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Package 599/658HostnameOS / ArchBUILDCHECKBUILD BIN
SpeCond 1.13.0
Florence Cavalli
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SpeCond
Last Changed Rev: 70052 / Revision: 74756
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
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 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: SpeCond
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SpeCond_1.13.0.tar.gz
StartedAt: 2013-03-24 10:30:01 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 10:33:00 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 178.7 seconds
RetCode: 0
Status:  OK 
CheckDir: SpeCond.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/SpeCond.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'SpeCond/DESCRIPTION' ... OK
* this is package 'SpeCond' version '1.13.0'
* 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 'SpeCond' can be installed ... [8s/8s] 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
SpeCond: warning in getSpecificOutliersStep1(expressionMatrix, fit =
  fit1, param.detection = param.detection, multitest.correction.method
  = "BY", prefix.file = prefix.file, print.hist.pv = FALSE): partial
  argument match of 'fit' to 'fit1'
SpeCond: warning in getSpecificResult(expressionMatrix, fit = fit2,
  specificOutlierStep1 = specificOutlierStep1, param.detection =
  param.detection, multitest.correction.method =
  multitest.correction.method, prefix.file = prefix.file, print.hist.pv
  = print.hist.pv): partial argument match of 'fit' to 'fit2'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
  = 1, nc = 2): partial argument match of 'nr' to 'nrow'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
  = 1, nc = 2): partial argument match of 'nc' to 'ncol'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
  1): partial argument match of 'nr' to 'nrow'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
  1): partial argument match of 'nc' to 'ncol'
getHeatmap: warning in heatmap(M_values, scale = "none", margin = c(8,
  8), col = colors): partial argument match of 'margin' to 'margins'
getHeatmap: warning in heatmap(M_values, scale = "none", margin = c(8,
  8), col = colors, RowSideColors = colRowSide): partial argument match
  of 'margin' to 'margins'
getHeatmap: warning in heatmap(M_values[rownames(M_values) %in%
  probe_set, ], scale = "none", margin = c(8, 8), col = colors):
  partial argument match of 'margin' to 'margins'
getProfileHeatmap: warning in heatmap(M_profile, scale = "none", margin
  = c(8, 8), col = colors): partial argument match of 'margin' to
  'margins'
* 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 ... [90s/91s] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
getFullHtmlSpeCondResult         12.381  0.430  13.354
getGeneHtmlPage                  10.946  0.332  11.579
writeSpeCondResult                7.743  0.068   7.859
SpeCond                           7.706  0.089   8.062
writeGeneResult                   7.606  0.059   7.704
writeUniqueProfileSpecificResult  7.569  0.056   7.661
getProfile                        7.562  0.062   7.869
getSpecificResult                 7.380  0.062   7.473
fitNoPriorWithExclusion           6.645  0.064   6.889
* 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-2.12-bioc/meat/SpeCond.Rcheck/00check.log'
for details.

SpeCond.Rcheck/00install.out:

* installing *source* package 'SpeCond' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'SpeCond.Rnw' 
** testing if installed package can be loaded
* DONE (SpeCond)

SpeCond.Rcheck/SpeCond-Ex.timings:

nameusersystemelapsed
SpeCond7.7060.0898.062
createParameterMatrix0.0120.0020.014
expSetSpeCondExample0.0120.0010.014
expressionSpeCondExample0.0120.0010.013
fitNoPriorWithExclusion6.6450.0646.889
fitPrior3.9530.0394.190
getDefaultParameter0.0080.0000.009
getFullHtmlSpeCondResult12.381 0.43013.354
getGeneHtmlPage10.946 0.33211.579
getMatrixFromExpressionSet0.4020.0080.412
getProfile7.5620.0627.869
getSpecificOutliersStep14.4310.0394.505
getSpecificResult7.3800.0627.473
simulatedSpeCondData0.0140.0020.016
writeGeneResult7.6060.0597.704
writeSpeCondResult7.7430.0687.859
writeUniqueProfileSpecificResult7.5690.0567.661