Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

Package 573/631HostnameOS / ArchBUILDCHECKBUILD BIN
SpeCond 1.13.0
Florence Cavalli
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SpeCond
Last Changed Rev: 70052 / Revision: 72575
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 
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: SpeCond
Version: 1.13.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings SpeCond_1.13.0.tar.gz
StartedAt: 2013-01-16 06:32:10 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 06:35:31 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 201.3 seconds
RetCode: 0
Status:  OK 
CheckDir: SpeCond.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/SpeCond.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
getFullHtmlSpeCondResult         7.888  0.080  15.942
getGeneHtmlPage                  7.252  0.028  14.552
SpeCond                          5.956  0.032  11.986
writeUniqueProfileSpecificResult 5.833  0.020  11.709
writeGeneResult                  5.777  0.028  11.623
getProfile                       5.772  0.024  11.593
writeSpeCondResult               5.736  0.008  11.496
getSpecificResult                5.452  0.020  10.936
fitNoPriorWithExclusion          5.172  0.008  10.349
getSpecificOutliersStep1         3.656  0.004   7.311
fitPrior                         3.065  0.004   6.127
* 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
  ‘/loc/home/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
SpeCond 5.956 0.03211.986
createParameterMatrix0.0120.0000.033
expSetSpeCondExample0.0160.0000.032
expressionSpeCondExample0.0080.0000.032
fitNoPriorWithExclusion 5.172 0.00810.349
fitPrior3.0650.0046.127
getDefaultParameter0.1120.0000.233
getFullHtmlSpeCondResult 7.888 0.08015.942
getGeneHtmlPage 7.252 0.02814.552
getMatrixFromExpressionSet0.2890.0040.595
getProfile 5.772 0.02411.593
getSpecificOutliersStep13.6560.0047.311
getSpecificResult 5.452 0.02010.936
simulatedSpeCondData0.0120.0000.029
writeGeneResult 5.777 0.02811.623
writeSpeCondResult 5.736 0.00811.496
writeUniqueProfileSpecificResult 5.833 0.02011.709