Package: RDAVIDWebService

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RDAVIDWebService.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RDAVIDWebService_1.20.0.tar.gz

StartedAt: 2019-04-13 04:55:05 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:59:49 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 283.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RDAVIDWebService.Rcheck

Warnings: 2

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RDAVIDWebService.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RDAVIDWebService_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RDAVIDWebService.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RDAVIDWebService/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RDAVIDWebService' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* 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 ... OK
* checking whether package 'RDAVIDWebService' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 24.0Mb
  sub-directories of 1Mb or more:
    java  21.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
benjaminis,DAVIDGODag: no visible global function definition for
  'nodeData'
benjaminis,DAVIDGODag: no visible global function definition for
  'goDag'
bonferronis,DAVIDGODag: no visible global function definition for
  'nodeData'
bonferronis,DAVIDGODag: no visible global function definition for
  'goDag'
coerce,data.frame-DAVIDFunctionalAnnotationChart: no visible global
  function definition for 'validObject'
coerce,data.frame-DAVIDFunctionalAnnotationTable: no visible global
  function definition for 'validObject'
coerce,data.frame-DAVIDGenes: no visible global function definition for
  'validObject'
counts,DAVIDGODag: no visible global function definition for 'nodeData'
counts,DAVIDGODag: no visible global function definition for 'goDag'
duplicateIds,DAVIDGenes: no visible global function definition for
  'validObject'
fdrs,DAVIDGODag: no visible global function definition for 'nodeData'
fdrs,DAVIDGODag: no visible global function definition for 'goDag'
foldEnrichments,DAVIDGODag: no visible global function definition for
  'nodeData'
foldEnrichments,DAVIDGODag: no visible global function definition for
  'goDag'
genes,DAVIDGenes: no visible global function definition for
  'validObject'
initialize,DAVIDCluster : <anonymous>: no visible global function
  definition for 'type.convert'
initialize,DAVIDCluster: no visible global function definition for
  'type.convert'
initialize,DAVIDFunctionalAnnotationChart: no visible global function
  definition for 'callNextMethod'
initialize,DAVIDFunctionalAnnotationChart: no visible global function
  definition for 'read.csv'
initialize,DAVIDFunctionalAnnotationChart: no visible global function
  definition for 'validObject'
initialize,DAVIDFunctionalAnnotationTable: no visible global function
  definition for 'callNextMethod'
initialize,DAVIDFunctionalAnnotationTable: no visible global function
  definition for 'validObject'
initialize,DAVIDFunctionalAnnotationTable: no visible global function
  definition for 'read.csv'
initialize,DAVIDGODag: no visible global function definition for
  'callNextMethod'
initialize,DAVIDGODag: no visible global function definition for
  'nodeDataDefaults<-'
initialize,DAVIDGODag: no visible global function definition for
  'GOGraph'
initialize,DAVIDGODag: no visible global function definition for
  'getFromNamespace'
initialize,DAVIDGODag: no visible global function definition for
  'inEdges'
initialize,DAVIDGODag: no visible global function definition for
  'removeNode'
initialize,DAVIDGODag: no visible global function definition for
  'nodes'
initialize,DAVIDGODag : <anonymous>: no visible global function
  definition for 'nodeData<-'
initialize,DAVIDGODag : <anonymous>: no visible global function
  definition for 'Term'
initialize,DAVIDGODag: no visible global function definition for
  'nodeData<-'
initialize,DAVIDGODag: no visible global function definition for
  'nodeData'
initialize,DAVIDGODag: no visible global function definition for
  'na.omit'
initialize,DAVIDGeneCluster: no visible global function definition for
  'callNextMethod'
initialize,DAVIDGenes: no visible global function definition for
  'callNextMethod'
initialize,DAVIDGenes: no visible global function definition for
  'read.csv'
initialize,DAVIDGenes: no visible global function definition for
  'validObject'
initialize,DAVIDTermCluster: no visible global function definition for
  'callNextMethod'
listTotals,DAVIDGODag: no visible global function definition for
  'nodeData'
listTotals,DAVIDGODag: no visible global function definition for
  'goDag'
percentages,DAVIDGODag: no visible global function definition for
  'nodeData'
percentages,DAVIDGODag: no visible global function definition for
  'goDag'
plot2D,DAVIDFunctionalAnnotationChart: no visible global function
  definition for 'callNextMethod'
plot2D,DAVIDFunctionalAnnotationTable: no visible global function
  definition for 'callNextMethod'
plot2D,DAVIDGeneCluster: no visible global function definition for
  'callNextMethod'
plot2D,DAVIDResult: no visible binding for global variable 'y'
plot2D,DAVIDResult: no visible binding for global variable 'x'
plot2D,DAVIDResult: no visible binding for global variable 'fill'
popHits,DAVIDGODag: no visible global function definition for
  'nodeData'
popHits,DAVIDGODag: no visible global function definition for 'goDag'
popTotals,DAVIDGODag: no visible global function definition for
  'nodeData'
popTotals,DAVIDGODag: no visible global function definition for 'goDag'
show,DAVIDCluster: no visible global function definition for
  'callNextMethod'
show,DAVIDFunctionalAnnotationChart: no visible global function
  definition for 'callNextMethod'
show,DAVIDFunctionalAnnotationTable: no visible global function
  definition for 'callNextMethod'
show,DAVIDGenes: no visible global function definition for
  'callNextMethod'
summary,DAVIDGODag: no visible global function definition for
  'callNextMethod'
terms,DAVIDGODag: no visible global function definition for 'nodeData'
terms,DAVIDGODag: no visible global function definition for 'goDag'
uniqueIds,DAVIDGenes: no visible global function definition for
  'validObject'
upsideDown,graph: no visible global function definition for 'nodes'
upsideDown,graph: no visible global function definition for 'edges'
upsideDown,graph : <anonymous>: no visible global function definition
  for 'edges'
upsideDown,graph : <anonymous> : <anonymous>: no visible global
  function definition for 'addEdge'
Undefined global functions or variables:
  GOGraph Term addEdge callNextMethod edges fill getFromNamespace goDag
  inEdges na.omit nodeData nodeData<- nodeDataDefaults<- nodes read.csv
  removeNode type.convert validObject x y
Consider adding
  importFrom("methods", "callNextMethod", "validObject")
  importFrom("stats", "na.omit")
  importFrom("utils", "getFromNamespace", "read.csv", "type.convert")
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpas6BgE', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpas6BgE', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpas6BgE', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpas6BgE', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpas6BgE', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpas6BgE', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpas6BgE', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpas6BgE', resetting
Examples with CPU or elapsed time > 5s
                          user system elapsed
DAVIDWebService-accessors 0.64   0.13    8.92
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpiQton3', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpiQton3', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpiQton3', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpiQton3', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpiQton3', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpiQton3', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpiQton3', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpiQton3', resetting
* 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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/RDAVIDWebService.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RDAVIDWebService_1.20.0.tar.gz && rm -rf RDAVIDWebService.buildbin-libdir && mkdir RDAVIDWebService.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RDAVIDWebService.buildbin-libdir RDAVIDWebService_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RDAVIDWebService_1.20.0.zip && rm RDAVIDWebService_1.20.0.tar.gz RDAVIDWebService_1.20.0.zip
###
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install for i386

* installing *source* package 'RDAVIDWebService' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RDAVIDWebService'
    finding HTML links ... done
    DAVIDClasses-categories                 html  
    DAVIDClasses-constructor                html  
    DAVIDClasses-genes                      html  
    DAVIDClasses-ids                        html  
    DAVIDClasses-plot2D                     html  
    DAVIDClasses-show                       html  
    DAVIDClasses-summary                    html  
    DAVIDCluster-class                      html  
    DAVIDCluster-methods                    html  
    DAVIDFunctionalAnnotationChart-class    html  
    DAVIDFunctionalAnnotationTable-class    html  
    DAVIDFunctionalAnnotationTable-methods
                                            html  
    DAVIDGODag-class                        html  
    DAVIDGODag-methods                      html  
    DAVIDGeneCluster-class                  html  
    DAVIDGenes-class                        html  
    DAVIDGenes-methods                      html  
    DAVIDResult-class                       html  
    DAVIDResult-getters                     html  
    DAVIDTermCluster-class                  html  
    DAVIDWebService-accessors               html  
    DAVIDWebService-class                   html  
    DAVIDWebService-methods                 html  
    DAVIDWebService-package                 html  
    DAVIDWebService-reports                 html  
    DAVIDdemo-annotationSummary             html  
    DAVIDdemo-annotationTable               html  
    DAVIDdemo-clusterReport                 html  
    DAVIDdemo-functionalAnnotationChart     html  
    DAVIDdemo-geneList                      html  
    DAVIDdemo-ids                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RDAVIDWebService' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RDAVIDWebService' as RDAVIDWebService_1.20.0.zip
* DONE (RDAVIDWebService)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RDAVIDWebService' successfully unpacked and MD5 sums checked
In R CMD INSTALL