CRAN Package Check Results for Package phangorn

Last updated on 2014-10-02 17:48:18.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.99-7 5.88 133.56 139.44 NOTE
r-devel-linux-x86_64-debian-gcc 1.99-7 6.68 128.94 135.62 NOTE
r-devel-linux-x86_64-fedora-clang 1.99-7 298.69 NOTE
r-devel-linux-x86_64-fedora-gcc 1.99-7 278.49 NOTE
r-devel-osx-x86_64-clang 1.99-7 229.86 NOTE
r-devel-windows-ix86+x86_64 1.99-7 22.00 207.00 229.00 NOTE
r-patched-linux-x86_64 1.99-7 6.88 135.10 141.98 NOTE
r-patched-solaris-sparc 1.99-7 1108.50 NOTE --no-vignettes
r-patched-solaris-x86 1.99-7 374.60 NOTE
r-release-linux-ix86 1.99-7 8.03 162.00 170.03 NOTE
r-release-linux-x86_64 1.99-7 7.43 133.33 140.76 NOTE
r-release-osx-x86_64-mavericks 1.99-7 NOTE
r-release-osx-x86_64-snowleopard 1.99-7 NOTE
r-release-windows-ix86+x86_64 1.99-7 19.00 220.00 239.00 NOTE
r-oldrel-windows-ix86+x86_64 1.99-7 26.00 221.00 247.00 OK

Check Details

Version: 1.99-7
Check: foreign function calls
Result: NOTE
    Calls with DUP:
     .C("C_reorder", edge[, 1], edge[, 2], as.integer(l + 2L), as.integer(m +
     2L), integer(l + 2L), as.integer(nTips + 1L), DUP = FALSE,
     PACKAGE = "phangorn")
     .C("C_cisort", as.integer(x), as.integer(y), k, l, integer(k +
     l), DUP = FALSE)
     .C("get_single_index_integer", as.integer(edge[, 2L]), as.integer(tip),
     integer(1L), PACKAGE = "phangorn", NAOK = TRUE, DUP = FALSE)
     .C("get_two_index_integer", as.integer(edge[, 1L]), as.integer(node),
     integer(2L), PACKAGE = "phangorn", NAOK = TRUE, DUP = FALSE)
     .C("C_reorder", parents, child, as.integer(n), as.integer(m),
     integer(n), as.integer(root - 1L), DUP = FALSE, PACKAGE = "phangorn")
    DUP is no longer supported and will be ignored.
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

Version: 1.99-7
Check: R code for possible problems
Result: NOTE
    NJ: no visible global function definition for ‘nj’
    PNJ: no visible global function definition for ‘old2new.phylo’
    RF.dist: no visible global function definition for ‘is.rooted’
    RF.dist: no visible global function definition for ‘unroot’
    RF.dist: no visible global function definition for ‘is.binary.tree’
    add.tip: no visible global function definition for ‘new2old.phylo’
    add.tip: no visible global function definition for ‘old2new.phylo’
    as.alignment.phyDat: no visible global function definition for
     ‘as.alignment’
    as.phylo.splits: no visible global function definition for ‘di2multi’
    as.splits.multiPhylo: no visible global function definition for
     ‘.uncompressTipLabel’
    as.splits.multiPhylo: no visible binding for global variable ‘root’
    as.splits.multiPhylo: no visible global function definition for
     ‘prop.part’
    bipartition: no visible global function definition for ‘is.rooted’
    bipartition: no visible global function definition for ‘unroot’
    bootstrap.phyDat: no visible global function definition for ‘mclapply’
    bootstrap.pml: no visible global function definition for ‘mclapply’
    coalSpeciesTree: no visible global function definition for
     ‘speciesTree’
    densiTree: no visible global function definition for ‘plotPhyloCoor’
    densiTree: no visible global function definition for ‘cladogram.plot’
    densiTree: no visible global function definition for ‘phylogram.plot’
    designTree: no visible global function definition for ‘is.rooted’
    designUnrooted: no visible global function definition for ‘is.rooted’
    designUnrooted: no visible global function definition for ‘unroot’
    dn: no visible global function definition for ‘is.binary.tree’
    dn: no visible global function definition for ‘multi2di’
    getAges : fun: no visible global function definition for
     ‘node.depth.edgelength’
    getAges: no visible global function definition for
     ‘.uncompressTipLabel’
    getClans: no visible global function definition for ‘is.rooted’
    getClans: no visible global function definition for ‘unroot’
    getDiv: no visible global function definition for ‘drop.tip’
    getDiversity: no visible global function definition for ‘is.rooted’
    getDiversity: no visible global function definition for ‘unroot’
    getE: no visible global function definition for ‘is.rooted’
    getE: no visible global function definition for ‘unroot’
    lowerBound: no visible global function definition for ‘stree’
    mRF: no visible global function definition for ‘.compressTipLabel’
    mRF: no visible global function definition for ‘.uncompressTipLabel’
    mRF: no visible binding for global variable ‘is.rooted’
    mRF: no visible binding for global variable ‘unroot’
    mRF : <anonymous>: no visible global function definition for
     ‘is.binary.tree’
    mRF2: no visible global function definition for ‘.compressTipLabel’
    mRF2: no visible global function definition for ‘.uncompressTipLabel’
    mRF2: no visible binding for global variable ‘is.rooted’
    mRF2: no visible binding for global variable ‘unroot’
    mRF2 : <anonymous>: no visible global function definition for
     ‘is.binary.tree’
    midpoint: no visible global function definition for ‘unroot’
    modelTest: no visible global function definition for ‘mclapply’
    my.supertree: no visible global function definition for ‘prop.part’
    my.supertree: no visible global function definition for ‘rtree’
    nnls.tree: no visible global function definition for ‘is.rooted’
    nnls.tree: no visible global function definition for ‘unroot’
    oneOf4: no visible global function definition for ‘is.binary.tree’
    optim.fitch: no visible global function definition for ‘is.binary.tree’
    optim.fitch: no visible global function definition for ‘multi2di’
    optim.fitch: no visible global function definition for ‘is.rooted’
    optim.fitch: no visible global function definition for ‘unroot’
    optim.pml: no visible global function definition for ‘is.binary.tree’
    optim.pml: no visible global function definition for ‘multi2di’
    optim.pml: no visible global function definition for ‘is.rooted’
    optim.pml: no visible global function definition for ‘unroot’
    optim.pml: no visible global function definition for ‘is.ultrametric’
    optim.sankoff: no visible global function definition for ‘is.rooted’
    optim.sankoff: no visible global function definition for ‘unroot’
    parsimony.plot: no visible binding for global variable ‘.PlotPhyloEnv’
    parsimony.plot: no visible global function definition for ‘edgelabels’
    plot2D: no visible global function definition for ‘cladogram.plot’
    plotAnc: no visible binding for global variable ‘.PlotPhyloEnv’
    plotAnc: no visible global function definition for ‘BOTHlabels’
    plotBS : prop.clades: no visible global function definition for
     ‘prop.part’
    plotBS : prop.clades: no visible global function definition for
     ‘postprocess.prop.part’
    plotBS: no visible global function definition for ‘is.rooted’
    plotBS: no visible binding for global variable ‘.PlotPhyloEnv’
    plotBS: no visible global function definition for ‘nodelabels’
    plotBS: no visible global function definition for ‘edgelabels’
    plotBSOld : prop.clades: no visible global function definition for
     ‘prop.part’
    plotBSOld : prop.clades: no visible global function definition for
     ‘postprocess.prop.part’
    plotBSOld: no visible global function definition for ‘is.rooted’
    plotBSOld: no visible binding for global variable ‘.PlotPhyloEnv’
    plotBSOld: no visible global function definition for ‘nodelabels’
    plotBSOld: no visible global function definition for ‘edgelabels’
    plotRGL: no visible global function definition for ‘segments3d’
    plotRGL: no visible global function definition for ‘spheres3d’
    plotRGL: no visible global function definition for ‘rgl.texts’
    pml: no visible global function definition for ‘is.ultrametric’
    pratchet: no visible global function definition for ‘nj’
    pruneTree: no visible global function definition for ‘is.rooted’
    pruneTree: no visible global function definition for ‘unroot’
    pruneTree: no visible global function definition for ‘di2multi’
    read.phyDat: no visible global function definition for
     ‘read.nexus.data’
    read.phyDat: no visible global function definition for ‘read.dna’
    reroot: no visible global function definition for ‘collapse.singles’
    rooted.nni: no visible global function definition for ‘reorder.phylo’
    rooted.nni: no visible global function definition for ‘is.rooted’
    sankoff.nni: no visible global function definition for ‘is.rooted’
    sankoff.nni: no visible global function definition for ‘unroot’
    sprMove: no visible global function definition for ‘is.rooted’
    sprMove: no visible global function definition for ‘unroot’
    sprMove: no visible global function definition for ‘is.binary.tree’
    sprMove : changeEdge: no visible global function definition for
     ‘collapse.singles’
    superTree: no visible global function definition for
     ‘.uncompressTipLabel’
    superTree: no visible global function definition for ‘root’
    superTree: no visible global function definition for ‘drop.tip’
    treedist: no visible global function definition for ‘unroot’
    treedist: no visible global function definition for ‘is.binary.tree’
    treedist: no visible global function definition for ‘dist.nodes’
    update.pml: no visible global function definition for ‘is.ultrametric’
    upperBound: no visible global function definition for ‘stree’
    write.phyDat: no visible global function definition for ‘write.dna’
    write.phyDat: no visible global function definition for
     ‘write.nexus.data’
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

Version: 1.99-7
Check: foreign function calls
Result: NOTE
    Calls with DUP != TRUE:
     .C("C_reorder", edge[, 1], edge[, 2], as.integer(l + 2L), as.integer(m +
     2L), integer(l + 2L), as.integer(nTips + 1L), DUP = FALSE,
     PACKAGE = "phangorn")
     .C("C_cisort", as.integer(x), as.integer(y), k, l, integer(k +
     l), DUP = FALSE)
     .C("get_single_index_integer", as.integer(edge[, 2L]), as.integer(tip),
     integer(1L), PACKAGE = "phangorn", NAOK = TRUE, DUP = FALSE)
     .C("get_two_index_integer", as.integer(edge[, 1L]), as.integer(node),
     integer(2L), PACKAGE = "phangorn", NAOK = TRUE, DUP = FALSE)
     .C("C_reorder", parents, child, as.integer(n), as.integer(m),
     integer(n), as.integer(root - 1L), DUP = FALSE, PACKAGE = "phangorn")
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavors: r-patched-linux-x86_64, r-patched-solaris-x86

Version: 1.99-7
Flags: --no-vignettes
Check: foreign function calls
Result: NOTE
    Calls with DUP != TRUE:
     .C("C_reorder", edge[, 1], edge[, 2], as.integer(l + 2L), as.integer(m +
     2L), integer(l + 2L), as.integer(nTips + 1L), DUP = FALSE,
     PACKAGE = "phangorn")
     .C("C_cisort", as.integer(x), as.integer(y), k, l, integer(k +
     l), DUP = FALSE)
     .C("get_single_index_integer", as.integer(edge[, 2L]), as.integer(tip),
     integer(1L), PACKAGE = "phangorn", NAOK = TRUE, DUP = FALSE)
     .C("get_two_index_integer", as.integer(edge[, 1L]), as.integer(node),
     integer(2L), PACKAGE = "phangorn", NAOK = TRUE, DUP = FALSE)
     .C("C_reorder", parents, child, as.integer(n), as.integer(m),
     integer(n), as.integer(root - 1L), DUP = FALSE, PACKAGE = "phangorn")
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavor: r-patched-solaris-sparc

Version: 1.99-7
Check: foreign function calls
Result: NOTE
    Calls with DUP = FALSE:
     .C("C_reorder", edge[, 1], edge[, 2], as.integer(l + 2L), as.integer(m +
     2L), integer(l + 2L), as.integer(nTips + 1L), DUP = FALSE,
     PACKAGE = "phangorn")
     .C("C_cisort", as.integer(x), as.integer(y), k, l, integer(k +
     l), DUP = FALSE)
     .C("get_single_index_integer", as.integer(edge[, 2L]), as.integer(tip),
     integer(1L), PACKAGE = "phangorn", NAOK = TRUE, DUP = FALSE)
     .C("get_two_index_integer", as.integer(edge[, 1L]), as.integer(node),
     integer(2L), PACKAGE = "phangorn", NAOK = TRUE, DUP = FALSE)
     .C("C_reorder", parents, child, as.integer(n), as.integer(m),
     integer(n), as.integer(root - 1L), DUP = FALSE, PACKAGE = "phangorn")
    DUP = FALSE is deprecated and may be disabled in future versions of R.
Flavors: r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.99-7
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘seqLogo’
Flavor: r-release-osx-x86_64-mavericks

Version: 1.99-7
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: ape
    
    Attaching package: ‘phangorn’
    
    The following object is masked from ‘package:ape’:
    
     as.prop.part
    
    Loading required package: seqLogo
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘seqLogo’
    Loading required package: seqLogo
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘seqLogo’
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'Ancestral.tex' failed.
    LaTeX errors:
    !pdfTeX error: pdflatex (file ./Ancestral-figLOGO.pdf): PDF inclusion: required
     page does not exist <0>
     ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.99-7
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘seqLogo’ ‘phytools’
Flavor: r-release-osx-x86_64-snowleopard

Version: 1.99-7
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: ape
    Loading required package: seqLogo
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘seqLogo’
    Loading required package: seqLogo
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘seqLogo’
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'Ancestral.tex' failed.
    LaTeX errors:
    !pdfTeX error: pdflatex (file ./Ancestral-figLOGO.pdf): PDF inclusion: required
     page does not exist <0>
     ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64-snowleopard