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Package 610/671HostnameOS / ArchBUILDCHECKBUILD BIN
SpeCond 1.14.0
Florence Cavalli
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/SpeCond
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 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 Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: SpeCond
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SpeCond_1.14.0.tar.gz
StartedAt: 2013-05-01 11:11:05 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 11:13:59 -0700 (Wed, 01 May 2013)
EllapsedTime: 173.9 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 Patched (2013-04-08 r62531)
* 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 '1.14.0'
* 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 ... [88s/90s] OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
getFullHtmlSpeCondResult         12.116  0.450  13.269
getGeneHtmlPage                  10.801  0.337  11.534
writeSpeCondResult                7.520  0.066   7.715
SpeCond                           7.464  0.083   7.799
writeGeneResult                   7.413  0.071   7.566
writeUniqueProfileSpecificResult  7.352  0.054   7.458
getSpecificResult                 7.315  0.057   7.486
getProfile                        7.121  0.059   7.402
fitNoPriorWithExclusion           6.612  0.063   6.727
* 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
** testing if installed package can be loaded
* DONE (SpeCond)

SpeCond.Rcheck/SpeCond-Ex.timings:

nameusersystemelapsed
SpeCond7.4640.0837.799
createParameterMatrix0.0120.0010.015
expSetSpeCondExample0.0160.0030.019
expressionSpeCondExample0.0100.0010.011
fitNoPriorWithExclusion6.6120.0636.727
fitPrior3.8100.0374.051
getDefaultParameter0.0100.0010.011
getFullHtmlSpeCondResult12.116 0.45013.269
getGeneHtmlPage10.801 0.33711.534
getMatrixFromExpressionSet0.3850.0090.401
getProfile7.1210.0597.402
getSpecificOutliersStep14.5200.0394.760
getSpecificResult7.3150.0577.486
simulatedSpeCondData0.0120.0020.014
writeGeneResult7.4130.0717.566
writeSpeCondResult7.5200.0667.715
writeUniqueProfileSpecificResult7.3520.0547.458