BioC 2.11: CHECK report for HTqPCR on lamb1

Package: HTqPCR

Version: 1.12.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings HTqPCR_1.12.0.tar.gz

StartedAt: 2013-03-25 02:11:22 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:13:04 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 102.0 seconds

RetCode: 0

Status: OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/HTqPCR.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.12.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
setCategory 8.308  0.008   8.432
* 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-2.11-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	4.784	0.032	4.889
cbind	0.112	0.000	0.114
changeCtLayout	0.160	0.000	0.173
clusterCt	0.368	0.020	0.414
filterCategory	0.212	0.008	0.231
filterCtData	0.208	0.012	0.235
heatmapSig	1.284	0.004	1.305
limmaCtData	0.756	0.012	0.784
mannwhitneyCtData	1.356	0.000	1.357
normalizeCtData	0.364	0.004	0.371
plotCVBoxes	0.156	0.000	0.156
plotCtArray	0.112	0.008	0.121
plotCtBoxes	0.052	0.004	0.057
plotCtCard	0.064	0.004	0.068
plotCtCategory	4.889	0.048	4.953
plotCtCor	0.040	0.004	0.054
plotCtDensity	0.036	0.000	0.035
plotCtHeatmap	2.296	0.008	2.342
plotCtHistogram	0.016	0.000	0.018
plotCtOverview	0.140	0.004	0.144
plotCtPCA	0.040	0.004	0.044
plotCtPairs	0.584	0.004	0.590
plotCtRQ	0.344	0.000	0.347
plotCtReps	0.116	0.008	0.123
plotCtScatter	0.028	0.000	0.026
plotCtSignificance	0.592	0.000	0.591
plotCtVariation	0.644	0.000	0.645
plotGenes	0.024	0.000	0.025
qPCRpros	0.004	0.000	0.004
qPCRraw	0.000	0.004	0.004
qPCRset-class	0.076	0.004	0.083
readCtData	0.108	0.000	0.116
setCategory	8.308	0.008	8.432
ttestCtData	0.880	0.000	0.897

Summary

Command output