Brad Friedman
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/AnalysisPageServer |
| Branch: master |
| Last Commit: 1877999 |
| Last Changed Date: 2018-10-30 11:54:33 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:30:55 -0400 (Tue, 09 Apr 2019).
| Package 49/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AnalysisPageServer 1.17.0 Brad Friedman
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: AnalysisPageServer |
| Version: 1.17.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnalysisPageServer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnalysisPageServer_1.17.0.tar.gz |
| StartedAt: 2019-04-08 23:11:52 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:13:13 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 80.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AnalysisPageServer.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AnalysisPageServer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AnalysisPageServer_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AnalysisPageServer.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (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 ‘1.17.0’ * 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/[email protected]/st/og-image.png AnalysisPageServer/inst/doc/static-example/jspm_packages/github/marionettejs/[email protected]/marionette-logo.png AnalysisPageServer/inst/doc/static-example/jspm_packages/github/select2/[email protected]/select2-spinner.gif AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.eot AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.svg AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.ttf AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/[email 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AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/marionettejs/[email protected]/marionette-logo.png AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/select2/[email protected]/select2-spinner.gif AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.eot AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.svg AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.ttf AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff2 AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/twbs/[email 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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/[email protected]/marionette-logo.png AnalysisPageServer/vignettes/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.eot AnalysisPageServer/vignettes/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.svg AnalysisPageServer/vignettes/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.ttf AnalysisPageServer/vignettes/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff AnalysisPageServer/vignettes/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff2 AnalysisPageServer/vignettes/jspm_packages/github/twbs/[email protected]/img/glyphicons-halflings-white.png AnalysisPageServer/vignettes/static-example/jspm_packages/github/RubaXa/[email protected]/st/og-image.png AnalysisPageServer/vignettes/static-example/jspm_packages/github/marionettejs/[email protected]/marionette-logo.png AnalysisPageServer/vignettes/static-example/jspm_packages/github/select2/[email protected]/select2-spinner.gif AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.eot AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.svg AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.ttf AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff2 AnalysisPageServer/vignettes/static-example/jspm_packages/github/twbs/[email protected]/img/glyphicons-halflings-white.png AnalysisPageServer/vignettes/static-example/jspm_packages/github/twbs/[email protected]/img/glyphicons-halflings.png AnalysisPageServer/vignettes/static-example/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.eot AnalysisPageServer/vignettes/static-example/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.svg AnalysisPageServer/vignettes/static-example/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.ttf AnalysisPageServer/vignettes/static-example/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.woff AnalysisPageServer/vignettes/static-example/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.woff2 AnalysisPageServer/vignettes/static-example2/jspm_packages/github/RubaXa/[email protected]/st/og-image.png AnalysisPageServer/vignettes/static-example2/jspm_packages/github/marionettejs/[email protected]/marionette-logo.png AnalysisPageServer/vignettes/static-example2/jspm_packages/github/select2/[email protected]/select2-spinner.gif AnalysisPageServer/vignettes/static-example2/jspm_packages/github/select2/[email protected]/select2x2.png AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.eot AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.svg AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.ttf AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff2 AnalysisPageServer/vignettes/static-example2/jspm_packages/github/twbs/[email protected]/img/glyphicons-halflings-white.png AnalysisPageServer/vignettes/static-example2/jspm_packages/github/twbs/[email protected]/img/glyphicons-halflings.png AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.eot AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.svg AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.ttf AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.woff AnalysisPageServer/vignettes/static-example2/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.woff2 AnalysisPageServer/vignettes/static-example3/jspm_packages/github/RubaXa/[email protected]/st/og-image.png AnalysisPageServer/vignettes/static-example3/jspm_packages/github/marionettejs/[email protected]/marionette-logo.png AnalysisPageServer/vignettes/static-example3/jspm_packages/github/select2/[email protected]/select2-spinner.gif AnalysisPageServer/vignettes/static-example3/jspm_packages/github/select2/[email protected]/select2x2.png AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.eot AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.svg AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.ttf AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff2 AnalysisPageServer/vignettes/static-example3/jspm_packages/github/twbs/[email protected]/img/glyphicons-halflings-white.png AnalysisPageServer/vignettes/static-example3/jspm_packages/github/twbs/[email protected]/img/glyphicons-halflings.png AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.eot AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.svg AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.ttf AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.woff AnalysisPageServer/vignettes/static-example3/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.woff2 AnalysisPageServer/vignettes/static-example4/jspm_packages/github/RubaXa/[email protected]/st/og-image.png AnalysisPageServer/vignettes/static-example4/jspm_packages/github/marionettejs/[email protected]/marionette-logo.png AnalysisPageServer/vignettes/static-example4/jspm_packages/github/select2/[email protected]/select2-spinner.gif AnalysisPageServer/vignettes/static-example4/jspm_packages/github/select2/[email protected]/select2x2.png AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.eot AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.svg AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.ttf AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/[email protected]/_jekyll/fonts/glyphicons-halflings-regular.woff2 AnalysisPageServer/vignettes/static-example4/jspm_packages/github/twbs/[email protected]/img/glyphicons-halflings-white.png AnalysisPageServer/vignettes/static-example4/jspm_packages/github/twbs/[email protected]/img/glyphicons-halflings.png AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.eot AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.svg AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.ttf AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.woff AnalysisPageServer/vignettes/static-example4/jspm_packages/npm/[email protected]/fonts/fontawesome-webfont.woff2 AnalysisPageServer/inst/doc/static-example/jspm_packages/github/marionettejs/[email protected] AnalysisPageServer/inst/doc/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/marionettejs/[email protected] AnalysisPageServer/inst/doc/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/marionettejs/[email protected] AnalysisPageServer/inst/doc/static-example3/jspm_packages/github/t0m/[email protected]/_jekyll/fonts AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/marionettejs/[email protected] AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/t0m/[email protected]/_jekyll/fonts AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/marionettejs/[email protected] AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/t0m/[email protected]/_jekyll/fonts AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/marionettejs/[email protected] AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/t0m/[email protected]/_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/[email protected] AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/[email protected]/_jekyll/fonts AnalysisPageServer/vignettes/static-example2/jspm_packages/github/marionettejs/[email protected] AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/[email protected]/_jekyll/fonts AnalysisPageServer/vignettes/static-example3/jspm_packages/github/marionettejs/[email protected] AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/[email protected]/_jekyll/fonts AnalysisPageServer/vignettes/static-example4/jspm_packages/github/marionettejs/[email protected] AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/[email protected]/_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 9.4Mb sub-directories of 1Mb or more: htdocs 8.0Mb * 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 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 is not available * 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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/AnalysisPageServer.Rcheck/00check.log’ for details.
AnalysisPageServer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AnalysisPageServer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘AnalysisPageServer’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c AnalysisPageSVG.cpp -o AnalysisPageSVG.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c SearchReplace2.cpp -o SearchReplace2.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c catch.c -o catch.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c cor.cpp -o cor.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c tinyxml2.cpp -o tinyxml2.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o AnalysisPageServer.so AnalysisPageSVG.o R_init_AnalysisPageServer.o SearchReplace2.o catch.o cor.o tinyxml2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/libs ** 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 ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (AnalysisPageServer)
AnalysisPageServer.Rcheck/tests/unit_tests.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.analysis.page.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.annotate.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.aps.urlEncode.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.data.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.error.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.eval.within.time.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.events.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.filter.widget.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.knitAPS.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.links.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.memory.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.messages.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.param.transformer.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.params.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.persistent.params.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.plot.pars.transformer.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.rapache.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.registry.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.remove.old.files.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.response.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.rook.analysis.page.server.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.search.replace.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.static.analysis.page.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/AnalysisPageServer/unitTests/test.tests.R
/Library/Frameworks/R.framework/Versions/3.6/Resources/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>
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.knitAPS ... Loading required namespace: knitr
Creating outdir /tmp/Rtmpmh8emi/filec9f049bb1340
processing file: /Library/Frameworks/R.framework/Versions/3.6/Resources/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 ... 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 ... [ 2019-04-08 23:12:55 ] INFO sourcing startup.script
[ 2019-04-08 23:12:55 ] INFO sourced startup.script
[ 2019-04-08 23:12:55 ] 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))
}
<bytecode: 0x7fc942e94f00>
<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/Rtmpmh8emi/filec9f05d621349/data/dataset-2.svg
Writing JSON file /tmp/Rtmpmh8emi/filec9f05d621349/data/dataset-2.json
Yes data
Writing plot file /tmp/Rtmpmh8emi/filec9f05d621349/data/dataset-3.svg
Writing JSON file /tmp/Rtmpmh8emi/filec9f05d621349/data/dataset-3.json
done successfully.
Executing test function test.static.analysis.page ... Yes data
Writing plot file /tmp/Rtmpmh8emi/filec9f04e5059bd/data/dataset-4.svg
Writing JSON file /tmp/Rtmpmh8emi/filec9f04e5059bd/data/dataset-4.json
Yes data
Writing plot file /tmp/Rtmpmh8emi/filec9f04e5059bd/data/dataset-5.svg
Writing JSON file /tmp/Rtmpmh8emi/filec9f04e5059bd/data/dataset-5.json
No data
Writing plot file /tmp/Rtmpmh8emi/filec9f04e5059bd/data/dataset-6.svg
Writing JSON file /tmp/Rtmpmh8emi/filec9f04e5059bd/data/dataset-6.json
Yes data
Writing JSON file /tmp/Rtmpmh8emi/filec9f04e5059bd/data/dataset-7.json
done successfully.
Executing test function test.static.page.group.length.vec ... Yes data
Writing plot file /tmp/Rtmpmh8emi/filec9f072c4d2e8/data/dataset-8.svg
Writing JSON file /tmp/Rtmpmh8emi/filec9f072c4d2e8/data/dataset-8.json
Yes data
Writing plot file /tmp/Rtmpmh8emi/filec9f072c4d2e8/data/dataset-9.svg
Writing JSON file /tmp/Rtmpmh8emi/filec9f072c4d2e8/data/dataset-9.json
Yes data
Writing plot file /tmp/Rtmpmh8emi/filec9f0211af537/data/dataset-10.svg
Writing JSON file /tmp/Rtmpmh8emi/filec9f0211af537/data/dataset-10.json
Yes data
Writing plot file /tmp/Rtmpmh8emi/filec9f0211af537/data/dataset-11.svg
Writing JSON file /tmp/Rtmpmh8emi/filec9f0211af537/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 ... 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 -- Mon Apr 8 23:13:03 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 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
5.663 0.486 13.277
AnalysisPageServer.Rcheck/AnalysisPageServer-Ex.timings
| name | user | system | elapsed | |
| add.event | 0.001 | 0.000 | 0.001 | |
| add.event.handler | 0.002 | 0.001 | 0.002 | |
| analysis.page.link | 0.002 | 0.000 | 0.003 | |
| aps.urlEncode | 0.001 | 0.000 | 0.002 | |
| array.param | 0.002 | 0.001 | 0.002 | |
| bool.param | 0.001 | 0.000 | 0.001 | |
| build.service | 0.002 | 0.000 | 0.002 | |
| checkPackageInstalled | 0.003 | 0.001 | 0.003 | |
| clear.event.handlers | 0.001 | 0.000 | 0.002 | |
| client.ip | 0.000 | 0.000 | 0.001 | |
| combobox.param | 0.001 | 0.000 | 0.001 | |
| compound.param | 0.002 | 0.000 | 0.003 | |
| copy.front.end | 0 | 0 | 0 | |
| data.frame.to.json | 0.006 | 0.001 | 0.006 | |
| data.frame.to.list | 0.003 | 0.001 | 0.005 | |
| default.param | 0.002 | 0.000 | 0.002 | |
| default.param.set | 0.001 | 0.001 | 0.001 | |
| dies.ok | 0.008 | 0.002 | 0.011 | |
| embed.APS.dataset | 0.001 | 0.000 | 0.001 | |
| event.names | 0.000 | 0.000 | 0.001 | |
| execute.handler | 0.152 | 0.011 | 0.164 | |
| file.param | 0.001 | 0.000 | 0.001 | |
| get.APS.libbase.prefix | 0.000 | 0.000 | 0.001 | |
| get.APS.outdir | 0 | 0 | 0 | |
| get.page | 0.058 | 0.005 | 0.066 | |
| getTraceback | 0.004 | 0.000 | 0.004 | |
| has.event | 0 | 0 | 0 | |
| has.page | 0.051 | 0.002 | 0.054 | |
| lives.ok | 0.000 | 0.000 | 0.001 | |
| new.FastRWeb.analysis.page.run | 0.001 | 0.000 | 0.000 | |
| new.analysis.page | 0.036 | 0.002 | 0.038 | |
| new.datanode.array | 0.014 | 0.002 | 0.017 | |
| new.datanode.html | 0.000 | 0.000 | 0.001 | |
| new.datanode.simple | 0.001 | 0.000 | 0.000 | |
| new.event.registry | 0.001 | 0.000 | 0.000 | |
| new.registry | 0 | 0 | 0 | |
| new.response | 0.001 | 0.000 | 0.001 | |
| new.rook.analysis.page.app | 0 | 0 | 0 | |
| pages | 0.040 | 0.002 | 0.042 | |
| param.set | 0.001 | 0.000 | 0.001 | |
| register.page | 0.037 | 0.001 | 0.038 | |
| remove.event | 0.000 | 0.001 | 0.001 | |
| requestEnv | 0.001 | 0.000 | 0.001 | |
| reset.APS.outdir | 0.000 | 0.000 | 0.001 | |
| rook.analysis.page.server.landing.page | 0.000 | 0.001 | 0.000 | |
| select.param | 0.001 | 0.000 | 0.001 | |
| set.APS.libbase.prefix | 0.000 | 0.000 | 0.001 | |
| set.APS.outdir | 0.000 | 0.001 | 0.000 | |
| setup.APS.knitr | 0 | 0 | 0 | |
| simple.param | 0 | 0 | 0 | |
| slider.param | 0.000 | 0.000 | 0.001 | |
| startRookAnalysisPageServer | 0.000 | 0.001 | 0.001 | |
| static.analysis.page | 0 | 0 | 0 | |
| trig.registry | 0.092 | 0.002 | 0.095 | |
| trigger.event | 0.000 | 0.000 | 0.001 | |
| tryKeepConditions | 0.002 | 0.000 | 0.002 | |
| tryKeepTraceback | 0.003 | 0.000 | 0.004 | |
| uniquify.ids.in.svg.files | 0.045 | 0.006 | 0.051 | |
| validate.param.value | 0.001 | 0.000 | 0.001 | |
| vwc.conditions | 0.002 | 0.000 | 0.003 | |
| vwc.error | 0.001 | 0.000 | 0.001 | |
| vwc.error.condition | 0.001 | 0.000 | 0.002 | |
| vwc.error.traceback | 0.005 | 0.000 | 0.005 | |
| vwc.is.error | 0.001 | 0.000 | 0.001 | |
| vwc.messages | 0.001 | 0.000 | 0.001 | |
| vwc.messages.conditions | 0.001 | 0.000 | 0.002 | |
| vwc.messages.tracebacks | 0.01 | 0.00 | 0.01 | |
| vwc.n | 0.001 | 0.000 | 0.001 | |
| vwc.n.messages | 0.001 | 0.000 | 0.001 | |
| vwc.n.warnings | 0.001 | 0.000 | 0.001 | |
| vwc.tracebacks | 0.011 | 0.000 | 0.011 | |
| vwc.value | 0.001 | 0.000 | 0.001 | |
| vwc.warnings | 0.002 | 0.000 | 0.002 | |
| vwc.warnings.conditions | 0.001 | 0.000 | 0.002 | |
| vwc.warnings.tracebacks | 0.007 | 0.000 | 0.007 | |