CRAN Package Check Results for Package phangorn

Last updated on 2014-04-24 10:48:53.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.99-7 6.17 136.05 142.22 NOTE
r-devel-linux-x86_64-debian-gcc 1.99-7 6.74 134.18 140.92 NOTE
r-devel-linux-x86_64-fedora-clang 1.99-7 308.01 NOTE
r-devel-linux-x86_64-fedora-gcc 1.99-7 297.94 NOTE
r-devel-osx-x86_64-clang 1.99-7 241.55 NOTE
r-devel-osx-x86_64-gcc 1.99-7 ERROR
r-devel-windows-ix86+x86_64 1.99-7 22.00 211.00 233.00 NOTE
r-patched-linux-x86_64 1.99-7 6.87 131.54 138.41 NOTE
r-patched-solaris-sparc 1.99-7 1115.80 NOTE --no-vignettes
r-patched-solaris-x86 1.99-7 362.90 NOTE
r-release-linux-ix86 1.99-7 10.00 202.00 212.00 NOTE
r-release-linux-x86_64 1.99-7 7.30 132.43 139.73 NOTE
r-release-osx-x86_64-mavericks 1.99-7 WARN
r-release-osx-x86_64-snowleopard 1.99-7 NOTE
r-release-windows-ix86+x86_64 1.99-7 20.00 220.00 240.00 NOTE
r-oldrel-windows-ix86+x86_64 1.99-7 22.00 213.00 235.00 OK

Check Details

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-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-x86, 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: ERROR
    Package required but not available: ‘igraph’
    
    Packages suggested but not available for checking: ‘seqLogo’ ‘phytools’
    
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavor: r-devel-osx-x86_64-gcc

Version: 1.99-7
Flags: --no-vignettes
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.
Flavor: r-patched-solaris-sparc

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: PDF version of manual
Result: WARNING
    LaTeX errors when creating PDF version.
    This typically indicates Rd problems.
    LaTeX errors found:
    ! LaTeX Error: File `upquote.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    0989f2/Rd2.tex:8: ==> Fatal error occurred, no output PDF file produced!
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