CRAN Package Check Results for Package phylobase

Last updated on 2014-03-07 22:46:49.

Memtest notes: UBSAN valgrind

Check Details

Version: 0.6.5.2
Check: installed package size
Result: NOTE
     installed size is 18.0Mb
     sub-directories of 1Mb or more:
     libs 16.8Mb
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-macosx-x86_64-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-macosx-x86_64

Version: 0.6.5.2
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘Rcpp’ ‘ape’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
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-macosx-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-x86_64

Version: 0.6.5.2
Check: for old-style vignette sources
Result: NOTE
    Vignette sources only in ‘inst/doc’:
     ‘developer.Rnw’, ‘phylobase.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-macosx-x86_64-clang, r-devel-macosx-x86_64-gcc, r-patched-solaris-sparc, r-patched-solaris-x86

Version: 0.6.5.2
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: 0.6.5.2
Check: Rd line widths
Result: NOTE
    Rd file ‘as-methods.Rd’:
     \examples lines wider than 100 characters:
     tree.owls <- read.tree(text="(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);")
    
    Rd file ‘phylobubbles.Rd’:
     \usage lines wider than 90 characters:
     phylobubbles(type, place.tip.label, show.node.label, rot, edge.color, node.color, tip.color, edge.width, newpage, ..., XXYY, square = F ... [TRUNCATED]
    
    Rd file ‘phylomat-class.Rd’:
     \examples lines wider than 100 characters:
     tree.owls <- read.tree(text="(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);")
    
    Rd file ‘tip.data.plot.Rd’:
     \usage lines wider than 90 characters:
     tip.data.plot(xxyy, type = c("phylogram", "cladogram", "fan"), show.tip.label = TRUE, show.node.label = FALSE, rot = 0, tip.plot.fun = ... [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: 0.6.5.2
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘Rcpp’ ‘ape’
     These packages need to be imported from for the case when
     this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavor: r-devel-macosx-x86_64-gcc

Version: 0.6.5.2
Check: for old-style vignette sources
Result: NOTE
    Vignette sources only in 'inst/doc':
     'developer.Rnw', 'phylobase.Rnw'
    A 'vignettes' directory is required as from R 3.1.0
    and these will not be indexed nor checked
    * checking examples ...
Flavor: r-devel-windows-ix86+x86_64

Version: 0.6.5.2
Check: for old-style vignette sources
Result: NOTE
    Vignette sources only in ‘inst/doc’:
     ‘developer.Rnw’, ‘phylobase.Rnw’
    A ‘vignettes’ directory will be required as from R 3.1.0
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.6.5.2
Check: tests
Result: ERROR
    Running the tests in ‘tests/doRUnit.R’ failed.
    Last 13 lines of output:
     Number of test functions: 99
     Number of errors: 0
     Number of failures: 1
    
    
     1 Test Suite :
     phylobase unit testing - 99 test functions, 0 errors, 1 failure
     FAILURE in test.nodeDepth.phylo4: Error in checkIdentical(nodeDepth(phy.alt), allDepths) : FALSE
     Error:
    
     unit testing failed (#test failures: 1, #R errors: 0)
    
     Execution halted
Flavor: r-patched-solaris-sparc

Version: 0.6.5.2
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘Rcpp’ ‘ape’
     These packages needs to imported from for the case when
     this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-release-linux-ix86, r-release-macosx-x86_64, r-release-windows-ix86+x86_64