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Package 266/553HostnameOS / ArchBUILDCHECKBUILD BIN
HTqPCR 1.10.0
Heidi Dvinge
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/HTqPCR
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: HTqPCR
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTqPCR_1.10.0.tar.gz
StartedAt: 2012-09-24 00:34:19 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:36:07 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 108.8 seconds
RetCode: 0
Status:  OK 
CheckDir: HTqPCR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/HTqPCR.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... 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
  '/Users/biocbuild/bbs-2.10-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
   'HTqPCR.Rnw' 
** testing if installed package can be loaded

* DONE (HTqPCR)

HTqPCR.Rcheck/HTqPCR-Ex.timings:

nameusersystemelapsed
HTqPCR-package4.3580.0454.404
cbind0.1590.0020.162
changeCtLayout0.1310.0040.135
clusterCt0.3950.0350.430
filterCategory0.0810.0040.086
filterCtData0.2230.0080.231
heatmapSig1.4070.0171.424
limmaCtData0.6900.0120.706
mannwhitneyCtData1.2080.0031.210
normalizeCtData0.4040.0300.433
plotCVBoxes0.1860.0060.192
plotCtArray0.1260.0100.136
plotCtBoxes0.0570.0060.063
plotCtCard0.0620.0100.071
plotCtCategory3.0780.0353.113
plotCtCor0.0560.0050.061
plotCtDensity0.0420.0060.048
plotCtHeatmap2.3950.0262.423
plotCtHistogram0.0200.0030.023
plotCtOverview0.0860.0080.095
plotCtPCA0.0400.0060.046
plotCtPairs0.5990.0140.614
plotCtRQ0.4690.0090.479
plotCtReps0.1530.0060.159
plotCtScatter0.0340.0050.039
plotCtSignificance0.4830.0180.501
plotCtVariation0.6180.0150.635
plotGenes0.0280.0060.034
qPCRpros0.0050.0010.006
qPCRraw0.0060.0010.006
qPCRset-class0.0750.0040.080
readCtData0.1250.0030.128
setCategory10.538 0.26510.809
ttestCtData1.4330.0031.436