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BioC 3.4: CHECK report for SpeCond on malbec1

This page was generated on 2017-04-15 16:09:59 -0400 (Sat, 15 Apr 2017).

Package 1174/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpeCond 1.28.0
Florence Cavalli
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/SpeCond
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: 1.28.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SpeCond_1.28.0.tar.gz
StartedAt: 2017-04-15 01:24:46 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:26:04 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 77.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SpeCond.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SpeCond_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SpeCond.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpeCond/DESCRIPTION’ ... OK
* this is package ‘SpeCond’ version ‘1.28.0’
* 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 ‘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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
getFullHtmlSpeCondResult 5.56  0.424   6.338
getGeneHtmlPage          4.76  0.332   5.399
* 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
  ‘/home/biocbuild/bbs-3.4-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
SpeCond3.3560.0123.371
createParameterMatrix0.0000.0000.001
expSetSpeCondExample0.0000.0000.003
expressionSpeCondExample0.0040.0000.002
fitNoPriorWithExclusion3.1920.0043.198
fitPrior1.8480.0001.850
getDefaultParameter0.0000.0040.000
getFullHtmlSpeCondResult5.5600.4246.338
getGeneHtmlPage4.7600.3325.399
getMatrixFromExpressionSet0.1680.0040.171
getProfile3.4520.0003.453
getSpecificOutliersStep11.9720.0001.975
getSpecificResult3.5280.0003.529
simulatedSpeCondData0.0040.0000.003
writeGeneResult3.4680.0003.470
writeSpeCondResult3.3840.0043.390
writeUniqueProfileSpecificResult3.2840.0003.287