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BioC 3.5: CHECK report for QDNAseq on oaxaca

This page was generated on 2017-03-04 16:47:06 -0500 (Sat, 04 Mar 2017).

Package 1000/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QDNAseq 1.11.0
Daoud Sie
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QDNAseq
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: QDNAseq
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.11.0.tar.gz
StartedAt: 2017-03-04 07:31:42 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 07:35:12 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 210.3 seconds
RetCode: 0
Status:  OK 
CheckDir: QDNAseq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.11.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/QDNAseq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QDNAseq/DESCRIPTION’ ... OK
* this is package ‘QDNAseq’ version ‘1.11.0’
* 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 ‘QDNAseq’ 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 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
frequencyPlot          15.236  0.237  15.479
callBins               14.606  0.220  14.831
normalizeSegmentedBins  6.020  0.118   6.140
segmentBins             5.689  0.086   5.779
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QDNAseq,reproducibility.R’
  Running ‘QDNAseq.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

QDNAseq.Rcheck/00install.out:

* installing *source* package ‘QDNAseq’ ...
** 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 (QDNAseq)

QDNAseq.Rcheck/QDNAseq-Ex.timings:

nameusersystemelapsed
addPhenodata0.1220.0100.132
applyFilters0.1740.0110.185
binReadCounts000
callBins14.606 0.22014.831
compareToReference1.4130.0631.477
correctBins0.7000.0340.735
createBins0.0010.0000.001
estimateCorrection0.6690.0310.701
exportBins0.0010.0010.001
frequencyPlot15.236 0.23715.479
getBinAnnotations000
highlightFilters0.6510.0550.722
isobarPlot0.6130.0230.646
makeCgh0.8670.0590.926
noisePlot0.8860.0450.932
normalizeBins0.5880.0350.623
normalizeSegmentedBins6.0200.1186.140
plot1.2460.0721.319
poolRuns0.2340.0150.249
segmentBins5.6890.0865.779
smoothOutlierBins0.6590.0470.705