BioC 2.12: CHECK report for HTqPCR on lamb2

Package: HTqPCR

Version: 1.13.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings HTqPCR_1.13.1.tar.gz

StartedAt: 2013-01-16 03:32:25 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:34:07 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 101.4 seconds

RetCode: 0

Status: OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/HTqPCR.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setCategory    8.176  0.004   8.181
plotCtCategory 5.089  0.056   5.140
HTqPCR-package 5.024  0.028   5.089
* 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
  ‘/loc/home/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	5.024	0.028	5.089
cbind	0.140	0.000	0.141
changeCtLayout	0.268	0.004	0.272
clusterCt	0.436	0.012	0.449
filterCategory	0.092	0.000	0.093
filterCtData	0.216	0.004	0.221
heatmapSig	1.416	0.016	1.434
limmaCtData	0.728	0.004	0.733
mannwhitneyCtData	1.152	0.000	1.150
normalizeCtData	0.472	0.012	0.481
plotCVBoxes	0.176	0.000	0.180
plotCtArray	0.156	0.000	0.154
plotCtBoxes	0.084	0.000	0.081
plotCtCard	0.212	0.008	0.219
plotCtCategory	5.089	0.056	5.140
plotCtCor	0.048	0.000	0.048
plotCtDensity	0.048	0.004	0.049
plotCtHeatmap	2.228	0.008	2.243
plotCtHistogram	0.020	0.004	0.023
plotCtOverview	0.140	0.000	0.141
plotCtPCA	0.048	0.004	0.054
plotCtPairs	0.524	0.016	0.539
plotCtRQ	0.316	0.000	0.314
plotCtReps	0.116	0.000	0.116
plotCtScatter	0.032	0.000	0.030
plotCtSignificance	0.412	0.000	0.410
plotCtVariation	0.600	0.004	0.602
plotGenes	0.044	0.000	0.045
qPCRpros	0.008	0.004	0.011
qPCRraw	0.008	0.000	0.011
qPCRset-class	0.100	0.004	0.105
readCtData	0.148	0.004	0.151
setCategory	8.176	0.004	8.181
ttestCtData	0.933	0.000	0.931

Summary

Command output