CRAN Package Check Results for Package geiger

Last updated on 2015-05-28 15:47:29.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.3 18.88 56.70 75.57 NOTE --no-vignettes
r-devel-linux-x86_64-debian-gcc 2.0.3 20.99 52.76 73.75 NOTE --no-vignettes
r-devel-linux-x86_64-fedora-clang 2.0.3 143.10 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0.3 139.85 NOTE
r-devel-osx-x86_64-clang 2.0.3 120.95 NOTE --no-build-vignettes
r-devel-windows-ix86+x86_64 2.0.3 55.00 93.00 148.00 NOTE
r-patched-linux-x86_64 2.0.3 21.38 51.86 73.24 NOTE --no-vignettes
r-patched-solaris-sparc 2.0.3 883.70 NOTE --no-vignettes
r-patched-solaris-x86 2.0.3 167.90 NOTE
r-release-linux-x86_64 2.0.3 22.17 54.07 76.24 NOTE --no-vignettes
r-release-osx-x86_64-mavericks 2.0.3 NOTE
r-release-osx-x86_64-snowleopard 2.0.3 NOTE
r-release-windows-ix86+x86_64 2.0.3 56.00 90.00 146.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0.3 55.00 106.00 161.00 NOTE

Check Details

Version: 2.0.3
Flags: --no-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Flags: --no-vignettes
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘colorspace’ ‘msm’ ‘ncbit’ ‘parallel’ ‘pls’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Flags: --no-vignettes
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.phylo.hphylo
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Flags: --no-vignettes
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .C("r_mkn_core", k = as.integer(k), n = length(order.C) - 1L,
     order = order.C, children = children.C, pij = pij, init = branch.init,
     base = branch.base, lq = lq, NAOK = TRUE, DUP = FALSE, PACKAGE = "geiger")
    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-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    .branchcol.plot: no visible global function definition for
     ‘diverge_hcl’
    .get.parallel: no visible global function definition for ‘detectCores’
    .get.parallel : fx: no visible global function definition for
     ‘mclapply’
    .jumps.plot: no visible global function definition for ‘diverge_hcl’
    .shifts.plot: no visible global function definition for ‘diverge_hcl’
    gbcontain: no visible global function definition for ‘ncbit’
    gbresolve.default: no visible global function definition for ‘ncbit’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64

Version: 2.0.3
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘colorspace’ ‘msm’ ‘ncbit’ ‘parallel’ ‘pls’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0.3
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.phylo.hphylo
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 2.0.3
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .C("r_mkn_core", k = as.integer(k), n = length(order.C) - 1L,
     order = order.C, children = children.C, pij = pij, init = branch.init,
     base = branch.base, lq = lq, NAOK = TRUE, DUP = FALSE, PACKAGE = "geiger")
    DUP is no longer supported and will be ignored.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64

Version: 2.0.3
Check: R code for possible problems
Result: NOTE
    .branchcol.plot: no visible global function definition for
     ‘diverge_hcl’
    .get.parallel: no visible global function definition for ‘detectCores’
    .get.parallel : fx: no visible global function definition for
     ‘mclapply’
    .jumps.plot: no visible global function definition for ‘diverge_hcl’
    .shifts.plot: no visible global function definition for ‘diverge_hcl’
    gbcontain: no visible global function definition for ‘ncbit’
    gbresolve.default: no visible global function definition for ‘ncbit’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0.3
Flags: --no-build-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Flags: --no-build-vignettes
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘colorspace’ ‘msm’ ‘ncbit’ ‘parallel’ ‘pls’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Flags: --no-build-vignettes
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.phylo.hphylo
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Flags: --no-build-vignettes
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .C("r_mkn_core", k = as.integer(k), n = length(order.C) - 1L,
     order = order.C, children = children.C, pij = pij, init = branch.init,
     base = branch.base, lq = lq, NAOK = TRUE, DUP = FALSE, PACKAGE = "geiger")
    DUP is no longer supported and will be ignored.
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    .branchcol.plot: no visible global function definition for
     ‘diverge_hcl’
    .get.parallel: no visible global function definition for ‘detectCores’
    .get.parallel : fx: no visible global function definition for
     ‘mclapply’
    .jumps.plot: no visible global function definition for ‘diverge_hcl’
    .shifts.plot: no visible global function definition for ‘diverge_hcl’
    gbcontain: no visible global function definition for ‘ncbit’
    gbresolve.default: no visible global function definition for ‘ncbit’
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘phytools’
Flavor: r-release-osx-x86_64-snowleopard

Version: 2.0.3
Check: foreign function calls
Result: NOTE
    Call with DUP != TRUE:
     .C("r_mkn_core", k = as.integer(k), n = length(order.C) - 1L,
     order = order.C, children = children.C, pij = pij, init = branch.init,
     base = branch.base, lq = lq, NAOK = TRUE, DUP = FALSE, PACKAGE = "geiger")
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavor: r-oldrel-windows-ix86+x86_64