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RMesquite log file (check_x86_64_mac)

Fri Feb 22 15:14:15 2013: Checking package RMesquite (SVN revision 27) ...
Additional arguments to R CMD check: --no-examples --no-tests --no-vignettes
* using log directory ‘/srv/rf/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/RMesquite.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-apple-darwin9.8.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-examples --no-tests --no-vignettes’
* checking for file ‘RMesquite/DESCRIPTION’ ... OK
* this is package ‘RMesquite’ version ‘0.5-0’
* checking CRAN incoming feasibility ... NOTE
New submission
* 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 executable files ... OK
* checking whether package ‘RMesquite’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
File ‘RMesquite/R/zzz.R’:
  .First.lib calls:
    require(rJava)
    require(ape)

Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.

editTree: no visible binding for global variable
  ‘.mesquite.GUIAvailable’
getPhyloTreeFromVector: no visible binding for global variable ‘tree’
showTree: no visible binding for global variable
  ‘.mesquite.GUIAvailable’
startMesquite: no visible binding for global variable ‘.jgr.works’
* checking Rd files ... NOTE
prepare_Rd: Rmesquite-package.Rd:52-54: Dropping empty section \seealso
prepare_Rd: startMesquite.Rd:57-63: Dropping empty section \value
prepare_Rd: startMesquite.Rd:70-72: Dropping empty section \note
prepare_Rd: startMesquite.Rd:67-69: Dropping empty section \author
prepare_Rd: startMesquite.Rd:64-66: Dropping empty section \references
prepare_Rd: startMesquite.Rd:76-78: Dropping empty section \seealso
prepare_Rd: ancestralStatesCategorical.rd:38-44: Dropping empty section \value
prepare_Rd: ancestralStatesCategorical.rd:51-53: Dropping empty section \note
prepare_Rd: ancestralStatesCategorical.rd:48-50: Dropping empty section \author
prepare_Rd: ancestralStatesCategorical.rd:45-47: Dropping empty section \references
prepare_Rd: ancestralStatesCategorical.rd:57-59: Dropping empty section \seealso
prepare_Rd: ancestralStatesCategorical.rd:60-61: Dropping empty section \examples
prepare_Rd: editTree.rd:32-34: Dropping empty section \note
prepare_Rd: editTree.rd:29-31: Dropping empty section \author
prepare_Rd: editTree.rd:26-28: Dropping empty section \references
prepare_Rd: editTree.rd:38-40: Dropping empty section \seealso
prepare_Rd: getMatrixInWindow.rd:30-32: Dropping empty section \note
prepare_Rd: getMatrixInWindow.rd:27-29: Dropping empty section \author
prepare_Rd: getMatrixInWindow.rd:24-26: Dropping empty section \references
prepare_Rd: getMatrixInWindow.rd:36-38: Dropping empty section \seealso
prepare_Rd: getTreeInWindow.rd:29-31: Dropping empty section \note
prepare_Rd: getTreeInWindow.rd:26-28: Dropping empty section \author
prepare_Rd: getTreeInWindow.rd:23-25: Dropping empty section \references
prepare_Rd: getTreeInWindow.rd:35-37: Dropping empty section \seealso
prepare_Rd: showTree.rd:23-29: Dropping empty section \value
prepare_Rd: showTree.rd:36-38: Dropping empty section \note
prepare_Rd: showTree.rd:33-35: Dropping empty section \author
prepare_Rd: showTree.rd:30-32: Dropping empty section \references
prepare_Rd: showTree.rd:42-44: Dropping empty section \seealso
prepare_Rd: stopMesquite.rd:15-17: Dropping empty section \details
prepare_Rd: stopMesquite.rd:18-24: Dropping empty section \value
prepare_Rd: stopMesquite.rd:31-33: Dropping empty section \note
prepare_Rd: stopMesquite.rd:28-30: Dropping empty section \author
prepare_Rd: stopMesquite.rd:25-27: Dropping empty section \references
prepare_Rd: stopMesquite.rd:37-39: Dropping empty section \seealso
prepare_Rd: stopMesquite.rd:40-42: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘as.matrix.jobjRef’ ‘as.phylo.jobjRef’ ‘availableMesquiteModules’
  ‘bisseLikelihood’ ‘evaluateTreeAndCharacter’ ‘from.CharacterMatrix’
  ‘from.RNumericMatrix’ ‘getCategoricalMatrices’ ‘getColumnNames’
  ‘getCommands’ ‘getContinuousMatrices’ ‘getDNAMatrices’
  ‘getNumberOfCharacters’ ‘getNumberOfTaxa’ ‘getNumberOfTrees’
  ‘getPhyloTreeFromVector’ ‘getProjectContents’ ‘getRowNames’
  ‘getTaxaBlocks’ ‘getTaxonNames’ ‘getTreeVectors’ ‘mesquite.classpath’
  ‘mesquiteApply.AncestralStateCategChar’
  ‘mesquiteApply.NumberForTreeAndCategChar’
  ‘mesquiteApply.TreeAndCategChar’ ‘mesquiteCategoricalMatrix’
  ‘mesquiteReadFile’ ‘mesquiteTaxaBlock’ ‘mesquiteTree’
  ‘setInteractive’ ‘showCommands’ ‘showDuties’ ‘showModules’
  ‘showProjectContents’ ‘startMesquiteModule’
  ‘startMesquiteModuleOfDutyClass’ ‘stopMesquiteModule’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/srv/rf/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/RMesquite.Rcheck/00check.log’
for details.

Run time: 62.63 seconds.
Additional Logs:
00install.out