BioC 2.14: CHECK report for HTqPCR on morelia

Package: HTqPCR

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTqPCR_1.18.0.tar.gz

StartedAt: 2014-10-07 23:30:35 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:32:01 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 86.4 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTqPCR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/HTqPCR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.18.0’
* 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 ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘limma’ ‘RColorBrewer’
A package should be listed in only one of these fields.
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
setCategory 5.232  0.035   5.271
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	3.090	0.029	3.128
cbind	0.087	0.002	0.089
changeCtLayout	0.121	0.002	0.123
clusterCt	0.238	0.007	0.248
filterCategory	0.179	0.003	0.181
filterCtData	0.184	0.004	0.190
heatmapSig	1.101	0.008	1.136
limmaCtData	0.620	0.005	0.628
mannwhitneyCtData	1.079	0.003	1.085
normalizeCtData	0.342	0.013	0.360
plotCVBoxes	0.155	0.003	0.160
plotCtArray	0.134	0.004	0.139
plotCtBoxes	0.052	0.002	0.055
plotCtCard	0.055	0.005	0.060
plotCtCategory	0.675	0.005	0.682
plotCtCor	0.048	0.002	0.051
plotCtDensity	0.032	0.003	0.035
plotCtHeatmap	1.694	0.009	1.707
plotCtHistogram	0.017	0.002	0.019
plotCtOverview	0.111	0.004	0.117
plotCtPCA	0.033	0.003	0.037
plotCtPairs	0.497	0.008	0.507
plotCtRQ	0.272	0.003	0.277
plotCtReps	0.100	0.003	0.102
plotCtScatter	0.025	0.002	0.029
plotCtSignificance	0.419	0.005	0.424
plotCtVariation	0.515	0.007	0.526
plotGenes	0.023	0.003	0.025
qPCRpros	0.006	0.000	0.006
qPCRraw	0.004	0.000	0.004
qPCRset-class	0.074	0.003	0.077
readCtData	0.227	0.004	0.232
setCategory	5.232	0.035	5.271
ttestCtData	0.859	0.002	0.862