Package: HTqPCR

Version: 1.13.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTqPCR_1.13.1.tar.gz

StartedAt: 2013-03-25 03:05:33 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:07:26 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 112.6 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/HTqPCR.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 ... [8s/8s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
setCategory 6.727  0.279   7.018
* 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
  '/Users/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	4.271	0.080	4.359
cbind	0.112	0.014	0.130
changeCtLayout	0.144	0.013	0.158
clusterCt	0.298	0.043	0.345
filterCategory	0.114	0.012	0.125
filterCtData	0.306	0.021	0.328
heatmapSig	1.442	0.034	1.478
limmaCtData	0.727	0.030	0.758
mannwhitneyCtData	1.250	0.011	1.261
normalizeCtData	0.440	0.053	0.500
plotCVBoxes	0.201	0.016	0.218
plotCtArray	0.135	0.018	0.154
plotCtBoxes	0.065	0.013	0.080
plotCtCard	0.077	0.020	0.100
plotCtCategory	2.950	0.042	2.995
plotCtCor	0.142	0.010	0.153
plotCtDensity	0.043	0.012	0.058
plotCtHeatmap	2.236	0.039	2.280
plotCtHistogram	0.025	0.010	0.035
plotCtOverview	0.141	0.024	0.165
plotCtPCA	0.049	0.015	0.065
plotCtPairs	0.646	0.023	0.674
plotCtRQ	0.357	0.018	0.379
plotCtReps	0.136	0.015	0.152
plotCtScatter	0.034	0.013	0.049
plotCtSignificance	0.505	0.024	0.618
plotCtVariation	0.731	0.033	0.829
plotGenes	0.035	0.014	0.063
qPCRpros	0.009	0.006	0.015
qPCRraw	0.010	0.005	0.014
qPCRset-class	0.090	0.019	0.109
readCtData	0.137	0.014	0.151
setCategory	6.727	0.279	7.018
ttestCtData	1.108	0.011	1.119