BioC 2.13: CHECK report for HTqPCR on zin1

Package: HTqPCR

Version: 1.16.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings HTqPCR_1.16.0.tar.gz

StartedAt: 2014-04-05 01:52:44 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:53:57 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 72.2 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/HTqPCR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.16.0’
* 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 ... [4s/4s] 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘HTqPCR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [21s/21s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	3.008	0.016	3.026
cbind	0.080	0.000	0.078
changeCtLayout	0.116	0.000	0.118
clusterCt	0.18	0.00	0.18
filterCategory	0.076	0.004	0.078
filterCtData	0.176	0.000	0.179
heatmapSig	0.932	0.004	0.938
limmaCtData	0.568	0.000	0.570
mannwhitneyCtData	0.924	0.000	0.928
normalizeCtData	0.332	0.004	0.335
plotCVBoxes	0.140	0.000	0.141
plotCtArray	0.176	0.000	0.175
plotCtBoxes	0.044	0.000	0.045
plotCtCard	0.052	0.000	0.051
plotCtCategory	2.468	0.012	2.482
plotCtCor	0.036	0.004	0.040
plotCtDensity	0.032	0.000	0.032
plotCtHeatmap	1.668	0.000	1.668
plotCtHistogram	0.016	0.000	0.017
plotCtOverview	0.108	0.000	0.107
plotCtPCA	0.032	0.004	0.037
plotCtPairs	0.452	0.000	0.453
plotCtRQ	0.284	0.004	0.286
plotCtReps	0.100	0.000	0.103
plotCtScatter	0.024	0.000	0.025
plotCtSignificance	0.348	0.000	0.349
plotCtVariation	0.488	0.004	0.521
plotGenes	0.028	0.000	0.029
qPCRpros	0.004	0.000	0.007
qPCRraw	0.008	0.000	0.006
qPCRset-class	0.072	0.004	0.076
readCtData	0.108	0.004	0.109
setCategory	4.857	0.008	4.873
ttestCtData	0.744	0.000	0.746