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BioC 3.2: CHECK report for QDNAseq on oaxaca

This page was generated on 2016-04-23 10:27:40 -0700 (Sat, 23 Apr 2016).

Package 820/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QDNAseq 1.6.1
Daoud Sie
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/QDNAseq
Last Changed Rev: 111627 / Revision: 116712
Last Changed Date: 2015-12-18 02:52:38 -0800 (Fri, 18 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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 UNNEEDED, same version exists in internal repository

Summary

Package: QDNAseq
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QDNAseq_1.6.1.tar.gz
StartedAt: 2016-04-23 03:21:38 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 03:25:10 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 211.9 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_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/QDNAseq.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.6.1’
* 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 ... [12s/14s] 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 ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::.showAnnotatedDataFrame’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2adhoc’ ‘sqrtadhoc’
* 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 ... [54s/56s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
frequencyPlot          13.991  0.157  14.361
callBins               13.616  0.143  14.466
normalizeSegmentedBins  5.865  0.080   5.948
segmentBins             5.266  0.057   5.325
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QDNAseq,reproducibility.R’ [8s/8s]
  Running ‘QDNAseq.R’ [14s/15s]
 [22s/24s] 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-3.2-bioc/meat/QDNAseq.Rcheck/00check.log’
for details.


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
addPhenodata0.2080.0110.220
applyFilters0.4190.0090.429
binReadCounts000
callBins13.616 0.14314.466
compareToReference1.1400.0521.192
correctBins0.8490.0410.892
createBins0.0010.0000.001
estimateCorrection0.8140.0400.854
exportBins0.0000.0000.001
frequencyPlot13.991 0.15714.361
getBinAnnotations0.0010.0010.001
highlightFilters0.4950.0460.549
isobarPlot0.9070.0310.961
makeCgh0.9360.0540.990
noisePlot0.7430.0360.780
normalizeBins0.7630.0340.797
normalizeSegmentedBins5.8650.0805.948
plot0.8710.0510.924
poolRuns0.1600.0090.170
segmentBins5.2660.0575.325
smoothOutlierBins0.8310.0390.870