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BioC 2.14: CHECK report for SpeCond on moscato2

This page was generated on 2014-10-08 08:53:09 -0700 (Wed, 08 Oct 2014).

Package 743/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpeCond 1.18.0
Florence Cavalli
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/SpeCond
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: SpeCond
Version: 1.18.0
Command: rm -rf SpeCond.buildbin-libdir && mkdir SpeCond.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpeCond.buildbin-libdir SpeCond_1.18.0.tar.gz >SpeCond-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=SpeCond.buildbin-libdir --install="check:SpeCond-install.out" --force-multiarch --no-vignettes --timings SpeCond_1.18.0.tar.gz
StartedAt: 2014-10-08 05:19:28 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 05:22:54 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 206.6 seconds
RetCode: 0
Status:  OK  
CheckDir: SpeCond.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SpeCond.buildbin-libdir && mkdir SpeCond.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpeCond.buildbin-libdir SpeCond_1.18.0.tar.gz >SpeCond-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=SpeCond.buildbin-libdir --install="check:SpeCond-install.out" --force-multiarch --no-vignettes --timings SpeCond_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/SpeCond.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SpeCond/DESCRIPTION' ... OK
* this is package 'SpeCond' version '1.18.0'
* 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 whether package 'SpeCond' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'fields' 'hwriter' 'mclust' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [54s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
getFullHtmlSpeCondResult 6.28   0.38    7.35
getGeneHtmlPage          5.55   0.25    6.01
SpeCond                  4.85   0.00    5.09
** running examples for arch 'x64' ... [66s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
getFullHtmlSpeCondResult         7.40   0.35    8.17
getGeneHtmlPage                  7.36   0.25    8.63
getProfile                       6.37   0.00    6.37
writeUniqueProfileSpecificResult 6.07   0.00    6.07
writeSpeCondResult               5.94   0.00    5.95
writeGeneResult                  5.46   0.02    5.47
SpeCond                          5.42   0.02    5.43
getSpecificResult                5.20   0.00    5.19
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/SpeCond.Rcheck/00check.log'
for details.

SpeCond.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'SpeCond' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpeCond' as SpeCond_1.18.0.zip
* DONE (SpeCond)

SpeCond.Rcheck/examples_i386/SpeCond-Ex.timings:

nameusersystemelapsed
SpeCond4.850.005.09
createParameterMatrix000
expSetSpeCondExample000
expressionSpeCondExample0.020.000.01
fitNoPriorWithExclusion4.300.004.31
fitPrior2.640.002.64
getDefaultParameter000
getFullHtmlSpeCondResult6.280.387.35
getGeneHtmlPage5.550.256.01
getMatrixFromExpressionSet0.230.000.23
getProfile4.460.014.48
getSpecificOutliersStep12.690.022.70
getSpecificResult4.570.004.57
simulatedSpeCondData0.010.000.01
writeGeneResult4.780.004.78
writeSpeCondResult4.650.014.66
writeUniqueProfileSpecificResult4.750.044.79

SpeCond.Rcheck/examples_x64/SpeCond-Ex.timings:

nameusersystemelapsed
SpeCond5.420.025.43
createParameterMatrix000
expSetSpeCondExample000
expressionSpeCondExample0.010.000.01
fitNoPriorWithExclusion4.930.014.95
fitPrior2.980.002.98
getDefaultParameter000
getFullHtmlSpeCondResult7.400.358.17
getGeneHtmlPage7.360.258.63
getMatrixFromExpressionSet0.480.000.48
getProfile6.370.006.37
getSpecificOutliersStep13.270.003.28
getSpecificResult5.200.005.19
simulatedSpeCondData0.020.000.02
writeGeneResult5.460.025.47
writeSpeCondResult5.940.005.95
writeUniqueProfileSpecificResult6.070.006.07