CRAN Package Check Results for Package maticce

Last updated on 2014-09-12 01:48:08.

Check Details

Version: 1.0-3
Check: DESCRIPTION meta-information
Result: NOTE
    Package listed in more than one of Depends, Imports, Suggests, Enhances:
     ‘ouch’
    A package should be listed in only one of these fields.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0-3
Check: for old-style vignette sources
Result: NOTE
    Vignette sources only in ‘inst/doc’:
     ‘maticce.Rnw’
    A ‘vignettes’ directory is required as from R 3.1.0
    and these will not be indexed nor checked
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.0-3
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘misc’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0-3
Check: Rd line widths
Result: NOTE
    Rd file 'carex.Rd':
     \examples lines wider than 100 characters:
     # for expedience, only tests for changes at up to 2 of the first 4 nodes on 2 trees visited in the MCMC phylogenetic analysis
     trialBayesTrees <- runBatchHansen(trees, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2)
     summary(trialBayesTrees) # summarizes results using summary.hansenBatch and displays the results using print.hansenSummary
     trialBayesConsensus <- runBatchHansen(contree, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2)
    
    Rd file 'multiModel.Rd':
     \usage lines wider than 90 characters:
     multiModel(phy, dat, node, models = c("whole.brown", "whole.ou1", "whole.ou2", "part.brown", "part.ou"))
     \examples lines wider than 100 characters:
     mm2 <- multiModel(carex$ovales.tree, ovales.data, ovales.nodes[[2]]) # compares five different models of character change at node 2
     pie(mm2$IC$AICcwi, labels = mm2$IC$name, col = rainbow(length(mm2$IC$name)), main = "AICc weights")
     barplot(c(noChangeAICwi, changeAICwi), ylim = c(0,1), names.arg = c('no transition', 'transition'),
    
    Rd file 'ouSim.Rd':
     \usage lines wider than 90 characters:
     ouSim(object, rootState = 0, shiftBranches = NULL, shiftStates = NULL, sqrt.alpha = 0, variance = 1, theta = rootState, model = "OU", b ... [TRUNCATED]
     ouSim(object, rootState = 0, sqrt.alpha = 0, variance = 1, theta = rootState, steps = 1000, ...)
    
    Rd file 'regimeMaker.Rd':
     \examples lines wider than 100 characters:
     # if we are interested in comparing the single-change models that allow changes only at nodes 1, 2, 4, 5, and 8, as well as the no-ch ... [TRUNCATED]
    
    Rd file 'regimeMatrix.Rd':
     \examples lines wider than 100 characters:
     # evaluating a set of models allowing all possible permutations of changes at 15 nodes will be quite time-consuming:
     # paring that down to all possible permutations of changes at 15 nodes, up to a maximum of 5 changes, is much more manageable:
    
    Rd file 'runBatchHansen.Rd':
     \usage lines wider than 90 characters:
     runBatchHansen(ouchTrees, characterStates, cladeMembersList, filePrefix = NULL, di = NULL, nodeNames = NULL, maxNodes = length(cladeMem ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0-3
Check: top-level files
Result: NOTE
    File
     inst/LICENSE
    will install at top-level and is not mentioned in the DESCRIPTION file.
Flavors: r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0-3
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-release-osx-x86_64-snowleopard

Version: 1.0-3
Check: for old-style vignette sources
Result: NOTE
    Vignette sources only in 'inst/doc':
     'maticce.Rnw'
    A 'vignettes' directory will be required as from R 3.1.0
Flavor: r-oldrel-windows-ix86+x86_64