BioC 3.4: CHECK report for PureCN on malbec1

Package: PureCN

Version: 1.2.3

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.2.3.tar.gz

StartedAt: 2017-04-15 00:35:13 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:45:05 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 591.5 seconds

RetCode: 0

Status:  OK

CheckDir: PureCN.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings PureCN_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/PureCN.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.3’
* 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 ... 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 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 65.184  0.072  65.175
runAbsoluteCN     23.056  0.012  22.947
filterTargets     18.476  0.016  18.424
findFocal         14.820  0.008  14.760
segmentationCBS   11.880  0.000  11.814
* 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: 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
autoCurateResults	0.908	0.016	0.925
bootstrapResults	0.552	0.000	0.552
calculateBamCoverageByInterval	0.072	0.000	0.074
calculateGCContentByInterval	0.040	0.000	0.039
calculateLogRatio	0.304	0.000	0.301
calculatePowerDetectSomatic	1.440	0.008	1.447
callAlterations	0.116	0.008	0.125
callAlterationsFromSegmentation	1.024	0.000	0.974
callLOH	0.152	0.000	0.154
centromeres	0.004	0.000	0.002
correctCoverageBias	0.264	0.004	0.270
createCurationFile	0.320	0.008	0.329
createNormalDatabase	0.956	0.000	0.954
createSNPBlacklist	0.000	0.000	0.001
createTargetWeights	0.772	0.004	0.774
filterTargets	18.476	0.016	18.424
filterVcfBasic	0.276	0.012	0.287
filterVcfMuTect	0.304	0.000	0.304
findBestNormal	1.328	0.000	1.329
findFocal	14.820	0.008	14.760
getDiploid	0.108	0.000	0.107
getSexFromCoverage	0.164	0.000	0.162
getSexFromVcf	0.312	0.004	0.317
plotAbs	0.268	0.004	0.274
plotBestNormal	1.488	0.000	1.486
poolCoverage	1.364	0.004	1.371
predictSomatic	0.380	0.000	0.381
readCoverageGatk	0.140	0.000	0.139
readCurationFile	0.268	0.004	0.270
runAbsoluteCN	23.056	0.012	22.947
segmentationCBS	11.880	0.000	11.814
segmentationPSCBS	65.184	0.072	65.175
setMappingBiasVcf	0.156	0.004	0.161
setPriorVcf	0.156	0.004	0.160