Package: ENVISIONQuery

Version: 1.26.0

Command: rm -rf ENVISIONQuery.buildbin-libdir ENVISIONQuery.Rcheck && mkdir ENVISIONQuery.buildbin-libdir ENVISIONQuery.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ENVISIONQuery.buildbin-libdir ENVISIONQuery_1.26.0.tar.gz >ENVISIONQuery.Rcheck\00install.out 2>&1 && cp ENVISIONQuery.Rcheck\00install.out ENVISIONQuery-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ENVISIONQuery.buildbin-libdir --install="check:ENVISIONQuery-install.out" --force-multiarch --no-vignettes --timings ENVISIONQuery_1.26.0.tar.gz

StartedAt: 2018-04-11 23:47:25 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:48:14 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 49.6 seconds

RetCode: 0

Status:  OK

CheckDir: ENVISIONQuery.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ENVISIONQuery.buildbin-libdir ENVISIONQuery.Rcheck && mkdir ENVISIONQuery.buildbin-libdir ENVISIONQuery.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ENVISIONQuery.buildbin-libdir ENVISIONQuery_1.26.0.tar.gz >ENVISIONQuery.Rcheck\00install.out 2>&1 && cp ENVISIONQuery.Rcheck\00install.out ENVISIONQuery-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ENVISIONQuery.buildbin-libdir --install="check:ENVISIONQuery-install.out" --force-multiarch --no-vignettes --timings ENVISIONQuery_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ENVISIONQuery.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ENVISIONQuery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ENVISIONQuery' version '1.26.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ENVISIONQuery' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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 ... NOTE
Packages in Depends field not imported from:
  'XML' 'rJava'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'ENVISIONQuery/R/zzz.R':
  .onAttach calls:
    cat("This is ", pkgname, " ", desc$Version, " ", desc$Date, "\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

.First.lib: no visible global function definition for 'data'
.onAttach : getJavaVersion: no visible global function definition for
  '.jcall'
.onAttach : jpackage: no visible binding for global variable
  '.jniInitialized'
.onAttach : jpackage: no visible global function definition for
  '.jinit'
.onAttach : jpackage: no visible global function definition for
  '.jaddClassPath'
.onAttach : jpackage: no visible global function definition for
  '.jaddLibrary'
.onAttach: no visible global function definition for
  'packageDescription'
ENVISIONQuery.chunk: no visible global function definition for
  '.jarray'
formatIdMap: no visible global function definition for 'xmlTreeParse'
formatIdMap: no visible global function definition for 'xmlRoot'
formatIdMap: no visible global function definition for 'xmlChildren'
formatIntact: no visible global function definition for 'xmlTreeParse'
formatIntact: no visible global function definition for 'xmlRoot'
formatIntact: no visible global function definition for 'xmlChildren'
formatPicr: no visible global function definition for 'xmlTreeParse'
formatPicr: no visible global function definition for 'xmlRoot'
formatPicr: no visible global function definition for 'xmlChildren'
formatReactome: no visible global function definition for
  'xmlTreeParse'
formatReactome: no visible global function definition for 'xmlRoot'
formatReactome: no visible global function definition for 'xmlChildren'
getIdEntries: no visible global function definition for 'xmlChildren'
getIdEntries : <anonymous>: no visible global function definition for
  'xmlAttrs'
getIdMatchInfo: no visible global function definition for 'xmlChildren'
getIdMatchInfo : <anonymous>: no visible global function definition for
  'xmlAttrs'
getIdMatchInfo : <anonymous>: no visible global function definition for
  'xmlValue'
getIdMatchInfo : <anonymous>: no visible global function definition for
  'xmlChildren'
getInputIdEntries: no visible global function definition for
  'xmlChildren'
getInputIdEntries : <anonymous>: no visible global function definition
  for 'xmlAttrs'
getIntactMatchInfo: no visible global function definition for
  'xmlChildren'
getIntactMatchInfo : <anonymous>: no visible global function definition
  for 'xmlAttrs'
getIntactMatchInfo: no visible global function definition for
  'xmlAttrs'
getPicrMatchInfo: no visible global function definition for
  'xmlChildren'
getPicrMatchInfo : <anonymous>: no visible global function definition
  for 'xmlAttrs'
getPicrMatchInfo: no visible global function definition for 'xmlAttrs'
getPositiveResultSetIDs: no visible global function definition for
  'xmlChildren'
getPositiveResultSetIDs: no visible global function definition for
  'xmlAttrs'
getPositiveResultSetIDs : <anonymous>: no visible global function
  definition for 'xmlAttrs'
getReactomeMatchInfo: no visible global function definition for
  'xmlChildren'
getReactomeMatchInfo : <anonymous>: no visible global function
  definition for 'xmlAttrs'
getReactomeMatchInfo: no visible global function definition for
  'xmlValue'
getReactomeMatchInfo: no visible global function definition for
  'xmlAttrs'
getService: no visible global function definition for 'menu'
getServices: no visible global function definition for
  'assignInNamespace'
getTool: no visible global function definition for 'menu'
progressMsg: no visible global function definition for 'flush.console'
registerServices: no visible global function definition for 'new'
registerServices: no visible global function definition for 'J'
Undefined global functions or variables:
  .jaddClassPath .jaddLibrary .jarray .jcall .jinit .jniInitialized J
  assignInNamespace data flush.console menu new packageDescription
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "assignInNamespace", "data", "flush.console",
             "menu", "packageDescription")
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 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
Examples with CPU or elapsed time > 5s
              user system elapsed
ENVISIONQuery 1.66   0.09    5.06
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/ENVISIONQuery.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ENVISIONQuery' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ENVISIONQuery'
    finding HTML links ... done
    ENVISIONQuery-package                   html  
    ENVISIONQuery                           html  
    ENVISIONQuery.chunk                     html  
    ENVISIONQuery.loop                      html  
    ENVISIONServices                        html  
    formatIdMap                             html  
    formatIntact                            html  
    formatPicr                              html  
    formatReactome                          html  
    getFormatter                            html  
    getIdEntries                            html  
    getIdMatchInfo                          html  
    getInputIdEntries                       html  
    getInputTypes                           html  
    getIntactMatchInfo                      html  
    getMerger                               html  
    getPicrMatchInfo                        html  
    getPositiveResultSetIDs                 html  
    getReactomeMatchInfo                    html  
    getService                              html  
    getServiceClient                        html  
    getServiceNames                         html  
    getServiceOptions                       html  
    getServices                             html  
    getTool                                 html  
    getToolNames                            html  
    jgetOptions                             html  
    mergeFrameList                          html  
    mergeMatchRows                          html  
    progressMsg                             html  
    registerServices                        html  
    toChunks                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
This is  ENVISIONQuery   1.26.0   2013-08-20 
In R CMD INSTALL

install for x64

* installing *source* package 'ENVISIONQuery' ...
** testing if installed package can be loaded
This is  ENVISIONQuery   1.26.0   2013-08-20 
* MD5 sums
packaged installation of 'ENVISIONQuery' as ENVISIONQuery_1.26.0.zip
* DONE (ENVISIONQuery)
In R CMD INSTALL
In R CMD INSTALL