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BioC 3.3: CHECK report for AnalysisPageServer on moscato2

This page was generated on 2016-10-13 12:53:29 -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: rm -rf AnalysisPageServer.buildbin-libdir AnalysisPageServer.Rcheck && mkdir AnalysisPageServer.buildbin-libdir AnalysisPageServer.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnalysisPageServer.buildbin-libdir AnalysisPageServer_1.6.2.tar.gz >AnalysisPageServer.Rcheck\00install.out 2>&1 && cp AnalysisPageServer.Rcheck\00install.out AnalysisPageServer-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=AnalysisPageServer.buildbin-libdir --install="check:AnalysisPageServer-install.out" --force-multiarch --no-vignettes --timings AnalysisPageServer_1.6.2.tar.gz
StartedAt: 2016-10-13 00:54:01 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:01:59 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 478.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: AnalysisPageServer.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AnalysisPageServer.buildbin-libdir AnalysisPageServer.Rcheck && mkdir AnalysisPageServer.buildbin-libdir AnalysisPageServer.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AnalysisPageServer.buildbin-libdir AnalysisPageServer_1.6.2.tar.gz >AnalysisPageServer.Rcheck\00install.out 2>&1 && cp AnalysisPageServer.Rcheck\00install.out AnalysisPageServer-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=AnalysisPageServer.buildbin-libdir --install="check:AnalysisPageServer-install.out" --force-multiarch --no-vignettes --timings AnalysisPageServer_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/AnalysisPageServer.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnalysisPageServer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnalysisPageServer' version '1.6.2'
* 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 whether package 'AnalysisPageServer' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.8Mb
  sub-directories of 1Mb or more:
    doc     28.1Mb
    htdocs   5.1Mb
    libs     1.6Mb
* 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.3-bioc/meat/AnalysisPageServer.buildbin-libdir/AnalysisPageServer/libs/i386/AnalysisPageServer.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 10 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/AnalysisPageServer.Rcheck/00check.log'
for details.


AnalysisPageServer.Rcheck/00install.out:


install for i386

* installing *source* package 'AnalysisPageServer' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c AnalysisPageSVG.cpp -o AnalysisPageSVG.o
AnalysisPageSVG.cpp: In function 'int matchPlotPoints(XMLElementList, std::deque<double>, std::deque<double>, double, int, int)':
AnalysisPageSVG.cpp:154:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "x and y have different lengths";
        ^
AnalysisPageSVG.cpp:157:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(els.size() < start + n)  {
                 ^
AnalysisPageSVG.cpp:194:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < x.size(); i++)  {
                      ^
AnalysisPageSVG.cpp:210:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_x.size(); i++)  {
                        ^
AnalysisPageSVG.cpp:215:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_y.size(); i++)  {
                        ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c SearchReplace2.cpp -o SearchReplace2.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c catch.c -o catch.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cor.cpp -o cor.o
cor.cpp: In function 'double basic_cor(const std::deque<double>&, const std::deque<double>&)':
cor.cpp:24:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "different sizes";
        ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c tinyxml2.cpp -o tinyxml2.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o AnalysisPageServer.dll tmp.def AnalysisPageSVG.o R_init_AnalysisPageServer.o SearchReplace2.o catch.o cor.o tinyxml2.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/AnalysisPageServer.buildbin-libdir/AnalysisPageServer/libs/i386
** 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

install for x64

* installing *source* package 'AnalysisPageServer' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c AnalysisPageSVG.cpp -o AnalysisPageSVG.o
AnalysisPageSVG.cpp: In function 'int matchPlotPoints(XMLElementList, std::deque<double>, std::deque<double>, double, int, int)':
AnalysisPageSVG.cpp:154:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "x and y have different lengths";
        ^
AnalysisPageSVG.cpp:157:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(els.size() < start + n)  {
                 ^
AnalysisPageSVG.cpp:194:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < x.size(); i++)  {
                      ^
AnalysisPageSVG.cpp:210:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_x.size(); i++)  {
                        ^
AnalysisPageSVG.cpp:215:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int i = 0; i < els_y.size(); i++)  {
                        ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_init_AnalysisPageServer.cpp -o R_init_AnalysisPageServer.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c SearchReplace2.cpp -o SearchReplace2.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c catch.c -o catch.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c cor.cpp -o cor.o
cor.cpp: In function 'double basic_cor(const std::deque<double>&, const std::deque<double>&)':
cor.cpp:24:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(n != y.size())  throw "different sizes";
        ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c tinyxml2.cpp -o tinyxml2.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o AnalysisPageServer.dll tmp.def AnalysisPageSVG.o R_init_AnalysisPageServer.o SearchReplace2.o catch.o cor.o tinyxml2.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/AnalysisPageServer.buildbin-libdir/AnalysisPageServer/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnalysisPageServer' as AnalysisPageServer_1.6.2.zip
* DONE (AnalysisPageServer)

AnalysisPageServer.Rcheck/examples_i386/AnalysisPageServer-Ex.timings:

nameusersystemelapsed
add.event000
add.event.handler000
analysis.page.link0.000.000.33
aps.urlEncode000
array.param000
bool.param000
build.service000
checkPackageInstalled0.010.000.02
clear.event.handlers000
client.ip000
combobox.param000
compound.param0.020.000.01
copy.front.end000
data.frame.to.json000
data.frame.to.list0.020.000.02
default.param000
default.param.set000
dies.ok0.010.000.02
embed.APS.dataset000
event.names000
execute.handler0.350.010.48
file.param000
get.APS.outdir000
get.page0.120.021.30
getTraceback000
has.event000
has.page0.130.000.12
lives.ok000
new.FastRWeb.analysis.page.run000
new.analysis.page0.110.010.12
new.datanode.array0.020.000.02
new.datanode.html000
new.datanode.simple000
new.event.registry000
new.registry000
new.response000
new.rook.analysis.page.app000
pages0.110.050.15
param.set000
register.page0.160.020.17
remove.event000
requestEnv000
reset.APS.outdir000
rook.analysis.page.server.landing.page000
select.param000
set.APS.outdir000
setup.APS.knitr000
simple.param000
slider.param000
startRookAnalysisPageServer000
static.analysis.page000
trig.registry0.190.040.23
trigger.event000
tryKeepConditions000
tryKeepTraceback000
uniquify.ids.in.svg.files0.040.000.05
validate.param.value000
vwc.conditions000
vwc.error000
vwc.error.condition000
vwc.error.traceback000
vwc.is.error000
vwc.messages000
vwc.messages.conditions000
vwc.messages.tracebacks000
vwc.n000
vwc.n.messages000
vwc.n.warnings000
vwc.tracebacks000
vwc.value000
vwc.warnings000
vwc.warnings.conditions000
vwc.warnings.tracebacks0.010.000.01

AnalysisPageServer.Rcheck/examples_x64/AnalysisPageServer-Ex.timings:

nameusersystemelapsed
add.event0.010.000.02
add.event.handler000
analysis.page.link000
aps.urlEncode000
array.param000
bool.param000
build.service0.020.000.02
checkPackageInstalled000
clear.event.handlers000
client.ip000
combobox.param000
compound.param000
copy.front.end000
data.frame.to.json0.020.000.02
data.frame.to.list000
default.param000
default.param.set0.080.000.07
dies.ok0.010.000.02
embed.APS.dataset000
event.names000
execute.handler0.350.010.56
file.param000
get.APS.outdir000
get.page0.180.020.27
getTraceback000
has.event000
has.page0.160.030.17
lives.ok000
new.FastRWeb.analysis.page.run000
new.analysis.page0.170.000.17
new.datanode.array0.020.000.01
new.datanode.html000
new.datanode.simple000
new.event.registry000
new.registry000
new.response000
new.rook.analysis.page.app0.020.000.01
pages0.170.010.41
param.set0.020.000.02
register.page0.180.000.31
remove.event000
requestEnv000
reset.APS.outdir000
rook.analysis.page.server.landing.page000
select.param0.020.000.01
set.APS.outdir000
setup.APS.knitr000
simple.param000
slider.param000
startRookAnalysisPageServer0.010.000.02
static.analysis.page000
trig.registry0.300.040.33
trigger.event000
tryKeepConditions000
tryKeepTraceback0.010.000.02
uniquify.ids.in.svg.files0.050.010.06
validate.param.value000
vwc.conditions000
vwc.error000
vwc.error.condition000
vwc.error.traceback000
vwc.is.error0.020.000.01
vwc.messages000
vwc.messages.conditions000
vwc.messages.tracebacks0.020.000.02
vwc.n000
vwc.n.messages0.010.000.01
vwc.n.warnings000
vwc.tracebacks0.020.000.02
vwc.value000
vwc.warnings000
vwc.warnings.conditions000
vwc.warnings.tracebacks000