Package: HTqPCR

Version: 1.10.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings HTqPCR_1.10.0.tar.gz

StartedAt: 2012-04-01 01:38:04 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:39:20 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 75.9 seconds

RetCode: 0

Status:  OK

CheckDir: HTqPCR.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/HTqPCR.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HTqPCR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTqPCR' version '1.10.0'
* 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 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
  '/loc/home/hpages/test-puck5/bbs-2.10-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	3.156	0.008	3.180
cbind	0.136	0.004	0.141
changeCtLayout	0.108	0.004	0.121
clusterCt	0.492	0.008	0.507
filterCategory	0.072	0.000	0.077
filterCtData	0.200	0.000	0.202
heatmapSig	1.120	0.004	1.142
limmaCtData	0.664	0.008	0.689
mannwhitneyCtData	1.048	0.008	1.063
normalizeCtData	0.328	0.004	0.339
plotCVBoxes	0.148	0.000	0.155
plotCtArray	0.100	0.000	0.104
plotCtBoxes	0.044	0.000	0.050
plotCtCard	0.052	0.000	0.057
plotCtCategory	2.716	0.016	2.740
plotCtCor	0.040	0.000	0.045
plotCtDensity	0.024	0.012	0.040
plotCtHeatmap	2.160	0.008	2.179
plotCtHistogram	0.020	0.000	0.022
plotCtOverview	0.080	0.004	0.094
plotCtPCA	0.036	0.000	0.042
plotCtPairs	0.488	0.004	0.498
plotCtRQ	0.284	0.000	0.287
plotCtReps	0.104	0.000	0.110
plotCtScatter	0.024	0.000	0.028
plotCtSignificance	0.376	0.000	0.382
plotCtVariation	0.517	0.000	0.525
plotGenes	0.020	0.004	0.037
qPCRpros	0.004	0.000	0.012
qPCRraw	0.008	0.000	0.012
qPCRset-class	0.072	0.000	0.075
readCtData	0.100	0.000	0.104
setCategory	5.356	0.004	5.371
ttestCtData	0.852	0.004	0.863