamCoverageByInterval	0.497	0.004	0.509
calculateGCContentByInterval	0.499	0.022	0.537
calculateLogRatio	1.111	0.018	1.153
calculatePowerDetectSomatic	1.726	0.010	1.803
callAlterations	0.192	0.010	0.208
callAlterationsFromSegmentation	2.539	0.070	2.492
callLOH	0.218	0.006	0.234
callMutationBurden	1.528	0.010	1.564
centromeres	0.002	0.004	0.007
correctCoverageBias	21.034	0.125	21.776
createCurationFile	0.404	0.014	0.451
createNormalDatabase	2.053	0.004	2.122
createTargetWeights	1.917	0.008	1.991
filterTargets	29.862	0.344	30.515
filterVcfBasic	0.890	0.009	0.936
filterVcfMuTect	0.540	0.004	0.545
filterVcfMuTect2	0.546	0.005	0.561
findBestNormal	12.157	0.048	12.490
findFocal	22.429	0.304	22.837
getSexFromCoverage	0.399	0.001	0.410
getSexFromVcf	0.218	0.007	0.240
plotAbs	1.011	0.009	1.046
plotBestNormal	3.582	0.014	3.697
poolCoverage	3.764	0.027	3.895
predictSomatic	0.467	0.008	0.483
readCoverageFile	0.369	0.013	0.390
readCurationFile	0.287	0.008	0.300
runAbsoluteCN	35.558	0.732	35.549
segmentationCBS	19.089	0.307	19.281
segmentationPSCBS	142.750	0.736	147.084
setMappingBiasVcf	0.197	0.008	0.208
setPriorVcf	0.191	0.003	0.198