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BioC 3.5: CHECK report for PureCN on toluca2

This page was generated on 2017-04-23 14:41:38 -0400 (Sun, 23 Apr 2017).

Package 1026/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PureCN 1.5.75
Markus Riester
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN
Last Changed Rev: 129033 / Revision: 129046
Last Changed Date: 2017-04-21 19:10:34 -0400 (Fri, 21 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PureCN
Version: 1.5.75
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PureCN_1.5.75.tar.gz
StartedAt: 2017-04-23 08:19:47 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 08:38:23 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 1116.7 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_1.5.75.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PureCN.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.5.75’
* 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  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.3Mb
* 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   158.138  0.788 160.223
runAbsoluteCN        38.837  0.341  39.584
filterTargets        34.894  0.246  35.444
findFocal            24.794  0.182  25.130
segmentationCBS      21.425  0.176  21.746
correctCoverageBias  16.277  0.227  16.631
findBestNormal       12.375  0.054  12.485
* 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-3.5-bioc/meat/PureCN.Rcheck/00check.log’
for details.


PureCN.Rcheck/00install.out:

* 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)

PureCN.Rcheck/PureCN-Ex.timings:

nameusersystemelapsed
bootstrapResults1.4910.0521.556
calculateBamCoverageByInterval0.4280.0230.455
calculateGCContentByInterval0.4400.0210.467
calculateLogRatio1.1930.0131.241
calculatePowerDetectSomatic2.3330.0092.470
callAlterations0.1400.0090.151
callAlterationsFromSegmentation0.9810.0171.002
callLOH0.2040.0080.214
centromeres0.0030.0050.008
correctCoverageBias16.277 0.22716.631
createCurationFile0.3540.0130.369
createNormalDatabase1.9310.0071.942
createSNPBlacklist0.0010.0000.001
createTargetWeights1.3550.0071.374
filterTargets34.894 0.24635.444
filterVcfBasic1.0860.0111.103
filterVcfMuTect0.5550.0040.565
findBestNormal12.375 0.05412.485
findFocal24.794 0.18225.130
getSexFromCoverage0.2660.0020.268
getSexFromVcf0.2500.0080.258
plotAbs1.0840.0101.101
plotBestNormal2.8050.0142.836
poolCoverage2.7060.0112.726
predictSomatic0.4160.0140.433
readCoverageFile0.2530.0010.255
readCurationFile0.2470.0120.261
runAbsoluteCN38.837 0.34139.584
segmentationCBS21.425 0.17621.746
segmentationPSCBS158.138 0.788160.223
setMappingBiasVcf0.2170.0090.226
setPriorVcf0.2180.0030.222