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CHECK report for SpeCond on tokay2

This page was generated on 2020-10-17 11:57:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SpeCond PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1707/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpeCond 1.42.0
Florence Cavalli
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SpeCond
Branch: RELEASE_3_11
Last Commit: 8ed11c7
Last Changed Date: 2020-04-27 14:20:40 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SpeCond
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpeCond.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SpeCond_1.42.0.tar.gz
StartedAt: 2020-10-17 08:31:25 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 08:34:17 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 171.6 seconds
RetCode: 0
Status:  OK  
CheckDir: SpeCond.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpeCond.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SpeCond_1.42.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SpeCond.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.42.0'
* 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
* 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 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
  '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 '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 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", "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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
getFullHtmlSpeCondResult 5.64   0.42    6.49
getGeneHtmlPage          5.03   0.33    5.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
getFullHtmlSpeCondResult 6.00   0.39    6.61
getGeneHtmlPage          5.28   0.27    5.56
fitNoPriorWithExclusion  5.52   0.00    5.52
SpeCond                  5.37   0.01    5.40
getSpecificResult        5.23   0.00    5.23
* 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/SpeCond.Rcheck/00check.log'
for details.



Installation output

SpeCond.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SpeCond_1.42.0.tar.gz && rm -rf SpeCond.buildbin-libdir && mkdir SpeCond.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpeCond.buildbin-libdir SpeCond_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SpeCond_1.42.0.zip && rm SpeCond_1.42.0.tar.gz SpeCond_1.42.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1098k  100 1098k    0     0  10.9M      0 --:--:-- --:--:-- --:--:-- 11.7M

install for i386

* installing *source* package 'SpeCond' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SpeCond'
    finding HTML links ... done
    SpeCond                                 html  
    createParameterMatrix                   html  
    expSetSpeCondExample                    html  
    expressionSpeCondExample                html  
    fitNoPriorWithExclusion                 html  
    fitPrior                                html  
    getDefaultParameter                     html  
    getFullHtmlSpeCondResult                html  
    getGeneHtmlPage                         html  
    getMatrixFromExpressionSet              html  
    getProfile                              html  
    getSpecificOutliersStep1                html  
    getSpecificResult                       html  
    simulatedSpeCondData                    html  
    writeGeneResult                         html  
    writeSpeCondResult                      html  
    writeUniqueProfileSpecificResult        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SpeCond' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpeCond' as SpeCond_1.42.0.zip
* DONE (SpeCond)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SpeCond' successfully unpacked and MD5 sums checked

Tests output


Example timings

SpeCond.Rcheck/examples_i386/SpeCond-Ex.timings

nameusersystemelapsed
SpeCond4.060.034.09
createParameterMatrix000
expSetSpeCondExample0.010.000.02
expressionSpeCondExample000
fitNoPriorWithExclusion3.770.003.77
fitPrior2.260.052.31
getDefaultParameter000
getFullHtmlSpeCondResult5.640.426.49
getGeneHtmlPage5.030.335.52
getMatrixFromExpressionSet0.130.000.12
getProfile4.030.024.05
getSpecificOutliersStep12.650.002.66
getSpecificResult4.570.004.56
simulatedSpeCondData000
writeGeneResult4.500.014.53
writeSpeCondResult404
writeUniqueProfileSpecificResult4.030.004.03

SpeCond.Rcheck/examples_x64/SpeCond-Ex.timings

nameusersystemelapsed
SpeCond5.370.015.40
createParameterMatrix000
expSetSpeCondExample000
expressionSpeCondExample0.000.020.01
fitNoPriorWithExclusion5.520.005.52
fitPrior3.340.003.34
getDefaultParameter000
getFullHtmlSpeCondResult6.000.396.61
getGeneHtmlPage5.280.275.56
getMatrixFromExpressionSet0.110.000.11
getProfile4.870.004.87
getSpecificOutliersStep13.350.003.35
getSpecificResult5.230.005.23
simulatedSpeCondData0.000.010.02
writeGeneResult4.440.004.43
writeSpeCondResult4.450.004.46
writeUniqueProfileSpecificResult4.000.024.01