BioC 3.5: CHECK report for PureCN on malbec2

Package: PureCN

Version: 1.6.3

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.6.3.tar.gz

StartedAt: 2017-08-16 01:28:48 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:42:16 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 808.9 seconds

RetCode: 0

Status:  OK

CheckDir: PureCN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.6.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/PureCN.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.3’
* 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 ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.7Mb
* 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 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   140.228  0.060 140.321
filterTargets        28.440  0.008  28.361
runAbsoluteCN        26.964  0.004  26.762
findFocal            16.508  0.008  16.420
segmentationCBS      14.616  0.008  14.498
correctCoverageBias  10.572  0.056  10.633
findBestNormal        7.124  0.000   7.126
* 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
  ‘/home/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	1.084	0.008	1.095
calculateBamCoverageByInterval	0.240	0.012	0.253
calculateGCContentByInterval	0.236	0.012	0.250
calculateLogRatio	0.696	0.008	0.705
calculatePowerDetectSomatic	1.804	0.000	1.805
callAlterations	0.176	0.008	0.182
callAlterationsFromSegmentation	1.008	0.008	0.970
callLOH	0.232	0.004	0.239
centromeres	0.004	0.000	0.003
correctCoverageBias	10.572	0.056	10.633
createCurationFile	0.304	0.008	0.312
createNormalDatabase	1.236	0.000	1.236
createSNPBlacklist	0	0	0
createTargetWeights	0.860	0.004	0.864
filterTargets	28.440	0.008	28.361
filterVcfBasic	0.708	0.004	0.712
filterVcfMuTect	0.392	0.000	0.394
findBestNormal	7.124	0.000	7.126
findFocal	16.508	0.008	16.420
getSexFromCoverage	0.140	0.000	0.141
getSexFromVcf	0.188	0.000	0.188
plotAbs	0.904	0.004	0.910
plotBestNormal	1.616	0.004	1.623
poolCoverage	1.608	0.008	1.617
predictSomatic	0.300	0.000	0.301
readCoverageFile	0.160	0.000	0.157
readCurationFile	0.816	0.000	0.818
runAbsoluteCN	26.964	0.004	26.762
segmentationCBS	14.616	0.008	14.498
segmentationPSCBS	140.228	0.060	140.321
setMappingBiasVcf	0.152	0.004	0.156
setPriorVcf	0.164	0.000	0.162