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BioC 3.0: CHECK report for ENVISIONQuery on perceval

This page was generated on 2015-04-10 09:55:43 -0700 (Fri, 10 Apr 2015).

Package 277/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ENVISIONQuery 1.14.0
Alex Lisovich , Roger Day
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ENVISIONQuery
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: ENVISIONQuery
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ENVISIONQuery_1.14.0.tar.gz
StartedAt: 2015-04-10 01:09:43 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:10:48 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 65.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ENVISIONQuery.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ENVISIONQuery_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ENVISIONQuery.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.14.0’
* 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 ... [5s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
  ‘rJava’ ‘XML’
  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’
* 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 ... [4s/7s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ENVISIONQuery.Rcheck/00check.log’
for details.

ENVISIONQuery.Rcheck/00install.out:

* 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   1.14.0   2013-08-20 
* DONE (ENVISIONQuery)

ENVISIONQuery.Rcheck/ENVISIONQuery-Ex.timings:

nameusersystemelapsed
ENVISIONQuery1.1560.1183.903
getInputTypes0.0010.0000.001
getService0.0010.0000.001
getServiceClient0.0010.0000.001
getServiceNames0.0010.0000.001
getServiceOptions0.0230.0070.420
getServices0.0010.0000.000
getTool0.0020.0010.002
getToolNames0.0010.0000.001