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BioC 3.3: CHECK report for AnalysisPageServer on zin2

This page was generated on 2016-10-13 12:45:15 -0700 (Thu, 13 Oct 2016).

Package 40/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnalysisPageServer 1.6.2
Brad Friedman
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/AnalysisPageServer
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnalysisPageServer
Version: 1.6.2
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AnalysisPageServer_1.6.2.tar.gz
StartedAt: 2016-10-12 23:23:37 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:24:40 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 62.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: AnalysisPageServer.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AnalysisPageServer_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AnalysisPageServer.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.6.2’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/htdocs/client/.bowerrc
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Analysis/show/AnalysisPageShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Analysis/show/AnalysisPageShowRouter.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/ToolOverviewShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/itemview/ToolOverviewBodyView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/itemview/ToolOverviewListView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/layoutview/ToolOverviewView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/ToolOverview/tooloverview-app.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/show/APSLandingPageShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/show/EPLandingPageShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/show/EPStudyFormShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/show/LandingPageShowRouter.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/show/layoutview/APSLandingPageView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/show/layoutview/EPLandingPageView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Primary/show/PrimaryPageShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Primary/show/PrimaryPageShowRouter.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Primary/show/layoutview/PrimaryPageView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/fetch/AnalysisFetchController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/SuggestionsCallbackController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/models/ComboboxParameterModel.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/models/createComboboxParameterModel.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/models/multipleMixin.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/models/nonMultipleMixin.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/models/nonSelfDependentMixin.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/models/selfDependentMixin.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/show/ComboboxShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/show/Select2ComboboxBehavior.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Combobox/show/itemview/ComboboxParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/ConditionalPersistent/ConditionalPersistentController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/ConditionalPersistent/models/PersistentParameterCollection.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/DisplayCallbackController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Persistent/PersistentController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/models/SelectParameterModel.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/models/createSelectParameterModel.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/models/multipleMixin.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/models/nonMultipleMixin.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/show/Select2SelectBehavior.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/show/SelectShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/show/itemview/DropdownSelectParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/show/itemview/RadioSelectParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/show/itemview/SelectParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select/show/itemview/getSelectParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Select2Behavior/Select2Behavior.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/ShowIfAdvancedController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Summary/show/SummaryShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Summary/show/compositeview/ParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Summary/show/compositeview/ParametersSummaryView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/fetch/ParametersFetchController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/models/ArrayParameterModel.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/models/CompoundParameterModel.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/models/FileParameterModel.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/models/ParameterChildrenCollection.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/models/ParameterCollection.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/show/ArrayShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/show/ParametersShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/show/behaviors/ParameterBehavior.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/show/compositeview/ArrayParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/show/compositeview/CompoundParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/show/itemview/BoolParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/show/itemview/FileParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/show/itemview/SliderParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/show/itemview/TextParameterView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServerStatic/Pages/Datasets/show/DatasetsShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServerStatic/Pages/Datasets/show/DatasetsShowRouter.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServerStatic/Pages/Datasets/show/collectionview/DatasetsView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServerStatic/Pages/Datasets/show/layoutview/DatasetView.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServerStatic/Pages/fetch/AnalysisFetchController.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServerStatic/Pages/fetch/PagesFetchController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Arrays/show/collectionview/ArrayListView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Arrays/show/collectionview/TabsContentView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Arrays/show/collectionview/TabsNavView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Arrays/show/layoutview/ArrayListItemView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Arrays/show/layoutview/ArrayTabsView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/SideMenu/show/MenuShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/SideMenu/show/itemview/SideMenuView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Sidebar/show/SidebarShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Sidebar/show/behaviors/AccordionGroupBehavior.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Sidebar/show/compositeview/FilterItemView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Sidebar/show/compositeview/FiltersView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Sidebar/show/itemview/TaggingView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Sidebar/show/itemview/WarningsView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Sidebar/show/layoutview/ParametersView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Sidebar/show/layoutview/SidebarView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Svg/download/SvgDownloadController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Svg/show/PointDetailsShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Svg/show/d3BrushTaggingController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Svg/show/d3BrushZoomingController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Svg/show/d3TagsShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/Svg/show/d3ZoomingController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Plots/show/itemview/ProgressBarView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Tables/Tbody/show/TbodyShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Tables/Tbody/show/itemview/TbodyView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Tables/Thead/show/TheadShowController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Tables/Thead/show/compositeview/TheadItemView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Tables/Thead/show/compositeview/TheadView.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Tables/download/TableDataDownloadController.js
  AnalysisPageServer/inst/htdocs/client/js/src/Common/AnalysisData/Tables/models/TableDataLocalModel.js
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/itemview
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/layoutview
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/ConditionalPersistent/models
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServer/Parameters/Summary/show/compositeview
  AnalysisPageServer/inst/htdocs/client/js/src/AnalysisPageServerStatic/Pages/Datasets/show/collectionview

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 35.5Mb
  sub-directories of 1Mb or more:
    doc     28.2Mb
    htdocs   5.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
.event.registry.or.die: no visible global function definition for ‘is’
.graphIsAcyclic: no visible global function definition for ‘new’
.graphIsAcyclic: no visible global function definition for ‘is’
.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’
.is.registry.or.stop: no visible global function definition for ‘is’
.page.meta.info: no visible global function definition for ‘is’
.parse.url.query.string: no visible global function definition for
  ‘setNames’
.prepare.params: no visible binding for global variable ‘svg’
.prepare.params: no visible global function definition for ‘is’
.transform.param.value.compound: no visible global function definition
  for ‘setNames’
.validate.analysis.page: no visible global function definition for ‘is’
.validate.atomic: no visible global function definition for ‘is’
.validate.brand.builder: no visible global function definition for ‘is’
.validate.data.frame.list: no visible global function definition for
  ‘is’
.validate.decoder.list: no visible global function definition for ‘is’
.validate.device.list: no visible global function definition for ‘is’
.validate.param: no visible global function definition for ‘is’
.validate.param.bool: no visible global function definition for ‘is’
.validate.param.combobox: no visible global function definition for
  ‘is’
.validate.param.select: no visible global function definition for ‘is’
.validate.param.slider: no visible global function definition for ‘is’
.validate.paramset: no visible global function definition for ‘is’
.validate.persistent.params: no visible binding for global variable
  ‘is’
.validate.plot.pars.transformer: no visible global function definition
  for ‘is’
.validate.type: no visible global function definition for ‘is’
add.event: no visible global function definition for ‘setNames’
analysis.page.link: no visible global function definition for ‘is’
analysis.page.of.current.app: no visible global function definition for
  ‘is’
annotate.analysis.page.svg: no visible global function definition for
  ‘is’
annotate.data.frame: no visible global function definition for ‘as’
annotate.data.frame: no visible global function definition for ‘is’
annotate.data.frame: no visible binding for global variable ‘is’
appendCustomContent: no visible global function definition for ‘is’
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’
checkPackageVersion: no visible global function definition for ‘is’
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’
current.app : <anonymous>: no visible global function definition for
  ‘is’
default.param: no visible global function definition for ‘is’
embed.APS.dataset: no visible global function definition for ‘is’
embed.APS.dataset: no visible binding for global variable ‘svg’
embed.APS.dataset: no visible global function definition for ‘dev.off’
encode.datanode: no visible global function definition for ‘is’
execute.handler: no visible binding for global variable ‘svg’
execute.handler: no visible global function definition for ‘is’
execute.handler: no visible global function definition for ‘setNames’
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’
is.registry: no visible global function definition for ‘is’
new.FastRWeb.analysis.page.run: no visible global function definition
  for ‘is’
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.analysis.page: no visible global function definition for ‘is’
new.datanode.array: no visible binding for global variable ‘is’
new.datanode.plot: no visible global function definition for ‘is’
new.datanode.table: no visible global function definition for ‘is’
new.registry: no visible global function definition for ‘is’
new.rook.analysis.page.app: no visible global function definition for
  ‘is’
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’
param.set: no visible global function definition for ‘is’
param.set: no visible binding for global variable ‘is’
persistent.param.dependencies.AnalysisPageParamSet: no visible global
  function definition for ‘setNames’
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 ‘is’
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 ‘is’
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’
register.page: no visible global function definition for ‘is’
simple.param: no visible global function definition for ‘is’
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’
static.analysis.page: no visible global function definition for ‘is’
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’
tryKeepConditions: no visible global function definition for ‘is’
uniquify.ids.in.svg.files: no visible global function definition for
  ‘setNames’
validate.compound.param.value: no visible global function definition
  for ‘setNames’
vwc.conditions: no visible global function definition for ‘is’
vwc.is.error: no visible global function definition for ‘is’
vwc.messages: no visible global function definition for ‘is’
vwc.n: no visible global function definition for ‘is’
vwc.tracebacks: no visible global function definition for ‘is’
vwc.value: no visible global function definition for ‘is’
Undefined global functions or variables:
  App FILES GET POST SERVER WebResult all.pages analysis analysis.id as
  brand capture.output checkEquals clean.tmpdir defineTestSuite dev.cur
  dev.list dev.off events file.params handler handlers head in.analysis
  is is.textarea.wrap.request new 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
  setNames status str svg temp.plot.file
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "dev.off", "png", "svg")
  importFrom("graphics", "plot")
  importFrom("methods", "as", "is", "new")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output", "head", "packageVersion",
             "sessionInfo", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'paramSetToJSON'
  ‘ps’
Documented arguments not in \usage in documentation object 'paramSetToJSON':
  ‘ap’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: 1 WARNING, 9 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/AnalysisPageServer.Rcheck/00check.log’
for details.

AnalysisPageServer.Rcheck/00install.out:

* installing *source* package ‘AnalysisPageServer’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-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:154:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "x and y have different lengths";
                  ^
AnalysisPageSVG.cpp:157:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(els.size() < start + n)  {
                           ^
AnalysisPageSVG.cpp:194:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < x.size(); i++)  {
                               ^
AnalysisPageSVG.cpp:210:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_x.size(); i++)  {
                                     ^
AnalysisPageSVG.cpp:215:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_y.size(); i++)  {
                                     ^
g++ -I/home/biocbuild/bbs-3.3-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-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c SearchReplace2.cpp -o SearchReplace2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c catch.c -o catch.o
g++ -I/home/biocbuild/bbs-3.3-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:24:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "different sizes";
                  ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c tinyxml2.cpp -o tinyxml2.o
g++ -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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/AnalysisPageServer-Ex.timings:

nameusersystemelapsed
add.event0.0010.0000.001
add.event.handler0.0010.0000.002
analysis.page.link0.0020.0000.001
aps.urlEncode0.0010.0000.001
array.param0.0000.0000.002
bool.param0.0000.0000.001
build.service0.0020.0000.002
checkPackageInstalled0.0020.0000.002
clear.event.handlers0.0010.0000.001
client.ip0.0010.0000.001
combobox.param0.0000.0000.001
compound.param0.0030.0000.002
copy.front.end0.0000.0000.001
data.frame.to.json0.0040.0000.004
data.frame.to.list0.0020.0000.002
default.param0.0010.0000.001
default.param.set0.0020.0000.002
dies.ok0.0070.0000.007
embed.APS.dataset0.0000.0000.001
event.names0.0010.0000.001
execute.handler0.0820.0120.093
file.param0.0000.0000.001
get.APS.outdir0.0010.0000.001
get.page0.0480.0000.048
getTraceback0.0030.0000.003
has.event0.0010.0000.001
has.page0.0360.0000.035
lives.ok000
new.FastRWeb.analysis.page.run0.0010.0000.001
new.analysis.page0.0280.0040.032
new.datanode.array0.0120.0000.011
new.datanode.html0.0000.0000.001
new.datanode.simple0.0010.0000.001
new.event.registry0.0000.0000.001
new.registry0.0010.0000.000
new.response0.0010.0000.002
new.rook.analysis.page.app0.0010.0000.000
pages0.0330.0040.038
param.set0.0010.0000.001
register.page0.0320.0000.031
remove.event0.0000.0000.001
requestEnv0.0000.0000.001
reset.APS.outdir000
rook.analysis.page.server.landing.page0.0000.0000.001
select.param0.0010.0000.000
set.APS.outdir0.0000.0000.001
setup.APS.knitr0.0010.0000.001
simple.param0.0010.0000.000
slider.param0.0010.0000.001
startRookAnalysisPageServer0.0010.0000.002
static.analysis.page0.0010.0000.000
trig.registry0.0720.0040.077
trigger.event0.0010.0000.001
tryKeepConditions0.0000.0040.002
tryKeepTraceback0.0020.0000.002
uniquify.ids.in.svg.files0.0260.0000.026
validate.param.value0.0010.0000.001
vwc.conditions0.0020.0000.002
vwc.error0.0010.0000.001
vwc.error.condition0.0010.0000.001
vwc.error.traceback0.0030.0000.004
vwc.is.error0.0020.0000.001
vwc.messages0.0010.0000.001
vwc.messages.conditions0.0020.0000.001
vwc.messages.tracebacks0.0060.0000.007
vwc.n0.0010.0000.001
vwc.n.messages0.0010.0000.001
vwc.n.warnings0.0010.0000.001
vwc.tracebacks0.0070.0000.006
vwc.value0.0010.0000.001
vwc.warnings0.0010.0000.001
vwc.warnings.conditions0.0010.0000.001
vwc.warnings.tracebacks0.0070.0000.007