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BioC 2.14: CHECK report for affyQCReport on morelia

This page was generated on 2014-10-08 09:02:33 -0700 (Wed, 08 Oct 2014).

Package 26/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyQCReport 1.42.0
Craig Parman
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/affyQCReport
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: affyQCReport
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affyQCReport_1.42.0.tar.gz
StartedAt: 2014-10-07 21:05:40 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:08:12 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 152.0 seconds
RetCode: 0
Status:  OK 
CheckDir: affyQCReport.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affyQCReport_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/affyQCReport.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyQCReport/DESCRIPTION’ ... OK
* this is package ‘affyQCReport’ version ‘1.42.0’
* 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 ‘affyQCReport’ can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’ ‘Biobase’ ‘lattice’
A package should be listed in only one of these fields.
* 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 ... NOTE
borderQC1: warning in axis(1, label = ArrayIndex, at = seq(1 - 0.5,
  length(ArrayIndex) - 0.5), cex = 0.2): partial argument match of
  'label' to 'labels'
borderQC2: warning in axis(1, label = ArrayIndex, at = seq(1 - 0.5,
  length(ArrayIndex) - 0.5), cex = 0.2): partial argument match of
  'label' to 'labels'
correlationPlot: warning in axis(2, label = as.list(pretty(c, 10)), at
  = seq(0, 1, by = (1/(length(pretty(c, 10)) - 1)))): partial argument
  match of 'label' to 'labels'
correlationPlot: warning in axis(4, label =
  as.list(attr(object@phenoData, which = "varLabels")[1:phenodepth]),
  at = seq(1 - 0.5, phenodepth - 0.5), las = 1): partial argument match
  of 'label' to 'labels'
signalDist: warning in legend(((temppar$xaxp[2] -
  temppar$xaxp[1])/temppar$xaxp[3]) * (temppar$xaxp[3] - 1) +
  temppar$xaxp[1], temppar$yaxp[2], as.character(ArrayIndex), lt =
  1:length(ArrayIndex), col = 1:length(ArrayIndex), cex = 0.5): partial
  argument match of 'lt' to 'lty'
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
correlationPlot 5.507  0.079   5.596
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/affyQCReport.Rcheck/00check.log’
for details.

affyQCReport.Rcheck/00install.out:

* installing *source* package ‘affyQCReport’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affyQCReport)

affyQCReport.Rcheck/affyQCReport-Ex.timings:

nameusersystemelapsed
QCReport0.0000.0000.001
affyQAReport000
borderQC11.1330.0281.163
borderQC20.6390.0080.650
correlationPlot5.5070.0795.596
signalDist4.2590.1064.370
titlePage0.7070.0360.743