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CHECK report for AnalysisPageServer on tokay1

This page was generated on 2019-04-13 11:24:45 -0400 (Sat, 13 Apr 2019).

Package 46/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnalysisPageServer 1.16.0
Brad Friedman
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/AnalysisPageServer
Branch: RELEASE_3_8
Last Commit: 67b0635
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnalysisPageServer
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnalysisPageServer.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings AnalysisPageServer_1.16.0.tar.gz
StartedAt: 2019-04-13 00:28:43 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 00:31:26 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 163.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: AnalysisPageServer.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnalysisPageServer.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings AnalysisPageServer_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/AnalysisPageServer.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnalysisPageServer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnalysisPageServer' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Packages which this enhances but not available for checking:
  'fork' 'FastRWeb'
* 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 ... NOTE
Found the following non-portable file paths:
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/inst/doc/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/inst/doc/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/inst/doc/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/inst/doc/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/inst/doc/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/inst/doc/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/inst/doc/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/RubaXa/Sortable@1.4.2/st/logo.png
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/select2/select2@3.5.4/select2.png
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/select2/select2@3.5.4/select2x2.png
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/npm/font-awesome@4.5.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/npm/font-awesome@4.5.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/npm/font-awesome@4.5.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/npm/font-awesome@4.5.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/npm/font-awesome@4.5.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/RubaXa/Sortable@1.4.2/st/logo.png
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/select2/select2@3.5.4/select2.png
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/select2/select2@3.5.4/select2x2.png
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Forms/show/compositeview/landingTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Forms/show/compositeview/primaryTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Forms/show/compositeview/secondaryTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Analysis/show/AnalysisPageShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Analysis/show/AnalysisPageShowRouter.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/ToolOverviewShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/itemview/ToolOverviewBodyView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/itemview/ToolOverviewListView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/itemview/bodyTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/itemview/listTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/layoutview/ToolOverviewView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/layoutview/template.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/tooloverview-app.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/show/APSLandingPageShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/show/EPLandingPageShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/show/EPStudyFormShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/show/LandingPageShowRouter.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/show/layoutview/APSLandingPageView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/show/layoutview/APStemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/show/layoutview/EPLandingPageView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/show/layoutview/EPtemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/show/layoutview/ep-landing.less
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Primary/show/PrimaryPageShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Primary/show/PrimaryPageShowRouter.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Primary/show/layoutview/PrimaryPageView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Primary/show/layoutview/template.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/SuggestionsCallbackController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/models/ComboboxParameterModel.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/models/createComboboxParameterModel.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/models/multipleMixin.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/models/nonMultipleMixin.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/models/nonSelfDependentMixin.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/models/selfDependentMixin.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/show/ComboboxShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/show/Select2ComboboxBehavior.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/show/itemview/ComboboxParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Combobox/show/itemview/landingTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/ConditionalPersistent/ConditionalPersistentController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/ConditionalPersistent/models/PersistentParameterCollection.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/ConditionalPersistent/models/PersistentParameterModel.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/models/SelectParameterModel.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/models/createSelectParameterModel.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/models/multipleMixin.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/models/nonMultipleMixin.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/show/Select2SelectBehavior.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/show/SelectShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/show/itemview/DropdownSelectParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/show/itemview/RadioSelectParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/show/itemview/SelectParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/show/itemview/getSelectParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select/show/itemview/radioTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select2Behavior/Select2Behavior.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Select2Behavior/ep-select2-no-spinner.css
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Summary/show/SummaryShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Summary/show/compositeview/ParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Summary/show/compositeview/ParametersSummaryView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Summary/show/compositeview/itemTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/Summary/show/compositeview/template.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/fetch/ParametersFetchController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/models/ArrayParameterModel.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/models/CompoundParameterModel.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/models/ParameterChildrenCollection.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/models/ParameterCollection.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/ParametersShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/behaviors/ParameterBehavior.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/compositeview/ArrayParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/compositeview/CompoundParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/compositeview/arrayTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/compositeview/compoundTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/itemview/BoolParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/itemview/FileParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/itemview/SliderParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/itemview/TextParameterView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/itemview/boolTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/itemview/fileTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/itemview/sliderTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Parameters/show/itemview/textTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServerStatic/Pages/Datasets/show/DatasetsShowController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServerStatic/Pages/Datasets/show/DatasetsShowRouter.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServerStatic/Pages/Datasets/show/collectionview/DatasetsView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServerStatic/Pages/Datasets/show/layoutview/DatasetView.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServerStatic/Pages/Datasets/show/layoutview/template.html
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServerStatic/Pages/fetch/AnalysisFetchController.js
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServerStatic/Pages/fetch/PagesFetchController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Arrays/show/collectionview/ArrayListView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Arrays/show/collectionview/TabsContentView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Arrays/show/collectionview/TabsNavView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Arrays/show/collectionview/navItemTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Arrays/show/layoutview/ArrayListItemView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Arrays/show/layoutview/ArrayTabsView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Arrays/show/layoutview/itemTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Arrays/show/layoutview/tabsTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/SideMenu/show/MenuShowController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/SideMenu/show/itemview/SideMenuView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/SideMenu/show/itemview/template.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/SidebarShowController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/behaviors/AccordionGroupBehavior.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/compositeview/FilterItemView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/compositeview/FiltersView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/compositeview/itemTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/compositeview/template.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/itemview/CustomSectionView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/itemview/TaggingView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/itemview/sectionTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/itemview/taggingTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/layoutview/ParametersView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/layoutview/SidebarView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/layoutview/parametersTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Sidebar/show/layoutview/sidebarTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Svg/download/SvgDownloadController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Svg/show/PointDetailsShowController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Svg/show/d3BrushTaggingController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Svg/show/d3BrushZoomingController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Plots/Svg/show/itemview/popupTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Tbody/show/TbodyShowController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Tbody/show/itemview/TbodyView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Tbody/show/itemview/chunkTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Tbody/show/itemview/template.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Thead/show/TheadShowController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Thead/show/compositeview/TheadItemView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Thead/show/compositeview/TheadView.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Thead/show/compositeview/itemTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Thead/show/compositeview/summaryTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/Thead/show/compositeview/template.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/download/TableDataDownloadController.js
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/show/itemview/characterTemplate.html
  AnalysisPageServer/inst/htdocs/client/src/Common/AnalysisData/Tables/show/itemview/numericTemplate.html
  AnalysisPageServer/vignettes/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/vignettes/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
  AnalysisPageServer/vignettes/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
  AnalysisPageServer/vignettes/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/vignettes/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/vignettes/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/vignettes/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/vignettes/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/vignettes/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/vignettes/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/vignettes/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/vignettes/static-example/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/select2/select2@3.5.4/select2x2.png
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/vignettes/static-example3/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/vignettes/static-example3/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/vignettes/static-example3/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/vignettes/static-example3/jspm_packages/github/select2/select2@3.5.4/select2x2.png
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  AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
  AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
  AnalysisPageServer/vignettes/static-example3/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
  AnalysisPageServer/vignettes/static-example3/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/vignettes/static-example4/jspm_packages/github/RubaXa/Sortable@1.4.2/st/og-image.png
  AnalysisPageServer/vignettes/static-example4/jspm_packages/github/marionettejs/backbone.marionette@2.4.4/marionette-logo.png
  AnalysisPageServer/vignettes/static-example4/jspm_packages/github/select2/select2@3.5.4/select2-spinner.gif
  AnalysisPageServer/vignettes/static-example4/jspm_packages/github/select2/select2@3.5.4/select2x2.png
  AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
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  AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.ttf
  AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff
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  AnalysisPageServer/vignettes/static-example4/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings.png
  AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.eot
  AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.svg
  AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
  AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff
  AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.woff2
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
  AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
  AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
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  AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
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  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
  AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
  AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
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  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/itemview
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/layoutview
  AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServerStatic/Pages/Datasets/show/collectionview
  AnalysisPageServer/vignettes/static-example/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
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  AnalysisPageServer/vignettes/static-example2/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
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Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'AnalysisPageServer' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIzTqlh/R.INSTALLdf46d92414/AnalysisPageServer/man/check.same.svgs.Rd:17: file link 'checkEquals' in package 'RUnit' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIzTqlh/R.INSTALLdf46d92414/AnalysisPageServer/man/new.analysis.page.Rd:133: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIzTqlh/R.INSTALLdf46d92414/AnalysisPageServer/man/test.package.Rd:26: file link 'runTestSuite' in package 'RUnit' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIzTqlh/R.INSTALLdf46d92414/AnalysisPageServer/man/test.package.Rd:26: file link 'require' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/AnalysisPageServer.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 11.4Mb
  sub-directories of 1Mb or more:
    htdocs   7.9Mb
    libs     1.6Mb
* 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
'library' or 'require' calls in package code:
  'FastRWeb' 'RUnit' 'fork'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'log4r:::INFO'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.head.string: no visible global function definition for 'head'
.inject.file.params: no visible global function definition for 'str'
.inject.file.params : <anonymous>: no visible global function
  definition for 'str'
.prepare.params: no visible binding for global variable 'svg'
check.memory: no visible global function definition for
  'capture.output'
check.same.svgs: no visible global function definition for
  'checkEquals'
checkPackageVersion: no visible global function definition for
  'packageVersion'
checkRookForkForVignettes: no visible binding for '<<-' assignment to
  'no.rook.fork.msg'
checkRookForkForVignettes : <anonymous>: no visible binding for global
  variable 'no.rook.fork.msg'
checkRookForkForVignettes: no visible binding for global variable
  'no.rook.fork.msg'
client.ip: no visible binding for global variable 'SERVER'
cosine.handler: no visible global function definition for 'plot'
embed.APS.dataset: no visible binding for global variable 'svg'
embed.APS.dataset: no visible global function definition for 'dev.off'
execute.handler: no visible binding for global variable 'svg'
execute.handler: no visible global function definition for 'dev.cur'
execute.handler: no visible global function definition for 'dev.off'
execute.handler: no visible global function definition for 'dev.list'
getTraceback: no visible global function definition for
  'capture.output'
inches.png: no visible global function definition for 'png'
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to 'GET'
new.FastRWeb.analysis.page.run : handler: no visible global function
  definition for 'parse.multipart'
new.FastRWeb.analysis.page.run : handler: no visible global function
  definition for 'capture.output'
new.FastRWeb.analysis.page.run : handler: no visible binding for global
  variable 'request'
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to 'POST'
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to 'SERVER'
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to 'FILES'
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to 'setContentType'
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to 'setHeader'
new.FastRWeb.analysis.page.run : handler: no visible binding for '<<-'
  assignment to 'sendBin'
new.FastRWeb.analysis.page.run : handler: no visible binding for global
  variable 'SERVER'
new.FastRWeb.analysis.page.run : handler: no visible global function
  definition for 'WebResult'
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to 'POST'
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to 'GET'
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to 'SERVER'
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to 'FILES'
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to 'setContentType'
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to 'setHeader'
new.rook.analysis.page.app : handler: no visible binding for '<<-'
  assignment to 'sendBin'
new.rook.analysis.page.app : handler: no visible global function
  definition for 'capture.output'
new.rook.analysis.page.app: no visible binding for global variable
  'App'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'GET'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'POST'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'FILES'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'is.textarea.wrap.request'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'setContentType'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'setHeader'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'in.analysis'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'analysis.id'
rapache.app.from.registry : <anonymous>: no visible binding for '<<-'
  assignment to 'analysis.id'
rapache.app.from.registry : <anonymous>: no visible binding for '<<-'
  assignment to 'in.analysis'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'events'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'plot.file'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'sendBin'
rapache.app.from.registry : <anonymous> : <anonymous>: no visible
  global function definition for 'process.response'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'params'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'clean.tmpdir'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'file.params'
rapache.app.from.registry : <anonymous>: no visible binding for '<<-'
  assignment to 'plot.file'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'temp.plot.file'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'SERVER'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'analysis'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'brand'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'page.params'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'all.pages'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'status'
rapache.app.from.registry : <anonymous>: no visible binding for global
  variable 'retrieve'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'handlers'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'capture.output'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'dev.list'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'sessionInfo'
rapache.app.from.registry : <anonymous>: no visible global function
  definition for 'resources'
rapache.app.from.registry : <anonymous> : <anonymous>: no visible
  global function definition for 'handler'
sine.handler: no visible global function definition for 'plot'
startRookAnalysisPageServer: no visible binding for '<<-' assignment to
  'server.pid'
startRookAnalysisPageServer: no visible binding for global variable
  'server.pid'
test.package: no visible global function definition for
  'defineTestSuite'
test.package: no visible global function definition for 'runTestSuite'
test.package: no visible global function definition for
  'printTextProtocol'
Undefined global functions or variables:
  App FILES GET POST SERVER WebResult all.pages analysis analysis.id
  brand capture.output checkEquals clean.tmpdir defineTestSuite dev.cur
  dev.list dev.off events file.params handler handlers head in.analysis
  is.textarea.wrap.request no.rook.fork.msg packageVersion page.params
  params parse.multipart plot plot.file png printTextProtocol
  process.response request resources retrieve runTestSuite sendBin
  server.pid sessionInfo setContentType setHeader status str svg
  temp.plot.file
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "dev.off", "png", "svg")
  importFrom("graphics", "plot")
  importFrom("utils", "capture.output", "head", "packageVersion",
             "sessionInfo", "str")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/libs/i386/AnalysisPageServer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'unit_tests.R'
 OK
* 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: 1 WARNING, 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/AnalysisPageServer.Rcheck/00check.log'
for details.



Installation output

AnalysisPageServer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/AnalysisPageServer_1.16.0.tar.gz && rm -rf AnalysisPageServer.buildbin-libdir && mkdir AnalysisPageServer.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnalysisPageServer.buildbin-libdir AnalysisPageServer_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL AnalysisPageServer_1.16.0.zip && rm AnalysisPageServer_1.16.0.tar.gz AnalysisPageServer_1.16.0.zip
###
##############################################################################
##############################################################################


  % 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 16.7M  100 16.7M    0     0  26.0M      0 --:--:-- --:--:-- --:--:-- 26.2M

install for i386

* installing *source* package 'AnalysisPageServer' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c AnalysisPageSVG.cpp -o AnalysisPageSVG.o
AnalysisPageSVG.cpp: In function 'int matchPlotPoints(XMLElementList, std::deque<double>, std::deque<double>, double, int, int)':
AnalysisPageSVG.cpp:154:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "x and y have different lengths";
        ^
AnalysisPageSVG.cpp:157:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(els.size() < start + n)  {
                 ^
AnalysisPageSVG.cpp:194:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < x.size(); i++)  {
                      ^
AnalysisPageSVG.cpp:210:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_x.size(); i++)  {
                        ^
AnalysisPageSVG.cpp:215:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_y.size(); i++)  {
                        ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c SearchReplace2.cpp -o SearchReplace2.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c catch.c -o catch.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cor.cpp -o cor.o
cor.cpp: In function 'double basic_cor(const std::deque<double>&, const std::deque<double>&)':
cor.cpp:24:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "different sizes";
        ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c tinyxml2.cpp -o tinyxml2.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o AnalysisPageServer.dll tmp.def AnalysisPageSVG.o R_init_AnalysisPageServer.o SearchReplace2.o catch.o cor.o tinyxml2.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/AnalysisPageServer.buildbin-libdir/AnalysisPageServer/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
While loading AnalysisPageServer: urlEncode not found, providing a pure R implementation
While loading AnalysisPageServer: urlDecode not found, providing a pure R implementation
** help
*** installing help indices
  converting help for package 'AnalysisPageServer'
    finding HTML links ... done
    add.event                               html  
    add.event.handler                       html  
    analysis.link                           html  
    analysis.page.link                      html  
    analysis.page.of.current.app            html  
    annotate.analysis.page.svg              html  
    annotate.data.frame                     html  
    apache.httpd.conf                       html  
    aps.dataset.divs                        html  
    aps.one.dataset.div                     html  
    aps.urlEncode                           html  
    array.param                             html  
    autosignal.on.bloated.memory            html  
    bind.memory.checker                     html  
    bool.param                              html  
    build.service                           html  
    check.memory                            html  
    check.same.svgs                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIzTqlh/R.INSTALLdf46d92414/AnalysisPageServer/man/check.same.svgs.Rd:17: file link 'checkEquals' in package 'RUnit' does not exist and so has been treated as a topic
    check.signal                            html  
    checkPackageInstalled                   html  
    checkRookForkForVignettes               html  
    clear.event.handlers                    html  
    client.ip                               html  
    combobox.param                          html  
    compound.param                          html  
    config.js                               html  
    copy.front.end                          html  
    current.app                             html  
    custom.body.attr                        html  
    custom.body.html                        html  
    custom.html.headers                     html  
    data.frame.to.json                      html  
    data.frame.to.list                      html  
    default.param                           html  
    default.param.set                       html  
    default.service.paramset                html  
    default.stylesheets                     html  
    dieIfWindows                            html  
    dies.ok                                 html  
    embed.APS.dataset                       html  
    encode.datanode                         html  
    eval.within.time                        html  
    event.names                             html  
    execute.handler                         html  
    file.param                              html  
    filterWidget                            html  
    get.APS.libbase.prefix                  html  
    get.APS.outdir                          html  
    get.page                                html  
    getTraceback                            html  
    has.event                               html  
    has.page                                html  
    ignore.lots.of.stuff                    html  
    is.registry                             html  
    kill.process                            html  
    knitAPS                                 html  
    known.param.sizes                       html  
    lives.ok                                html  
    make.standard.ids                       html  
    messageSectionName                      html  
    new.FastRWeb.analysis.page.run          html  
    new.analysis.page                       html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIzTqlh/R.INSTALLdf46d92414/AnalysisPageServer/man/new.analysis.page.Rd:133: file link 'AnnotatedDataFrame' in package 'Biobase' does not exist and so has been treated as a topic
    new.datanode.array                      html  
    new.datanode.html                       html  
    new.datanode.plot                       html  
    new.datanode.simple                     html  
    new.datanode.table                      html  
    new.event.registry                      html  
    new.registry                            html  
    new.response                            html  
    new.rook.analysis.page.app              html  
    pages                                   html  
    param.set                               html  
    paramSetToJSON                          html  
    persistent.param.dependencies           html  
    persistent.params                       html  
    platformIsWindows                       html  
    protect.rapache.memory                  html  
    rapache.app.from.registry               html  
    rapache.trig.app                        html  
    register.page                           html  
    remove.event                            html  
    remove.old.files                        html  
    requestEnv                              html  
    reset.APS.outdir                        html  
    rook.analysis.page.server.landing.page
                                            html  
    search.replace                          html  
    select.param                            html  
    service.link                            html  
    set.APS.libbase.prefix                  html  
    set.APS.outdir                          html  
    setup.APS.knitr                         html  
    simple.param                            html  
    sine.handler                            html  
    slider.param                            html  
    startRookAnalysisPageServer             html  
    static.analysis.page                    html  
    static.analysis.page.query.string       html  
    test.package                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIzTqlh/R.INSTALLdf46d92414/AnalysisPageServer/man/test.package.Rd:26: file link 'runTestSuite' in package 'RUnit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpIzTqlh/R.INSTALLdf46d92414/AnalysisPageServer/man/test.package.Rd:26: file link 'require' in package 'base' does not exist and so has been treated as a topic
    trig.registry                           html  
    trigger.event                           html  
    tryKeepConditions                       html  
    tryKeepTraceback                        html  
    uniquify.ids.in.svg.files               html  
    urlDecode                               html  
    urlEncode                               html  
    validate.array.param.value              html  
    validate.bool.param.value               html  
    validate.combobox.param.value           html  
    validate.compound.param.value           html  
    validate.file.param.value               html  
    validate.labeled.param.value            html  
    validate.param.list                     html  
    validate.param.value                    html  
    validate.select.param.value             html  
    validate.text.param.value               html  
    vwc.conditions                          html  
    vwc.error                               html  
    vwc.error.condition                     html  
    vwc.error.traceback                     html  
    vwc.is.error                            html  
    vwc.messages                            html  
    vwc.messages.conditions                 html  
    vwc.messages.tracebacks                 html  
    vwc.n                                   html  
    vwc.n.messages                          html  
    vwc.n.warnings                          html  
    vwc.tracebacks                          html  
    vwc.value                               html  
    vwc.warnings                            html  
    vwc.warnings.conditions                 html  
    vwc.warnings.tracebacks                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'AnalysisPageServer' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c AnalysisPageSVG.cpp -o AnalysisPageSVG.o
AnalysisPageSVG.cpp: In function 'int matchPlotPoints(XMLElementList, std::deque<double>, std::deque<double>, double, int, int)':
AnalysisPageSVG.cpp:154:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "x and y have different lengths";
        ^
AnalysisPageSVG.cpp:157:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(els.size() < start + n)  {
                 ^
AnalysisPageSVG.cpp:194:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < x.size(); i++)  {
                      ^
AnalysisPageSVG.cpp:210:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_x.size(); i++)  {
                        ^
AnalysisPageSVG.cpp:215:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_y.size(); i++)  {
                        ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c SearchReplace2.cpp -o SearchReplace2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c catch.c -o catch.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cor.cpp -o cor.o
cor.cpp: In function 'double basic_cor(const std::deque<double>&, const std::deque<double>&)':
cor.cpp:24:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "different sizes";
        ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c tinyxml2.cpp -o tinyxml2.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o AnalysisPageServer.dll tmp.def AnalysisPageSVG.o R_init_AnalysisPageServer.o SearchReplace2.o catch.o cor.o tinyxml2.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/AnalysisPageServer.buildbin-libdir/AnalysisPageServer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnalysisPageServer' as AnalysisPageServer_1.16.0.zip
* DONE (AnalysisPageServer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'AnalysisPageServer' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

AnalysisPageServer.Rcheck/tests_i386/unit_tests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> AnalysisPageServer:::test.package()
Loading required package: RUnit
Loading required package: AnalysisPageServer

Pattern = /^test.*R$/

Matching test files:
 C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.analysis.page.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.annotate.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.aps.urlEncode.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.data.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.error.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.eval.within.time.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.events.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.filter.widget.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.knitAPS.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.links.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.memory.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.messages.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.param.transformer.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.params.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.persistent.params.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.plot.pars.transformer.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.rapache.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.registry.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.remove.old.files.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.response.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.rook.analysis.page.server.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.search.replace.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.static.analysis.page.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.tests.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.validate.param.list.R 



Executing test function test.analysis.page  ... 
exct.h> page <- new.analysis.page(AnalysisPageServer:::sine.handler)

exct.h> plot.file <- tempfile(fileext = ".svg")

exct.h> plist <- lapply(list(xmin=-2*pi, xmax=2*pi, n= 50), rjson::toJSON)

exct.h> sine.data <- AnalysisPageServer:::execute.handler(page, plist, plot.file=plot.file)

exct.h> # now sine.data is an AnnotatedDataFrame
exct.h> 
exct.h> 
exct.h> 
Skipping plot check in test.analysis.page on windows
 done successfully.



Executing test function test.annotate.data.frame  ...  done successfully.



Executing test function test.inject.file.params  ...  done successfully.



Executing test function test.prepare.params  ...  done successfully.



Executing test function test.annotator.heatmap  ...  done successfully.



Executing test function test.annotator.simple  ...  done successfully.



Executing test function test.double.annotation  ...  done successfully.



Executing test function test.uniquify.ids  ...  done successfully.



Executing test function test.aps.urlEncode  ...  done successfully.



Executing test function test.data.frame.to.json  ...  done successfully.



Executing test function test.data.nodes  ...  done successfully.



Executing test function test.error  ...  done successfully.



Executing test function test.eval.within.time  ... Skipping test.eval.within.time on windows
 done successfully.



Executing test function test.events  ...  done successfully.



Executing test function test.filter.widget  ...  done successfully.



Executing test function test.knitAPS  ... Loading required namespace: knitr
Creating outdir C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88ccb3699d


processing file: C:\Users\biocbuild\bbs-3.8-bioc\R\library\AnalysisPageServer\testdata\knitAPS\template.Rmd
label: setup (with options) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: iris (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

output file: template.md

 done successfully.



Executing test function test.links  ...  done successfully.



Executing test function test.autosignal.on.bloated.memory  ... Skipping autosignal.on.bloated.memory on windows
 done successfully.



Executing test function test.bind.memory.checker  ...  done successfully.



Executing test function test.check.memory  ...  done successfully.



Executing test function test.protect.rapache.memory  ... Skipping autosignal.on.bloated.memory on windows
 done successfully.



Executing test function test.messages  ...  done successfully.



Executing test function test.param.transformer  ...  done successfully.



Executing test function test.default.params  ... 
dflt..>   f <- function(A=1, B=2) {}

dflt..>   # param set with 2 form elements rendered as text inputs; something like   A [__________]     B [__________]
dflt..>   pset <- default.param.set(f)
 done successfully.



Executing test function test.equal.params  ...  done successfully.



Executing test function test.param.constructors  ... 
smpl.p>   x <- simple.param("xmin", label="X-min", description="Minimum x value", type="text")

smpl.p>   # Please see the "Persistent Parameters" and "Conditionally Persistent Parameters"
smpl.p>   # sections of the Interactive Apps vignette for demonstrations of these functionalities
smpl.p> 
smpl.p> 
smpl.p> 

fl.prm>   cov.param <- file.param("cov", label="Covariate Data", description="A two-column Excel file, first column being the sample ID (SAMID) and second being covariate data (with the name of the variable in the header)")

bl.prm>   show.ids <- bool.param("show_ids", label="Show IDs", description="Show sample IDs on the plot", value=TRUE)

sldr.p>   slider <- slider.param("children", label="No. Children", description="Number of Children", min = 0, max = 10, step = 0.5)

slct.p>   color <- select.param("color", label="Color", description="Color of your house", choices=c("red","green","mauve","tope"))

cmbbx.>   ## Note the :query parameter is dependent on the same gene element. This makes it a type-ahead query.
cmbbx.>   gene <- combobox.param(name="gene", uri="/find_gene_id/:genome/:query/", dependent.params=c(genome="genome", query="gene"), response.type="id-long_name-reason")

cmpnd.>   plist <- list(simple.param(name="study"), simple.param(name="comp"), simple.param("feature.type", value="gene"))

cmpnd.>   comp <- compound.param(name="comp", label="Comparison", children=param.set(plist))

arry.p>   one.gene <- simple.param(name="gene", label="Gene Symbol")

arry.p>   gene.set <- array.param(name="geneset", prototype=one.gene)
 done successfully.



Executing test function test.paramSetToJSON  ...  done successfully.



Executing test function test.persistent.params  ...  done successfully.



Executing test function test.persistent.params  ...  done successfully.



Executing test function test.validate.persistent.param.dependencies  ...  done successfully.



Executing test function test.plot.pars.transformer  ...  done successfully.



Executing test function test.device.list  ...  done successfully.



Executing test function test.page.meta.info  ...  done successfully.



Executing test function test.rapache  ... [ 2019-04-13 00:30:52 ] INFO sourcing startup.script 
[ 2019-04-13 00:30:52 ] INFO sourced startup.script 
[ 2019-04-13 00:30:52 ] INFO checking 'pages' response 
Skipping check.plot on windows (part of test.rapache)
 done successfully.



Executing test function test.registry  ... 
h..APR> example(register.page, ask=FALSE)  # register the sine page

rgstr.> # Make a new registry
rgstr.> registry <- new.registry()

rgstr.> # Now register it under the name "sine" (in the "example" registry)
rgstr.> # and keep the modified registry.
rgstr.> registry <- register.page(registry, "sine", AnalysisPageServer:::sine.handler)

h..APR> has.page(registry, "sine")         # should return TRUE now.
[1] TRUE

g..APR> example(register.page, ask=FALSE)  # register the sine page

rgstr.> # Make a new registry
rgstr.> registry <- new.registry()

rgstr.> # Now register it under the name "sine" (in the "example" registry)
rgstr.> # and keep the modified registry.
rgstr.> registry <- register.page(registry, "sine", AnalysisPageServer:::sine.handler)

g..APR> get.page(registry, "sine")         # should return the sine.handler function
$handler
function (xmin = 0, xmax = 3 * pi, n = 100) 
{
    xmin <- as.numeric(xmin)
    xmax <- as.numeric(xmax)
    n <- as.numeric(n)
    x <- seq(xmin, xmax, length = n)
    y <- sin(x)
    plot(x, y, pch = 19, col = "seagreen")
    ids <- make.unique(rep(LETTERS, length = n))
    return(data.frame(x = x, y = y, row.names = ids))
}
<bytecode: 0x047791d0>
<environment: namespace:AnalysisPageServer>

$params
$xmin
$name
[1] "xmin"

$label
[1] "xmin"

$description
[1] "xmin"

$value
[1] 0

$type
[1] "text"

$advanced
[1] 0

$show.if
NULL

$size
[1] "medium"

$required
[1] TRUE

attr(,"class")
[1] "AnalysisPageParam"

$xmax
$name
[1] "xmax"

$label
[1] "xmax"

$description
[1] "xmax"

$value
[1] 9.424778

$type
[1] "text"

$advanced
[1] 0

$show.if
NULL

$size
[1] "medium"

$required
[1] TRUE

attr(,"class")
[1] "AnalysisPageParam"

$n
$name
[1] "n"

$label
[1] "n"

$description
[1] "n"

$value
[1] 100

$type
[1] "text"

$advanced
[1] 0

$show.if
NULL

$size
[1] "medium"

$required
[1] TRUE

attr(,"class")
[1] "AnalysisPageParam"

attr(,"class")
[1] "AnalysisPageParamSet"

$annotate.plot
[1] TRUE

$standard.ids
[1] TRUE

$class.name
[1] "plot-point"

$plot.pars.transformer
NULL

$annotate.data.frame
[1] TRUE

$numeric.sig.digs
[1] 3

$no.plot
[1] FALSE

$name
[1] "sine"

$label
[1] "sine"

$description
[1] "sine"

$advanced
[1] 0

$service
[1] FALSE

$in.menu
[1] TRUE

$paramset.transformer
NULL

attr(,"class")
[1] "AnalysisPage"

pg.APR> empty.pages <- pages(new.registry())   # should be empty character vector

pg.APR> example(register.page, ask=FALSE)      # see register.page example---registers the sine handler

rgstr.> # Make a new registry
rgstr.> registry <- new.registry()

rgstr.> # Now register it under the name "sine" (in the "example" registry)
rgstr.> # and keep the modified registry.
rgstr.> registry <- register.page(registry, "sine", AnalysisPageServer:::sine.handler)

pg.APR> pages(registry)                        # should now be the character vector "sine"
[1] "sine"
 done successfully.



Executing test function test.remove.old.files  ...  done successfully.



Executing test function test.response  ...  done successfully.



Executing test function test.rook.analysis.page.server  ... Skipping test.rook.analysis.page.server on windows since the test requires fork
 done successfully.



Executing test function test.search.replace  ...  done successfully.



Executing test function test.custom.html  ... Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c13702baf/data/dataset-2.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c13702baf/data/dataset-2.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c13702baf/data/dataset-3.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c13702baf/data/dataset-3.json
 done successfully.



Executing test function test.static.analysis.page  ... Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c4faf3aa5/data/dataset-4.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c4faf3aa5/data/dataset-4.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c4faf3aa5/data/dataset-5.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c4faf3aa5/data/dataset-5.json
No data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c4faf3aa5/data/dataset-6.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c4faf3aa5/data/dataset-6.json
Yes data
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c4faf3aa5/data/dataset-7.json
 done successfully.



Executing test function test.static.page.group.length.vec  ... Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c3e557e55/data/dataset-8.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c3e557e55/data/dataset-8.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c3e557e55/data/dataset-9.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c3e557e55/data/dataset-9.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c69e641b/data/dataset-10.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c69e641b/data/dataset-10.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c69e641b/data/dataset-11.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpiKVCxI\file88c69e641b/data/dataset-11.json
 done successfully.



Executing test function test.valid.html4.ids  ...  done successfully.



Executing test function test.dies.ok  ...  done successfully.



Executing test function test.lives.ok  ...  done successfully.



Executing test function test.signal  ... Skipping test.signal on windows
 done successfully.



Executing test function test.validate.param.list  ... 
cmbbx.>   ## Note the :query parameter is dependent on the same gene element. This makes it a type-ahead query.
cmbbx.>   gene <- combobox.param(name="gene", uri="/find_gene_id/:genome/:query/", dependent.params=c(genome="genome", query="gene"), response.type="id-long_name-reason")

smpl.p>   x <- simple.param("xmin", label="X-min", description="Minimum x value", type="text")

smpl.p>   # Please see the "Persistent Parameters" and "Conditionally Persistent Parameters"
smpl.p>   # sections of the Interactive Apps vignette for demonstrations of these functionalities
smpl.p> 
smpl.p> 
smpl.p> 

cmpnd.>   plist <- list(simple.param(name="study"), simple.param(name="comp"), simple.param("feature.type", value="gene"))

cmpnd.>   comp <- compound.param(name="comp", label="Comparison", children=param.set(plist))

arry.p>   one.gene <- simple.param(name="gene", label="Gene Symbol")

arry.p>   gene.set <- array.param(name="geneset", prototype=one.gene)

slct.p>   color <- select.param("color", label="Color", description="Color of your house", choices=c("red","green","mauve","tope"))

bl.prm>   show.ids <- bool.param("show_ids", label="Show IDs", description="Show sample IDs on the plot", value=TRUE)

fl.prm>   cov.param <- file.param("cov", label="Covariate Data", description="A two-column Excel file, first column being the sample ID (SAMID) and second being covariate data (with the name of the variable in the header)")
 done successfully.



RUNIT TEST PROTOCOL -- Sat Apr 13 00:31:03 2019 
*********************************************** 
Number of test functions: 47 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnalysisPageServer RUnit Tests - 47 test functions, 0 errors, 0 failures
Number of test functions: 47 
Number of errors: 0 
Number of failures: 0 
Warning message:
In func() :
  Skipping check that plot was correctly annotated in test.static.analysis.page because ANALYSISPAGESERVER_FULL_TESTS is not set
> 
> proc.time()
   user  system elapsed 
   5.42    0.92   18.00 

AnalysisPageServer.Rcheck/tests_x64/unit_tests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> AnalysisPageServer:::test.package()
Loading required package: RUnit
Loading required package: AnalysisPageServer

Pattern = /^test.*R$/

Matching test files:
 C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.analysis.page.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.annotate.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.aps.urlEncode.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.data.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.error.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.eval.within.time.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.events.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.filter.widget.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.knitAPS.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.links.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.memory.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.messages.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.param.transformer.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.params.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.persistent.params.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.plot.pars.transformer.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.rapache.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.registry.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.remove.old.files.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.response.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.rook.analysis.page.server.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.search.replace.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.static.analysis.page.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.tests.R
  C:/Users/biocbuild/bbs-3.8-bioc/R/library/AnalysisPageServer/unitTests/test.validate.param.list.R 



Executing test function test.analysis.page  ... 
exct.h> page <- new.analysis.page(AnalysisPageServer:::sine.handler)

exct.h> plot.file <- tempfile(fileext = ".svg")

exct.h> plist <- lapply(list(xmin=-2*pi, xmax=2*pi, n= 50), rjson::toJSON)

exct.h> sine.data <- AnalysisPageServer:::execute.handler(page, plist, plot.file=plot.file)

exct.h> # now sine.data is an AnnotatedDataFrame
exct.h> 
exct.h> 
exct.h> 
Skipping plot check in test.analysis.page on windows
 done successfully.



Executing test function test.annotate.data.frame  ...  done successfully.



Executing test function test.inject.file.params  ...  done successfully.



Executing test function test.prepare.params  ...  done successfully.



Executing test function test.annotator.heatmap  ...  done successfully.



Executing test function test.annotator.simple  ...  done successfully.



Executing test function test.double.annotation  ...  done successfully.



Executing test function test.uniquify.ids  ...  done successfully.



Executing test function test.aps.urlEncode  ...  done successfully.



Executing test function test.data.frame.to.json  ...  done successfully.



Executing test function test.data.nodes  ...  done successfully.



Executing test function test.error  ...  done successfully.



Executing test function test.eval.within.time  ... Skipping test.eval.within.time on windows
 done successfully.



Executing test function test.events  ...  done successfully.



Executing test function test.filter.widget  ...  done successfully.



Executing test function test.knitAPS  ... Loading required namespace: knitr
Creating outdir C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc4fee14df


processing file: C:\Users\biocbuild\bbs-3.8-bioc\R\library\AnalysisPageServer\testdata\knitAPS\template.Rmd
label: setup (with options) 
List of 1
 $ echo: logi FALSE

  ordinary text without R code

label: iris (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

output file: template.md

 done successfully.



Executing test function test.links  ...  done successfully.



Executing test function test.autosignal.on.bloated.memory  ... Skipping autosignal.on.bloated.memory on windows
 done successfully.



Executing test function test.bind.memory.checker  ...  done successfully.



Executing test function test.check.memory  ...  done successfully.



Executing test function test.protect.rapache.memory  ... Skipping autosignal.on.bloated.memory on windows
 done successfully.



Executing test function test.messages  ...  done successfully.



Executing test function test.param.transformer  ...  done successfully.



Executing test function test.default.params  ... 
dflt..>   f <- function(A=1, B=2) {}

dflt..>   # param set with 2 form elements rendered as text inputs; something like   A [__________]     B [__________]
dflt..>   pset <- default.param.set(f)
 done successfully.



Executing test function test.equal.params  ...  done successfully.



Executing test function test.param.constructors  ... 
smpl.p>   x <- simple.param("xmin", label="X-min", description="Minimum x value", type="text")

smpl.p>   # Please see the "Persistent Parameters" and "Conditionally Persistent Parameters"
smpl.p>   # sections of the Interactive Apps vignette for demonstrations of these functionalities
smpl.p> 
smpl.p> 
smpl.p> 

fl.prm>   cov.param <- file.param("cov", label="Covariate Data", description="A two-column Excel file, first column being the sample ID (SAMID) and second being covariate data (with the name of the variable in the header)")

bl.prm>   show.ids <- bool.param("show_ids", label="Show IDs", description="Show sample IDs on the plot", value=TRUE)

sldr.p>   slider <- slider.param("children", label="No. Children", description="Number of Children", min = 0, max = 10, step = 0.5)

slct.p>   color <- select.param("color", label="Color", description="Color of your house", choices=c("red","green","mauve","tope"))

cmbbx.>   ## Note the :query parameter is dependent on the same gene element. This makes it a type-ahead query.
cmbbx.>   gene <- combobox.param(name="gene", uri="/find_gene_id/:genome/:query/", dependent.params=c(genome="genome", query="gene"), response.type="id-long_name-reason")

cmpnd.>   plist <- list(simple.param(name="study"), simple.param(name="comp"), simple.param("feature.type", value="gene"))

cmpnd.>   comp <- compound.param(name="comp", label="Comparison", children=param.set(plist))

arry.p>   one.gene <- simple.param(name="gene", label="Gene Symbol")

arry.p>   gene.set <- array.param(name="geneset", prototype=one.gene)
 done successfully.



Executing test function test.paramSetToJSON  ...  done successfully.



Executing test function test.persistent.params  ...  done successfully.



Executing test function test.persistent.params  ...  done successfully.



Executing test function test.validate.persistent.param.dependencies  ...  done successfully.



Executing test function test.plot.pars.transformer  ...  done successfully.



Executing test function test.device.list  ...  done successfully.



Executing test function test.page.meta.info  ...  done successfully.



Executing test function test.rapache  ... [ 2019-04-13 00:31:08 ] INFO sourcing startup.script 
[ 2019-04-13 00:31:08 ] INFO sourced startup.script 
[ 2019-04-13 00:31:08 ] INFO checking 'pages' response 
Skipping check.plot on windows (part of test.rapache)
 done successfully.



Executing test function test.registry  ... 
h..APR> example(register.page, ask=FALSE)  # register the sine page

rgstr.> # Make a new registry
rgstr.> registry <- new.registry()

rgstr.> # Now register it under the name "sine" (in the "example" registry)
rgstr.> # and keep the modified registry.
rgstr.> registry <- register.page(registry, "sine", AnalysisPageServer:::sine.handler)

h..APR> has.page(registry, "sine")         # should return TRUE now.
[1] TRUE

g..APR> example(register.page, ask=FALSE)  # register the sine page

rgstr.> # Make a new registry
rgstr.> registry <- new.registry()

rgstr.> # Now register it under the name "sine" (in the "example" registry)
rgstr.> # and keep the modified registry.
rgstr.> registry <- register.page(registry, "sine", AnalysisPageServer:::sine.handler)

g..APR> get.page(registry, "sine")         # should return the sine.handler function
$handler
function (xmin = 0, xmax = 3 * pi, n = 100) 
{
    xmin <- as.numeric(xmin)
    xmax <- as.numeric(xmax)
    n <- as.numeric(n)
    x <- seq(xmin, xmax, length = n)
    y <- sin(x)
    plot(x, y, pch = 19, col = "seagreen")
    ids <- make.unique(rep(LETTERS, length = n))
    return(data.frame(x = x, y = y, row.names = ids))
}
<bytecode: 0x000000000900a060>
<environment: namespace:AnalysisPageServer>

$params
$xmin
$name
[1] "xmin"

$label
[1] "xmin"

$description
[1] "xmin"

$value
[1] 0

$type
[1] "text"

$advanced
[1] 0

$show.if
NULL

$size
[1] "medium"

$required
[1] TRUE

attr(,"class")
[1] "AnalysisPageParam"

$xmax
$name
[1] "xmax"

$label
[1] "xmax"

$description
[1] "xmax"

$value
[1] 9.424778

$type
[1] "text"

$advanced
[1] 0

$show.if
NULL

$size
[1] "medium"

$required
[1] TRUE

attr(,"class")
[1] "AnalysisPageParam"

$n
$name
[1] "n"

$label
[1] "n"

$description
[1] "n"

$value
[1] 100

$type
[1] "text"

$advanced
[1] 0

$show.if
NULL

$size
[1] "medium"

$required
[1] TRUE

attr(,"class")
[1] "AnalysisPageParam"

attr(,"class")
[1] "AnalysisPageParamSet"

$annotate.plot
[1] TRUE

$standard.ids
[1] TRUE

$class.name
[1] "plot-point"

$plot.pars.transformer
NULL

$annotate.data.frame
[1] TRUE

$numeric.sig.digs
[1] 3

$no.plot
[1] FALSE

$name
[1] "sine"

$label
[1] "sine"

$description
[1] "sine"

$advanced
[1] 0

$service
[1] FALSE

$in.menu
[1] TRUE

$paramset.transformer
NULL

attr(,"class")
[1] "AnalysisPage"

pg.APR> empty.pages <- pages(new.registry())   # should be empty character vector

pg.APR> example(register.page, ask=FALSE)      # see register.page example---registers the sine handler

rgstr.> # Make a new registry
rgstr.> registry <- new.registry()

rgstr.> # Now register it under the name "sine" (in the "example" registry)
rgstr.> # and keep the modified registry.
rgstr.> registry <- register.page(registry, "sine", AnalysisPageServer:::sine.handler)

pg.APR> pages(registry)                        # should now be the character vector "sine"
[1] "sine"
 done successfully.



Executing test function test.remove.old.files  ...  done successfully.



Executing test function test.response  ...  done successfully.



Executing test function test.rook.analysis.page.server  ... Skipping test.rook.analysis.page.server on windows since the test requires fork
 done successfully.



Executing test function test.search.replace  ...  done successfully.



Executing test function test.custom.html  ... Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc5d414adf/data/dataset-2.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc5d414adf/data/dataset-2.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc5d414adf/data/dataset-3.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc5d414adf/data/dataset-3.json
 done successfully.



Executing test function test.static.analysis.page  ... Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc1fe3d36/data/dataset-4.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc1fe3d36/data/dataset-4.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc1fe3d36/data/dataset-5.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc1fe3d36/data/dataset-5.json
No data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc1fe3d36/data/dataset-6.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc1fe3d36/data/dataset-6.json
Yes data
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc1fe3d36/data/dataset-7.json
 done successfully.



Executing test function test.static.page.group.length.vec  ... Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc5e127c53/data/dataset-8.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc5e127c53/data/dataset-8.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc5e127c53/data/dataset-9.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc5e127c53/data/dataset-9.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc63f54861/data/dataset-10.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc63f54861/data/dataset-10.json
Yes data
Writing plot file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc63f54861/data/dataset-11.svg
Writing JSON file C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpCQXUQx\file16dc63f54861/data/dataset-11.json
 done successfully.



Executing test function test.valid.html4.ids  ...  done successfully.



Executing test function test.dies.ok  ...  done successfully.



Executing test function test.lives.ok  ...  done successfully.



Executing test function test.signal  ... Skipping test.signal on windows
 done successfully.



Executing test function test.validate.param.list  ... 
cmbbx.>   ## Note the :query parameter is dependent on the same gene element. This makes it a type-ahead query.
cmbbx.>   gene <- combobox.param(name="gene", uri="/find_gene_id/:genome/:query/", dependent.params=c(genome="genome", query="gene"), response.type="id-long_name-reason")

smpl.p>   x <- simple.param("xmin", label="X-min", description="Minimum x value", type="text")

smpl.p>   # Please see the "Persistent Parameters" and "Conditionally Persistent Parameters"
smpl.p>   # sections of the Interactive Apps vignette for demonstrations of these functionalities
smpl.p> 
smpl.p> 
smpl.p> 

cmpnd.>   plist <- list(simple.param(name="study"), simple.param(name="comp"), simple.param("feature.type", value="gene"))

cmpnd.>   comp <- compound.param(name="comp", label="Comparison", children=param.set(plist))

arry.p>   one.gene <- simple.param(name="gene", label="Gene Symbol")

arry.p>   gene.set <- array.param(name="geneset", prototype=one.gene)

slct.p>   color <- select.param("color", label="Color", description="Color of your house", choices=c("red","green","mauve","tope"))

bl.prm>   show.ids <- bool.param("show_ids", label="Show IDs", description="Show sample IDs on the plot", value=TRUE)

fl.prm>   cov.param <- file.param("cov", label="Covariate Data", description="A two-column Excel file, first column being the sample ID (SAMID) and second being covariate data (with the name of the variable in the header)")
 done successfully.



RUNIT TEST PROTOCOL -- Sat Apr 13 00:31:19 2019 
*********************************************** 
Number of test functions: 47 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnalysisPageServer RUnit Tests - 47 test functions, 0 errors, 0 failures
Number of test functions: 47 
Number of errors: 0 
Number of failures: 0 
Warning message:
In func() :
  Skipping check that plot was correctly annotated in test.static.analysis.page because ANALYSISPAGESERVER_FULL_TESTS is not set
> 
> proc.time()
   user  system elapsed 
   6.92    1.01   16.20 

Example timings

AnalysisPageServer.Rcheck/examples_i386/AnalysisPageServer-Ex.timings

nameusersystemelapsed
add.event000
add.event.handler000
analysis.page.link0.000.000.02
aps.urlEncode000
array.param0.020.000.01
bool.param000
build.service000
checkPackageInstalled000
clear.event.handlers000
client.ip000
combobox.param000
compound.param000
copy.front.end000
data.frame.to.json0.010.000.02
data.frame.to.list000
default.param000
default.param.set000
dies.ok000
embed.APS.dataset000
event.names000
execute.handler0.240.010.31
file.param0.010.000.01
get.APS.libbase.prefix000
get.APS.outdir000
get.page0.130.020.18
getTraceback000
has.event000
has.page0.110.010.12
lives.ok000
new.FastRWeb.analysis.page.run000
new.analysis.page0.080.050.13
new.datanode.array0.010.000.01
new.datanode.html000
new.datanode.simple000
new.event.registry000
new.registry000
new.response000
new.rook.analysis.page.app000
pages0.070.010.08
param.set000
register.page0.060.020.07
remove.event000
requestEnv000
reset.APS.outdir000
rook.analysis.page.server.landing.page000
select.param000
set.APS.libbase.prefix000
set.APS.outdir000
setup.APS.knitr000
simple.param000
slider.param000
startRookAnalysisPageServer000
static.analysis.page000
trig.registry0.130.010.14
trigger.event000
tryKeepConditions000
tryKeepTraceback000
uniquify.ids.in.svg.files0.020.000.01
validate.param.value000
vwc.conditions000
vwc.error000
vwc.error.condition000
vwc.error.traceback000
vwc.is.error000
vwc.messages000
vwc.messages.conditions000
vwc.messages.tracebacks000
vwc.n000
vwc.n.messages000
vwc.n.warnings000
vwc.tracebacks0.010.000.02
vwc.value000
vwc.warnings000
vwc.warnings.conditions000
vwc.warnings.tracebacks000

AnalysisPageServer.Rcheck/examples_x64/AnalysisPageServer-Ex.timings

nameusersystemelapsed
add.event000
add.event.handler000
analysis.page.link000
aps.urlEncode0.010.000.01
array.param000
bool.param000
build.service000
checkPackageInstalled000
clear.event.handlers000
client.ip000
combobox.param000
compound.param000
copy.front.end000
data.frame.to.json0.020.000.02
data.frame.to.list000
default.param000
default.param.set000
dies.ok000
embed.APS.dataset000
event.names0.010.000.02
execute.handler0.130.030.17
file.param000
get.APS.libbase.prefix000
get.APS.outdir000
get.page0.060.020.08
getTraceback000
has.event000
has.page0.080.000.08
lives.ok000
new.FastRWeb.analysis.page.run000
new.analysis.page0.060.020.08
new.datanode.array0.010.000.02
new.datanode.html000
new.datanode.simple000
new.event.registry000
new.registry000
new.response000
new.rook.analysis.page.app000
pages0.080.020.09
param.set000
register.page0.050.010.06
remove.event000
requestEnv0.010.000.02
reset.APS.outdir000
rook.analysis.page.server.landing.page000
select.param000
set.APS.libbase.prefix000
set.APS.outdir000
setup.APS.knitr000
simple.param000
slider.param000
startRookAnalysisPageServer000
static.analysis.page000
trig.registry0.090.030.12
trigger.event000
tryKeepConditions000
tryKeepTraceback000
uniquify.ids.in.svg.files0.030.000.03
validate.param.value000
vwc.conditions000
vwc.error000
vwc.error.condition000
vwc.error.traceback0.020.000.01
vwc.is.error000
vwc.messages000
vwc.messages.conditions000
vwc.messages.tracebacks000
vwc.n0.010.000.02
vwc.n.messages000
vwc.n.warnings000
vwc.tracebacks000
vwc.value000
vwc.warnings0.020.000.01
vwc.warnings.conditions000
vwc.warnings.tracebacks000