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BioC 3.4: CHECK report for RDAVIDWebService on tokay1

This page was generated on 2017-04-15 16:17:58 -0400 (Sat, 15 Apr 2017).

Package 1018/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RDAVIDWebService 1.12.0
Cristobal Fresno
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/RDAVIDWebService
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RDAVIDWebService
Version: 1.12.0
Command: rm -rf RDAVIDWebService.buildbin-libdir RDAVIDWebService.Rcheck && mkdir RDAVIDWebService.buildbin-libdir RDAVIDWebService.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RDAVIDWebService.buildbin-libdir RDAVIDWebService_1.12.0.tar.gz >RDAVIDWebService.Rcheck\00install.out 2>&1 && cp RDAVIDWebService.Rcheck\00install.out RDAVIDWebService-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RDAVIDWebService.buildbin-libdir --install="check:RDAVIDWebService-install.out" --force-multiarch --no-vignettes --timings RDAVIDWebService_1.12.0.tar.gz
StartedAt: 2017-04-15 00:23:25 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:27:35 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 250.3 seconds
RetCode: 0
Status:  OK  
CheckDir: RDAVIDWebService.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RDAVIDWebService.buildbin-libdir RDAVIDWebService.Rcheck && mkdir RDAVIDWebService.buildbin-libdir RDAVIDWebService.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RDAVIDWebService.buildbin-libdir RDAVIDWebService_1.12.0.tar.gz >RDAVIDWebService.Rcheck\00install.out 2>&1 && cp RDAVIDWebService.Rcheck\00install.out RDAVIDWebService-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RDAVIDWebService.buildbin-libdir --install="check:RDAVIDWebService-install.out" --force-multiarch --no-vignettes --timings RDAVIDWebService_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/RDAVIDWebService.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... 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 23.8Mb
  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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/RDAVIDWebService.Rcheck/00check.log'
for details.


RDAVIDWebService.Rcheck/00install.out:


install for i386

* installing *source* package 'RDAVIDWebService' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'RDAVIDWebService' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RDAVIDWebService' as RDAVIDWebService_1.12.0.zip
* DONE (RDAVIDWebService)

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

nameusersystemelapsed
DAVIDClasses-categories0.410.040.43

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

nameusersystemelapsed
DAVIDClasses-categories0.550.020.56