Brad Friedman
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/AnalysisPageServer |
| Branch: RELEASE_3_6 |
| Last Commit: 1465019 |
| Last Changed Date: 2017-10-30 12:40:47 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:13:06 -0400 (Thu, 12 Apr 2018).
| Package 42/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AnalysisPageServer 1.12.0 Brad Friedman
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: AnalysisPageServer |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings AnalysisPageServer_1.12.0.tar.gz |
| StartedAt: 2018-04-11 21:23:56 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 21:25:03 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 67.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AnalysisPageServer.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings AnalysisPageServer_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnalysisPageServer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnalysisPageServer’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... 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
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AnalysisPageServer/inst/doc/static-example/jspm_packages/github/twbs/bootstrap@2.3.2/img/glyphicons-halflings-white.png
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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 for sufficient/correct file permissions ... OK
* checking whether package ‘AnalysisPageServer’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 41.8Mb
sub-directories of 1Mb or more:
doc 31.5Mb
htdocs 8.6Mb
* 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
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following directories should probably not be installed:
‘images’, ‘img’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 7 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/00check.log’
for details.
AnalysisPageServer.Rcheck/00install.out
* installing *source* package ‘AnalysisPageServer’ ...
** libs
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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++) {
^
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c SearchReplace2.cpp -o SearchReplace2.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c catch.c -o catch.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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";
^
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c tinyxml2.cpp -o tinyxml2.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o AnalysisPageServer.so AnalysisPageSVG.o R_init_AnalysisPageServer.o SearchReplace2.o catch.o cor.o tinyxml2.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/libs
** R
** inst
** preparing 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnalysisPageServer)
AnalysisPageServer.Rcheck/tests/unit_tests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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:
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.analysis.page.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.annotate.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.aps.urlEncode.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.data.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.error.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.eval.within.time.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.events.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.filter.widget.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.links.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.memory.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.messages.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.param.transformer.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.params.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.persistent.params.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.plot.pars.transformer.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.rapache.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.registry.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.remove.old.files.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.response.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.rook.analysis.page.server.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.search.replace.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.static.analysis.page.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/AnalysisPageServer/unitTests/test.tests.R
/home/biocbuild/bbs-3.6-bioc/meat/AnalysisPageServer.Rcheck/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>
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 since fork is unavailable
done successfully.
Executing test function test.events ... done successfully.
Executing test function test.filter.widget ... done successfully.
Executing test function test.links ... done successfully.
Executing test function test.autosignal.on.bloated.memory ... 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 ... 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 ... [ 2018-04-11 21:24:48 ] INFO sourcing startup.script
[ 2018-04-11 21:24:48 ] INFO sourced startup.script
[ 2018-04-11 21:24:48 ] INFO checking 'pages' response
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))
}
<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 ... done successfully.
Executing test function test.search.replace ... done successfully.
Executing test function test.custom.html ... Yes data
Writing plot file /tmp/RtmpCNHuSl/file108760257d/data/dataset-1.svg
Writing JSON file /tmp/RtmpCNHuSl/file108760257d/data/dataset-1.json
Yes data
Writing plot file /tmp/RtmpCNHuSl/file108760257d/data/dataset-2.svg
Writing JSON file /tmp/RtmpCNHuSl/file108760257d/data/dataset-2.json
done successfully.
Executing test function test.static.analysis.page ... Yes data
Writing plot file /tmp/RtmpCNHuSl/file108720c89f6a/data/dataset-3.svg
Writing JSON file /tmp/RtmpCNHuSl/file108720c89f6a/data/dataset-3.json
Yes data
Writing plot file /tmp/RtmpCNHuSl/file108720c89f6a/data/dataset-4.svg
Writing JSON file /tmp/RtmpCNHuSl/file108720c89f6a/data/dataset-4.json
No data
Writing plot file /tmp/RtmpCNHuSl/file108720c89f6a/data/dataset-5.svg
Writing JSON file /tmp/RtmpCNHuSl/file108720c89f6a/data/dataset-5.json
Yes data
Writing JSON file /tmp/RtmpCNHuSl/file108720c89f6a/data/dataset-6.json
done successfully.
Executing test function test.static.page.group.length.vec ... Yes data
Writing plot file /tmp/RtmpCNHuSl/file1087fb1e3b6/data/dataset-7.svg
Writing JSON file /tmp/RtmpCNHuSl/file1087fb1e3b6/data/dataset-7.json
Yes data
Writing plot file /tmp/RtmpCNHuSl/file1087fb1e3b6/data/dataset-8.svg
Writing JSON file /tmp/RtmpCNHuSl/file1087fb1e3b6/data/dataset-8.json
Yes data
Writing plot file /tmp/RtmpCNHuSl/file108715b08efe/data/dataset-9.svg
Writing JSON file /tmp/RtmpCNHuSl/file108715b08efe/data/dataset-9.json
Yes data
Writing plot file /tmp/RtmpCNHuSl/file108715b08efe/data/dataset-10.svg
Writing JSON file /tmp/RtmpCNHuSl/file108715b08efe/data/dataset-10.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 ... 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 -- Wed Apr 11 21:24:57 2018
***********************************************
Number of test functions: 46
Number of errors: 0
Number of failures: 0
1 Test Suite :
AnalysisPageServer RUnit Tests - 46 test functions, 0 errors, 0 failures
Number of test functions: 46
Number of errors: 0
Number of failures: 0
Warning messages:
1: In func() :
Rook (>= 1.1) or fork is not installed so Rook-based tests were not run
2: 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
8.976 0.164 16.183
AnalysisPageServer.Rcheck/AnalysisPageServer-Ex.timings
| name | user | system | elapsed | |
| add.event | 0.004 | 0.000 | 0.000 | |
| add.event.handler | 0.000 | 0.000 | 0.001 | |
| analysis.page.link | 0.000 | 0.000 | 0.001 | |
| aps.urlEncode | 0.000 | 0.000 | 0.001 | |
| array.param | 0.084 | 0.000 | 0.087 | |
| bool.param | 0.000 | 0.000 | 0.001 | |
| build.service | 0.000 | 0.000 | 0.001 | |
| checkPackageInstalled | 0.004 | 0.000 | 0.002 | |
| clear.event.handlers | 0.008 | 0.000 | 0.008 | |
| client.ip | 0.000 | 0.000 | 0.001 | |
| combobox.param | 0.000 | 0.000 | 0.001 | |
| compound.param | 0.008 | 0.008 | 0.016 | |
| copy.front.end | 0 | 0 | 0 | |
| data.frame.to.json | 0.040 | 0.000 | 0.037 | |
| data.frame.to.list | 0.016 | 0.000 | 0.015 | |
| default.param | 0.000 | 0.000 | 0.001 | |
| default.param.set | 0.004 | 0.000 | 0.001 | |
| dies.ok | 0.004 | 0.000 | 0.005 | |
| embed.APS.dataset | 0.000 | 0.000 | 0.001 | |
| event.names | 0.000 | 0.000 | 0.001 | |
| execute.handler | 0.360 | 0.012 | 0.373 | |
| file.param | 0 | 0 | 0 | |
| get.APS.outdir | 0.000 | 0.004 | 0.001 | |
| get.page | 0.064 | 0.000 | 0.064 | |
| getTraceback | 0.000 | 0.000 | 0.002 | |
| has.event | 0.000 | 0.000 | 0.001 | |
| has.page | 0.036 | 0.000 | 0.038 | |
| lives.ok | 0 | 0 | 0 | |
| new.FastRWeb.analysis.page.run | 0.000 | 0.000 | 0.001 | |
| new.analysis.page | 0.024 | 0.000 | 0.023 | |
| new.datanode.array | 0.012 | 0.000 | 0.011 | |
| new.datanode.html | 0 | 0 | 0 | |
| new.datanode.simple | 0 | 0 | 0 | |
| new.event.registry | 0 | 0 | 0 | |
| new.registry | 0 | 0 | 0 | |
| new.response | 0.000 | 0.000 | 0.001 | |
| new.rook.analysis.page.app | 0.004 | 0.000 | 0.001 | |
| pages | 0.020 | 0.004 | 0.027 | |
| param.set | 0.004 | 0.000 | 0.001 | |
| register.page | 0.024 | 0.000 | 0.024 | |
| remove.event | 0 | 0 | 0 | |
| requestEnv | 0.004 | 0.000 | 0.001 | |
| reset.APS.outdir | 0 | 0 | 0 | |
| rook.analysis.page.server.landing.page | 0 | 0 | 0 | |
| select.param | 0.012 | 0.000 | 0.010 | |
| set.APS.outdir | 0.000 | 0.000 | 0.001 | |
| setup.APS.knitr | 0 | 0 | 0 | |
| simple.param | 0.000 | 0.000 | 0.001 | |
| slider.param | 0.000 | 0.000 | 0.001 | |
| startRookAnalysisPageServer | 0.000 | 0.000 | 0.001 | |
| static.analysis.page | 0 | 0 | 0 | |
| trig.registry | 0.064 | 0.000 | 0.062 | |
| trigger.event | 0.000 | 0.000 | 0.001 | |
| tryKeepConditions | 0.004 | 0.000 | 0.001 | |
| tryKeepTraceback | 0.016 | 0.000 | 0.015 | |
| uniquify.ids.in.svg.files | 0.028 | 0.004 | 0.033 | |
| validate.param.value | 0.004 | 0.000 | 0.001 | |
| vwc.conditions | 0.000 | 0.000 | 0.001 | |
| vwc.error | 0.004 | 0.000 | 0.001 | |
| vwc.error.condition | 0.000 | 0.000 | 0.001 | |
| vwc.error.traceback | 0.004 | 0.000 | 0.003 | |
| vwc.is.error | 0.000 | 0.000 | 0.001 | |
| vwc.messages | 0.004 | 0.000 | 0.001 | |
| vwc.messages.conditions | 0.000 | 0.000 | 0.001 | |
| vwc.messages.tracebacks | 0.008 | 0.000 | 0.009 | |
| vwc.n | 0.000 | 0.000 | 0.001 | |
| vwc.n.messages | 0.000 | 0.000 | 0.001 | |
| vwc.n.warnings | 0.004 | 0.000 | 0.000 | |
| vwc.tracebacks | 0.004 | 0.000 | 0.006 | |
| vwc.value | 0.000 | 0.000 | 0.001 | |
| vwc.warnings | 0.000 | 0.000 | 0.001 | |
| vwc.warnings.conditions | 0.000 | 0.000 | 0.001 | |
| vwc.warnings.tracebacks | 0.004 | 0.000 | 0.004 | |