Package: affyQCReport

Version: 1.36.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings affyQCReport_1.36.0.tar.gz

StartedAt: 2013-03-24 23:04:54 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:08:03 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 188.9 seconds

RetCode: 0

Status:  OK

CheckDir: affyQCReport.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/affyQCReport.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyQCReport/DESCRIPTION’ ... OK
* this is package ‘affyQCReport’ version ‘1.36.0’
* 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 whether package ‘affyQCReport’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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 examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
correlationPlot 9.921  0.072  10.002
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/affyQCReport.Rcheck/00check.log’
for details.

* installing *source* package ‘affyQCReport’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: geneNames
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘affyQCReport.Rnw’ 
** testing if installed package can be loaded
No methods found in "Biobase" for requests: geneNames

* DONE (affyQCReport)

name	user	system	elapsed
QCReport	0	0	0
affyQAReport	0.000	0.000	0.001
borderQC1	1.484	0.040	1.562
borderQC2	0.732	0.016	0.751
correlationPlot	9.921	0.072	10.002
signalDist	4.208	0.060	4.374
titlePage	0.396	0.004	0.401