BioC 3.3: CHECK report for ENVISIONQuery on morelia

Package: ENVISIONQuery

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ENVISIONQuery_1.19.0.tar.gz

StartedAt: 2015-10-22 05:45:51 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 05:46:26 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 35.4 seconds

RetCode: 0

Status:  OK

CheckDir: ENVISIONQuery.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ENVISIONQuery_1.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ENVISIONQuery.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ENVISIONQuery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENVISIONQuery’ version ‘1.19.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ENVISIONQuery’ can be installed ... [2s/3s] 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
* 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'.

.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’
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’
registerServices: no visible global function definition for ‘J’
Undefined global functions or variables:
  .jaddClassPath .jaddLibrary .jarray .jcall .jinit .jniInitialized J
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/4s] 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/ENVISIONQuery.Rcheck/00check.log’
for details.

* installing *source* package ‘ENVISIONQuery’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
This is  ENVISIONQuery   1.19.0   2013-08-20 
* DONE (ENVISIONQuery)

name	user	system	elapsed
ENVISIONQuery	0.898	0.062	3.054
getInputTypes	0.001	0.000	0.001
getService	0.001	0.000	0.001
getServiceClient	0.001	0.001	0.002
getServiceNames	0.001	0.000	0.001
getServiceOptions	0.017	0.003	0.081
getServices	0.000	0.000	0.001
getTool	0.002	0.000	0.002
getToolNames	0.001	0.000	0.002