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Package 314/658HostnameOS / ArchBUILDCHECKBUILD BIN
HTqPCR 1.13.1
Heidi Dvinge
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HTqPCR
Last Changed Rev: 72298 / Revision: 74774
Last Changed Date: 2013-01-04 13:18:09 -0800 (Fri, 04 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / 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: 1.13.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings HTqPCR_1.13.1.tar.gz
StartedAt: 2013-03-25 02:23:33 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:25:56 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 142.8 seconds
RetCode: 0
Status:  OK 
CheckDir: HTqPCR.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/HTqPCR.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.13.1’
* 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 ... [9s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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 ... [45s/47s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
setCategory    10.388  0.008  10.630
plotCtCategory  7.156  0.080   7.453
HTqPCR-package  6.844  0.068   7.107
* 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
  ‘/home/biocbuild/bbs-2.12-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-package6.8440.0687.107
cbind0.2040.0000.202
changeCtLayout0.5080.0120.522
clusterCt0.4520.0040.461
filterCategory0.1160.0000.140
filterCtData0.2800.0040.308
heatmapSig1.9960.0242.082
limmaCtData1.0120.0121.026
mannwhitneyCtData1.7130.0001.838
normalizeCtData0.6840.0120.774
plotCVBoxes0.2360.0040.242
plotCtArray0.2400.0000.239
plotCtBoxes0.3040.0000.306
plotCtCard0.0920.0000.095
plotCtCategory7.1560.0807.453
plotCtCor0.0640.0080.071
plotCtDensity0.0560.0120.069
plotCtHeatmap3.1760.0203.559
plotCtHistogram0.0240.0120.036
plotCtOverview0.1840.0040.187
plotCtPCA0.0680.0000.067
plotCtPairs0.8080.0120.819
plotCtRQ0.4760.0120.488
plotCtReps0.1880.0000.188
plotCtScatter0.0520.0000.051
plotCtSignificance0.6880.0120.703
plotCtVariation0.9130.0120.924
plotGenes0.0600.0000.061
qPCRpros0.0080.0000.010
qPCRraw0.0120.0040.015
qPCRset-class0.1440.0000.143
readCtData0.1800.0080.190
setCategory10.388 0.00810.630
ttestCtData1.2640.0001.266