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BioC 2.13: CHECK report for HTqPCR on perceval

This page was generated on 2014-04-05 09:52:21 -0700 (Sat, 05 Apr 2014).

Package 350/750HostnameOS / ArchBUILDCHECKBUILD BIN
HTqPCR 1.16.0
Heidi Dvinge
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/HTqPCR
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: HTqPCR
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTqPCR_1.16.0.tar.gz
StartedAt: 2014-04-05 02:00:34 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:02:35 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 121.4 seconds
RetCode: 0
Status:  OK 
CheckDir: HTqPCR.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/HTqPCR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.16.0’
* 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 ... [7s/8s] 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 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 ... [34s/35s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setCategory    7.425  0.145   7.634
plotCtCategory 5.221  0.126   5.467
HTqPCR-package 5.130  0.079   5.304
* 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
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/HTqPCR.Rcheck/00check.log’
for details.

HTqPCR.Rcheck/00install.out:

* 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)

HTqPCR.Rcheck/HTqPCR-Ex.timings:

nameusersystemelapsed
HTqPCR-package5.1300.0795.304
cbind0.1160.0030.119
changeCtLayout0.1580.0030.166
clusterCt0.1430.0150.161
filterCategory0.1200.0040.127
filterCtData0.2350.0050.245
heatmapSig1.3700.0271.476
limmaCtData0.7450.0150.770
mannwhitneyCtData1.2220.0061.295
normalizeCtData0.4750.0180.542
plotCVBoxes0.1930.0060.226
plotCtArray0.1330.0070.158
plotCtBoxes0.0700.0040.076
plotCtCard0.0860.0090.096
plotCtCategory5.2210.1265.467
plotCtCor0.0540.0060.062
plotCtDensity0.0450.0080.054
plotCtHeatmap2.2760.0342.392
plotCtHistogram0.0250.0080.035
plotCtOverview0.1640.0170.183
plotCtPCA0.0510.0070.059
plotCtPairs0.6620.0220.744
plotCtRQ0.4860.0330.530
plotCtReps0.1410.0100.154
plotCtScatter0.0430.0090.055
plotCtSignificance0.5280.0240.560
plotCtVariation0.7390.0180.867
plotGenes0.2580.0090.273
qPCRpros0.0100.0060.016
qPCRraw0.0090.0030.012
qPCRset-class0.0840.0130.099
readCtData0.1550.0090.167
setCategory7.4250.1457.634
ttestCtData1.0370.0161.067