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BioC 3.4: CHECK report for PureCN on morelia

This page was generated on 2016-09-21 03:55:57 -0700 (Wed, 21 Sep 2016).

Package 941/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PureCN 1.1.50
Markus Riester
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN
Last Changed Rev: 121142 / Revision: 121152
Last Changed Date: 2016-09-19 09:27:55 -0700 (Mon, 19 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK YES, new version is higher than in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK YES, new version is higher than in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK YES, new version is higher than in internal repository

Summary

Package: PureCN
Version: 1.1.50
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.1.50.tar.gz
StartedAt: 2016-09-20 11:34:09 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:42:30 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 501.1 seconds
RetCode: 0
Status:  OK 
CheckDir: PureCN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.1.50.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/PureCN.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.50’
* 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 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
filterTargets   15.920  0.121  16.095
findFocal       13.387  0.079  13.471
runAbsoluteCN   12.742  0.089  12.848
segmentationCBS 11.383  0.098  11.523
* 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

PureCN.Rcheck/00install.out:

* 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)

PureCN.Rcheck/PureCN-Ex.timings:

nameusersystemelapsed
autoCurateResults0.7230.0310.754
bootstrapResults0.8810.0220.904
calculateBamCoverageByInterval0.0800.0050.086
calculateGCContentByInterval0.0360.0020.038
calculateLogRatio0.3980.0070.405
calculatePowerDetectSomatic1.6420.0391.682
callAlterations0.1380.0120.151
callLOH0.1910.0070.199
centromeres0.0020.0060.008
correctCoverageBias0.3310.0050.335
createCurationFile0.3650.0140.383
createNormalDatabase1.6530.0151.670
createSNPBlacklist0.0010.0000.000
createTargetWeights0.8610.0080.871
filterTargets15.920 0.12116.095
filterVcfBasic0.2700.0050.274
filterVcfMuTect0.2680.0070.275
findBestNormal1.3250.0091.335
findFocal13.387 0.07913.471
getDiploid0.1000.0070.106
getSexFromCoverage0.1610.0010.162
getSexFromVcf0.2920.0110.304
plotAbs0.2020.0140.216
plotBestNormal1.8390.0111.851
poolCoverage1.5690.0071.575
predictSomatic0.3410.0120.352
readCoverageGatk0.1740.0020.176
readCurationFile0.1940.0110.204
runAbsoluteCN12.742 0.08912.848
segmentationCBS11.383 0.09811.523
segmentationPSCBS0.0030.0000.004
setMappingBiasVcf0.1810.0030.186
setPriorVcf0.1680.0030.171