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BioC 2.13: CHECK report for affyQCReport on moscato1

This page was generated on 2014-04-05 09:49:13 -0700 (Sat, 05 Apr 2014).

Package 25/750HostnameOS / ArchBUILDCHECKBUILD BIN
affyQCReport 1.40.0
Craig Parman
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/affyQCReport
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: affyQCReport
Version: 1.40.0
Command: rm -rf affyQCReport.buildbin-libdir && mkdir affyQCReport.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyQCReport.buildbin-libdir affyQCReport_1.40.0.tar.gz >affyQCReport-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=affyQCReport.buildbin-libdir --install="check:affyQCReport-install.out" --force-multiarch --no-vignettes --timings affyQCReport_1.40.0.tar.gz && mv affyQCReport.buildbin-libdir/* affyQCReport.Rcheck/ && rmdir affyQCReport.buildbin-libdir
StartedAt: 2014-04-05 02:04:58 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:08:50 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 231.1 seconds
RetCode: 0
Status:  OK  
CheckDir: affyQCReport.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/affyQCReport.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyQCReport/DESCRIPTION' ... OK
* this is package 'affyQCReport' version '1.40.0'
* 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 whether package 'affyQCReport' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'affyQCReport.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [24s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
correlationPlot 6.26   0.09    6.35
signalDist      5.07   0.10    5.16
** running examples for arch 'x64' ... [27s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
correlationPlot 6.79   0.18    6.98
signalDist      4.88   0.19    5.07
* 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 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/affyQCReport.Rcheck/00check.log'
for details.

affyQCReport.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'affyQCReport' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyQCReport' as affyQCReport_1.40.0.zip
* DONE (affyQCReport)

affyQCReport.Rcheck/examples_i386/affyQCReport-Ex.timings:

nameusersystemelapsed
QCReport0.010.000.01
affyQAReport0.020.000.02
borderQC11.630.051.67
borderQC20.880.010.89
correlationPlot6.260.096.35
signalDist5.070.105.16
titlePage0.720.010.73

affyQCReport.Rcheck/examples_x64/affyQCReport-Ex.timings:

nameusersystemelapsed
QCReport0.000.010.02
affyQAReport000
borderQC11.920.071.98
borderQC20.840.031.10
correlationPlot6.790.186.98
signalDist4.880.195.07
titlePage0.580.000.58