Package: HTqPCR

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTqPCR_1.11.0.tar.gz

StartedAt: 2012-06-21 00:56:13 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:58:22 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 129.1 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 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.11.0'
* 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 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
* 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	5.432	0.065	5.857
cbind	0.235	0.004	0.239
changeCtLayout	0.176	0.010	0.192
clusterCt	0.415	0.055	0.477
filterCategory	0.109	0.007	0.120
filterCtData	0.296	0.009	0.310
heatmapSig	1.668	0.022	1.720
limmaCtData	1.001	0.016	1.024
mannwhitneyCtData	1.623	0.007	1.658
normalizeCtData	0.562	0.042	0.629
plotCVBoxes	0.251	0.009	0.268
plotCtArray	0.266	0.012	0.286
plotCtBoxes	0.067	0.006	0.076
plotCtCard	0.081	0.012	0.102
plotCtCategory	4.362	0.057	4.474
plotCtCor	0.067	0.005	0.073
plotCtDensity	0.056	0.009	0.065
plotCtHeatmap	2.991	0.045	3.085
plotCtHistogram	0.029	0.005	0.050
plotCtOverview	0.124	0.010	0.146
plotCtPCA	0.062	0.011	0.081
plotCtPairs	0.794	0.023	0.918
plotCtRQ	0.449	0.009	0.470
plotCtReps	0.179	0.008	0.188
plotCtScatter	0.038	0.006	0.046
plotCtSignificance	0.616	0.023	0.657
plotCtVariation	0.939	0.019	0.968
plotGenes	0.034	0.005	0.045
qPCRpros	0.008	0.002	0.009
qPCRraw	0.008	0.001	0.009
qPCRset-class	0.107	0.006	0.120
readCtData	0.169	0.004	0.174
setCategory	9.316	0.083	9.463
ttestCtData	1.265	0.005	1.274