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: 2013-03-24 06:35:12 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 06:37:24 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 131.3 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 beta (2013-03-21 r62346)
* 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 '1.13.1'
* 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/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/40s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setCategory    8.822  0.299   9.189
HTqPCR-package 5.406  0.091   5.634
plotCtCategory 5.268  0.103   5.381
* 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	5.406	0.091	5.634
cbind	0.269	0.005	0.275
changeCtLayout	0.194	0.009	0.203
clusterCt	0.461	0.023	0.495
filterCategory	0.105	0.003	0.108
filterCtData	0.280	0.009	0.293
heatmapSig	1.511	0.038	1.555
limmaCtData	0.916	0.025	0.940
mannwhitneyCtData	1.551	0.006	1.559
normalizeCtData	0.631	0.026	0.669
plotCVBoxes	0.396	0.009	0.413
plotCtArray	0.199	0.009	0.228
plotCtBoxes	0.080	0.007	0.088
plotCtCard	0.091	0.010	0.106
plotCtCategory	5.268	0.103	5.381
plotCtCor	0.062	0.008	0.072
plotCtDensity	0.053	0.007	0.064
plotCtHeatmap	2.785	0.113	2.923
plotCtHistogram	0.029	0.007	0.038
plotCtOverview	0.170	0.016	0.190
plotCtPCA	0.062	0.008	0.073
plotCtPairs	0.782	0.022	0.813
plotCtRQ	0.448	0.012	0.467
plotCtReps	0.169	0.011	0.183
plotCtScatter	0.042	0.008	0.054
plotCtSignificance	0.609	0.015	0.627
plotCtVariation	0.839	0.020	0.870
plotGenes	0.049	0.009	0.065
qPCRpros	0.013	0.004	0.017
qPCRraw	0.173	0.003	0.177
qPCRset-class	0.097	0.015	0.115
readCtData	0.247	0.013	0.261
setCategory	8.822	0.299	9.189
ttestCtData	1.400	0.020	1.425