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: 2017-10-18 01:41:23 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:55:13 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 830.1 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 3.4.2 (2017-09-28)
* 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   141.748  0.124 141.872
filterTargets        29.228  0.008  29.157
runAbsoluteCN        27.608  0.004  27.391
findFocal            17.696  0.016  17.605
segmentationCBS      15.204  0.004  15.100
correctCoverageBias  10.676  0.032  10.713
findBestNormal        7.372  0.008   7.386
* 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	1.244	0.012	1.257
calculateBamCoverageByInterval	0.328	0.004	0.332
calculateGCContentByInterval	0.276	0.024	0.300
calculateLogRatio	0.696	0.004	0.699
calculatePowerDetectSomatic	1.372	0.000	1.374
callAlterations	0.108	0.000	0.111
callAlterationsFromSegmentation	0.880	0.004	0.837
callLOH	0.280	0.000	0.281
centromeres	0.004	0.000	0.004
correctCoverageBias	10.676	0.032	10.713
createCurationFile	0.308	0.000	0.307
createNormalDatabase	1.212	0.000	1.213
createSNPBlacklist	0.000	0.000	0.001
createTargetWeights	0.876	0.000	0.876
filterTargets	29.228	0.008	29.157
filterVcfBasic	0.732	0.000	0.731
filterVcfMuTect	0.392	0.000	0.394
findBestNormal	7.372	0.008	7.386
findFocal	17.696	0.016	17.605
getSexFromCoverage	0.152	0.000	0.152
getSexFromVcf	0.208	0.000	0.207
plotAbs	0.756	0.000	0.753
plotBestNormal	2.444	0.004	2.451
poolCoverage	1.664	0.000	1.664
predictSomatic	0.324	0.008	0.332
readCoverageFile	0.144	0.000	0.144
readCurationFile	0.200	0.000	0.199
runAbsoluteCN	27.608	0.004	27.391
segmentationCBS	15.204	0.004	15.100
segmentationPSCBS	141.748	0.124	141.872
setMappingBiasVcf	0.164	0.004	0.171
setPriorVcf	0.152	0.000	0.154