BioC 2.12: CHECK report for HTqPCR on george2

Package: HTqPCR

Version: 1.13.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings HTqPCR_1.13.1.tar.gz

StartedAt: 2013-03-25 02:23:33 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:25:56 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 142.8 seconds

RetCode: 0

Status: OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/HTqPCR.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTqPCR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTqPCR’ version ‘1.13.1’
* 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 ‘HTqPCR’ can be installed ... [9s/9s] OK
* checking installed package size ... OK
* checking package 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 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
heatmapSig: warning in heatmap.2(data, trace = "none", density.info =
  "none", col = col, distfun = d, breaks = b, mar = mar, ...): partial
  argument match of 'mar' to 'margins'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
  partial argument match of 'n' to 'number'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
  partial argument match of 'sort' to 'sort.by'
plotCtCor: warning in heatmap.2(x, col = col, breaks = b, scale =
  "none", dendrogram = "row", trace = "none", main = main, density.info
  = "none", mar = mar, ...): partial argument match of 'mar' to
  'margins'
plotCtHeatmap: warning in heatmap.2(data, trace = "none", density.info
  = "none", main = main, col = col, distfun = d, breaks = breaks, mar =
  mar, ...): partial argument match of 'mar' to 'margins'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
  SD[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra = 0.001):
  partial argument match of 'sfra' to 'sfrac'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
  SD.ratio[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra =
  0.001): partial argument match of 'sfra' to 'sfrac'
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [45s/47s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
setCategory    10.388  0.008  10.630
plotCtCategory  7.156  0.080   7.453
HTqPCR-package  6.844  0.068   7.107
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/HTqPCR.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
HTqPCR-package	6.844	0.068	7.107
cbind	0.204	0.000	0.202
changeCtLayout	0.508	0.012	0.522
clusterCt	0.452	0.004	0.461
filterCategory	0.116	0.000	0.140
filterCtData	0.280	0.004	0.308
heatmapSig	1.996	0.024	2.082
limmaCtData	1.012	0.012	1.026
mannwhitneyCtData	1.713	0.000	1.838
normalizeCtData	0.684	0.012	0.774
plotCVBoxes	0.236	0.004	0.242
plotCtArray	0.240	0.000	0.239
plotCtBoxes	0.304	0.000	0.306
plotCtCard	0.092	0.000	0.095
plotCtCategory	7.156	0.080	7.453
plotCtCor	0.064	0.008	0.071
plotCtDensity	0.056	0.012	0.069
plotCtHeatmap	3.176	0.020	3.559
plotCtHistogram	0.024	0.012	0.036
plotCtOverview	0.184	0.004	0.187
plotCtPCA	0.068	0.000	0.067
plotCtPairs	0.808	0.012	0.819
plotCtRQ	0.476	0.012	0.488
plotCtReps	0.188	0.000	0.188
plotCtScatter	0.052	0.000	0.051
plotCtSignificance	0.688	0.012	0.703
plotCtVariation	0.913	0.012	0.924
plotGenes	0.060	0.000	0.061
qPCRpros	0.008	0.000	0.010
qPCRraw	0.012	0.004	0.015
qPCRset-class	0.144	0.000	0.143
readCtData	0.180	0.008	0.190
setCategory	10.388	0.008	10.630
ttestCtData	1.264	0.000	1.266

Summary

Command output