Package: HTqPCR

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTqPCR_1.12.0.tar.gz

StartedAt: 2013-03-25 00:01:32 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:03:14 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 101.5 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/HTqPCR.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.12.0'
* 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 'HTqPCR' 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
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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
setCategory 7.279  0.307   7.653
* 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-2.11-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	4.154	0.070	4.243
cbind	0.181	0.004	0.184
changeCtLayout	0.134	0.008	0.143
clusterCt	0.385	0.047	0.440
filterCategory	0.084	0.008	0.093
filterCtData	0.224	0.011	0.235
heatmapSig	1.235	0.024	1.269
limmaCtData	0.725	0.019	0.751
mannwhitneyCtData	1.179	0.004	1.185
normalizeCtData	0.431	0.044	0.486
plotCVBoxes	0.178	0.008	0.188
plotCtArray	0.205	0.012	0.218
plotCtBoxes	0.048	0.006	0.054
plotCtCard	0.056	0.010	0.067
plotCtCategory	3.813	0.054	3.961
plotCtCor	0.047	0.006	0.056
plotCtDensity	0.038	0.008	0.046
plotCtHeatmap	2.285	0.049	2.358
plotCtHistogram	0.022	0.004	0.029
plotCtOverview	0.130	0.016	0.151
plotCtPCA	0.042	0.009	0.051
plotCtPairs	0.590	0.020	0.614
plotCtRQ	0.343	0.010	0.356
plotCtReps	0.121	0.006	0.127
plotCtScatter	0.027	0.006	0.033
plotCtSignificance	0.460	0.024	0.486
plotCtVariation	0.670	0.023	0.704
plotGenes	0.026	0.007	0.039
qPCRpros	0.006	0.001	0.006
qPCRraw	0.006	0.001	0.006
qPCRset-class	0.080	0.004	0.085
readCtData	0.131	0.005	0.141
setCategory	7.279	0.307	7.653
ttestCtData	0.923	0.005	0.933