Package: HTqPCR

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTqPCR_1.14.0.tar.gz

StartedAt: 2013-05-01 06:52:11 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:54:24 -0700 (Wed, 01 May 2013)

EllapsedTime: 132.9 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/HTqPCR.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'HTqPCR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTqPCR' version '1.14.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'HTqPCR' can be installed ... [8s/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 ... [39s/41s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setCategory    8.876  0.442   9.526
plotCtCategory 5.865  0.124   6.069
HTqPCR-package 5.356  0.104   5.990
* 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
** testing if installed package can be loaded
* DONE (HTqPCR)

name	user	system	elapsed
HTqPCR-package	5.356	0.104	5.990
cbind	0.243	0.003	0.246
changeCtLayout	0.173	0.006	0.188
clusterCt	0.454	0.034	0.511
filterCategory	0.114	0.007	0.121
filterCtData	0.268	0.008	0.277
heatmapSig	1.649	0.029	1.863
limmaCtData	0.889	0.024	1.054
mannwhitneyCtData	1.516	0.012	1.541
normalizeCtData	0.572	0.025	0.609
plotCVBoxes	0.244	0.010	0.270
plotCtArray	0.224	0.012	0.242
plotCtBoxes	0.095	0.007	0.105
plotCtCard	0.109	0.009	0.131
plotCtCategory	5.865	0.124	6.069
plotCtCor	0.067	0.007	0.089
plotCtDensity	0.080	0.006	0.094
plotCtHeatmap	2.810	0.079	2.995
plotCtHistogram	0.032	0.008	0.042
plotCtOverview	0.195	0.017	0.222
plotCtPCA	0.066	0.010	0.082
plotCtPairs	0.736	0.018	0.858
plotCtRQ	0.421	0.012	0.439
plotCtReps	0.167	0.009	0.178
plotCtScatter	0.044	0.007	0.053
plotCtSignificance	0.805	0.055	0.872
plotCtVariation	0.784	0.026	0.833
plotGenes	0.045	0.010	0.059
qPCRpros	0.013	0.005	0.019
qPCRraw	0.016	0.005	0.021
qPCRset-class	0.119	0.016	0.138
readCtData	0.248	0.013	0.264
setCategory	8.876	0.442	9.526
ttestCtData	1.163	0.017	1.191