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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:24:45 -0400 (Sat, 13 Apr 2019).
| Package 46/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AnalysisPageServer 1.16.0 Brad Friedman
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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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
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AnalysisPageServer/inst/doc/static-example4/jspm_packages/npm/font-awesome@4.7.0/fonts/fontawesome-webfont.ttf
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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
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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
AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.eot
AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
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
AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.svg
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
AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts/glyphicons-halflings-regular.woff2
AnalysisPageServer/vignettes/static-example4/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
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
AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
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
AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
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
AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
AnalysisPageServer/vignettes/static-example2/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
AnalysisPageServer/vignettes/static-example3/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
AnalysisPageServer/vignettes/static-example4/jspm_packages/github/marionettejs/backbone.marionette@2.4.4
AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts
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.
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
|
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
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AnalysisPageServer.Rcheck/examples_i386/AnalysisPageServer-Ex.timings
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AnalysisPageServer.Rcheck/examples_x64/AnalysisPageServer-Ex.timings
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