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BioC 3.4: CHECK report for SpeCond on moscato1

This page was generated on 2016-09-21 03:42:54 -0700 (Wed, 21 Sep 2016).

Package 1144/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpeCond 1.27.0
Florence Cavalli
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SpeCond
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SpeCond
Version: 1.27.0
Command: rm -rf SpeCond.buildbin-libdir SpeCond.Rcheck && mkdir SpeCond.buildbin-libdir SpeCond.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpeCond.buildbin-libdir SpeCond_1.27.0.tar.gz >SpeCond.Rcheck\00install.out 2>&1 && cp SpeCond.Rcheck\00install.out SpeCond-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SpeCond.buildbin-libdir --install="check:SpeCond-install.out" --force-multiarch --no-vignettes --timings SpeCond_1.27.0.tar.gz
StartedAt: 2016-09-20 16:57:10 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 16:59:54 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 164.0 seconds
RetCode: 0
Status:  OK  
CheckDir: SpeCond.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SpeCond.buildbin-libdir SpeCond.Rcheck && mkdir SpeCond.buildbin-libdir SpeCond.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpeCond.buildbin-libdir SpeCond_1.27.0.tar.gz >SpeCond.Rcheck\00install.out 2>&1 && cp SpeCond.Rcheck\00install.out SpeCond-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=SpeCond.buildbin-libdir --install="check:SpeCond-install.out" --force-multiarch --no-vignettes --timings SpeCond_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/SpeCond.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SpeCond/DESCRIPTION' ... OK
* this is package 'SpeCond' version '1.27.0'
* 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.
* 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'
SpeCond: no visible global function definition for 'is'
SpeCond: no visible global function definition for 'new'
callMclustInStep2: no visible global function definition for 'Mclust'
callMclustInStep2: no visible global function definition for
  'priorControl'
createSingleGeneHtmlPage: no visible global function definition for
  'openPage'
createSingleGeneHtmlPage: no visible global function definition for
  'hwrite'
createSingleGeneHtmlPage: no visible global function definition for
  'sessionInfo'
createSingleGeneHtmlPage: no visible global function definition for
  'closePage'
fitNoPriorWithExclusion : <anonymous>: no visible global function
  definition for 'Mclust'
fitPrior : <anonymous>: no visible global function definition for
  'Mclust'
fitPrior : <anonymous>: no visible global function definition for
  'priorControl'
getDifferenceMedian: no visible global function definition for 'median'
getExpressionpatternLegend: no visible global function definition for
  'hwrite'
getFullHtmlSpeCondResult: no visible global function definition for
  'openPage'
getFullHtmlSpeCondResult: no visible global function definition for
  'is'
getFullHtmlSpeCondResult: no visible global function definition for
  'hwrite'
getFullHtmlSpeCondResult: no visible global function definition for
  'png'
getFullHtmlSpeCondResult: no visible global function definition for
  'barplot'
getFullHtmlSpeCondResult: no visible global function definition for
  'dev.off'
getFullHtmlSpeCondResult: no visible global function definition for
  'par'
getFullHtmlSpeCondResult: no visible global function definition for
  'plot'
getFullHtmlSpeCondResult: no visible global function definition for
  'axis'
getFullHtmlSpeCondResult: no visible global function definition for
  'points'
getFullHtmlSpeCondResult: no visible global function definition for
  'legend'
getFullHtmlSpeCondResult: no visible global function definition for
  'mtext'
getFullHtmlSpeCondResult: no visible global function definition for
  'hwriteImage'
getFullHtmlSpeCondResult: no visible global function definition for
  'colorRampPalette'
getFullHtmlSpeCondResult: no visible global function definition for
  'sessionInfo'
getFullHtmlSpeCondResult: no visible global function definition for
  'closePage'
getFullHtmlSpeCondResult: no visible global function definition for
  'write.table'
getGeneHtmlPage: no visible global function definition for 'is'
getGeneHtmlPage: no visible global function definition for 'openPage'
getGeneHtmlPage: no visible global function definition for 'hwrite'
getGeneHtmlPage: no visible global function definition for
  'sessionInfo'
getGeneHtmlPage: no visible global function definition for 'closePage'
getHeatmap: no visible global function definition for 'png'
getHeatmap: no visible global function definition for 'heatmap'
getHeatmap: no visible global function definition for 'colorbar.plot'
getHeatmap: no visible global function definition for 'dev.off'
getHeatmap: no visible global function definition for 'pdf'
getMatrixFromExpressionSet: no visible global function definition for
  'is'
getMatrixFromExpressionSet: no visible global function definition for
  'exprs'
getMinLoglikelihoodNull: no visible global function definition for
  'dnorm'
getPValueMean : <anonymous>: no visible global function definition for
  'pnorm'
getProfileHeatmap: no visible global function definition for 'png'
getProfileHeatmap: no visible global function definition for 'heatmap'
getProfileHeatmap: no visible global function definition for 'dev.off'
getProfileHeatmap: no visible global function definition for 'pdf'
getScaleMAD: no visible global function definition for 'mad'
getSpecific: no visible global function definition for 'pdf'
getSpecific: no visible global function definition for 'hist'
getSpecific: no visible global function definition for 'dev.off'
getSpecific: no visible global function definition for 'p.adjust'
getSpecific: no visible global function definition for 'new'
plotNormalMixture: no visible global function definition for 'png'
plotNormalMixture: no visible global function definition for 'plot'
plotNormalMixture: no visible global function definition for 'points'
plotNormalMixture: no visible global function definition for
  'hwriteImage'
plotNormalMixture: no visible global function definition for 'dev.off'
plotNormalMixture: no visible global function definition for 'hist'
plotNormalMixture : f1: no visible global function definition for
  'dnorm'
plotNormalMixture : f2: no visible global function definition for
  'dnorm'
plotNormalMixture : f3: no visible global function definition for
  'dnorm'
plotNormalMixture : f4: no visible global function definition for
  'dnorm'
plotNormalMixture : f5: no visible global function definition for
  'dnorm'
plotNormalMixture: no visible global function definition for 'lines'
plotNormalMixture: no visible global function definition for 'legend'
plotNormalMixture : f_null : <anonymous>: no visible global function
  definition for 'dnorm'
show.sp_list: no visible global function definition for 'is'
writeGeneResult: no visible global function definition for
  'write.table'
writeSpeCondResult: no visible global function definition for
  'write.table'
writeUniqueProfileSpecificResult: no visible global function definition
  for 'write.table'
Undefined global functions or variables:
  Mclust axis barplot closePage colorRampPalette colorbar.plot dev.off
  dnorm exprs heatmap hist hwrite hwriteImage is legend lines mad
  median mtext new openPage p.adjust par pdf plot png pnorm points
  priorControl sessionInfo write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "png")
  importFrom("graphics", "axis", "barplot", "hist", "legend", "lines",
             "mtext", "par", "plot", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm", "heatmap", "mad", "median", "p.adjust",
             "pnorm")
  importFrom("utils", "sessionInfo", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
getFullHtmlSpeCondResult 5.51   0.37    6.68
getGeneHtmlPage          5.05   0.27    5.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
getFullHtmlSpeCondResult 6.35   0.37    7.22
getGeneHtmlPage          5.49   0.30    5.90
getProfile               4.68   0.00    5.55
* 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
* DONE

Status: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-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_1.27.0.zip
* DONE (SpeCond)

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

nameusersystemelapsed
SpeCond4.040.034.32
createParameterMatrix000
expSetSpeCondExample000
expressionSpeCondExample0.000.010.01
fitNoPriorWithExclusion3.930.003.93
fitPrior2.260.022.28
getDefaultParameter000
getFullHtmlSpeCondResult5.510.376.68
getGeneHtmlPage5.050.275.77
getMatrixFromExpressionSet0.160.010.17
getProfile3.990.003.99
getSpecificOutliersStep12.390.002.39
getSpecificResult3.920.003.92
simulatedSpeCondData0.010.000.01
writeGeneResult3.890.003.89
writeSpeCondResult3.830.003.83
writeUniqueProfileSpecificResult3.870.023.89

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

nameusersystemelapsed
SpeCond4.440.024.51
createParameterMatrix000
expSetSpeCondExample0.000.000.01
expressionSpeCondExample000
fitNoPriorWithExclusion3.950.003.95
fitPrior2.760.002.76
getDefaultParameter0.010.000.02
getFullHtmlSpeCondResult6.350.377.22
getGeneHtmlPage5.490.305.90
getMatrixFromExpressionSet0.210.010.22
getProfile4.680.005.55
getSpecificOutliersStep12.790.002.79
getSpecificResult4.660.004.67
simulatedSpeCondData0.000.020.01
writeGeneResult4.850.004.86
writeSpeCondResult4.680.004.68
writeUniqueProfileSpecificResult4.730.004.72