CRAN Package Check Results for Maintainer ‘Martin R. Smith <martin.smith at durham.ac.uk>’

Last updated on 2025-03-15 08:52:41 CET.

Package WARN NOTE OK
CongreveLamsdell2016 15
PlotTools 15
Quartet 15
Rogue 15
TBRDist 15
Ternary 6 9
TotalCopheneticIndex 15
TreeDist 7 8
TreeSearch 1 9 5
TreeTools 4 11

Package CongreveLamsdell2016

Current CRAN status: OK: 15

Package PlotTools

Current CRAN status: OK: 15

Package Quartet

Current CRAN status: OK: 15

Package Rogue

Current CRAN status: OK: 15

Additional issues

rchk

Package TBRDist

Current CRAN status: NOTE: 15

Version: 1.0.2
Check: C++ specification
Result: NOTE Specified C++11: please drop specification unless essential 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-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 1.0.2
Check: LazyData
Result: NOTE 'LazyData' is specified without a 'data' directory Flavors: r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 1.0.2
Check: installed package size
Result: NOTE installed size is 5.3Mb sub-directories of 1Mb or more: libs 5.1Mb Flavor: r-oldrel-macos-arm64

Package Ternary

Current CRAN status: NOTE: 6, OK: 9

Version: 2.3.3
Check: installed package size
Result: NOTE installed size is 6.9Mb sub-directories of 1Mb or more: doc 5.9Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package TotalCopheneticIndex

Current CRAN status: OK: 15

Package TreeDist

Current CRAN status: NOTE: 7, OK: 8

Version: 2.9.2
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘TreeDistData’ Flavors: r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 2.9.2
Check: installed package size
Result: NOTE installed size is 9.0Mb sub-directories of 1Mb or more: doc 4.9Mb libs 3.4Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package TreeSearch

Current CRAN status: WARN: 1, NOTE: 9, OK: 5

Version: 1.5.1
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: AdditionTree.Rd: ImposeConstraint AllSPR.Rd: phylo CharacterLength.Rd: phylo ConcordantInformation.Rd: phylo Consistency.Rd: phylo DoubleNNI.Rd: phylo JackLabels.Rd: phylo Jackknife.Rd: phylo MaximizeParsimony.Rd: phylo, ImposeConstraint MorphyTreeLength.Rd: RenumberTips, phylo NNI.Rd: phylo PlotCharacter.Rd: phylo Ratchet.Rd: phylo RearrangeEdges.Rd: phylo SPR.Rd: phylo SiteConcordance.Rd: phylo StopUnlessBifurcating.Rd: phylo SuccessiveApproximations.Rd: phylo TBR.Rd: phylo TBRWarning.Rd: phylo TaxonInfluence.Rd: ClusteringInfoDistance, write.nexus, path_sanitize TreeSearch.Rd: phylo cSPR.Rd: phylo dot-NonDuplicateRoot.Rd: phylo inapplicable.datasets.Rd: read.nexus.data Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64

Version: 1.5.1
Check: whether package can be installed
Result: WARN Found the following significant warnings: Rd warning: AdditionTree.Rd:27: missing link ‘ImposeConstraint’ Rd warning: AllSPR.Rd:11: missing link ‘phylo’ Rd warning: AllSPR.Rd:14: missing link ‘phylo’ Rd warning: AllSPR.Rd:16: missing link ‘phylo’ Rd warning: CharacterLength.Rd:16: missing link ‘phylo’ Rd warning: ConcordantInformation.Rd:16: missing link ‘phylo’ Rd warning: Consistency.Rd:13: missing link ‘phylo’ Rd warning: DoubleNNI.Rd:11: missing link ‘phylo’ Rd warning: DoubleNNI.Rd:14: missing link ‘phylo’ Rd warning: JackLabels.Rd:20: missing link ‘phylo’ Rd warning: Jackknife.Rd:23: missing link ‘phylo’ Rd warning: MaximizeParsimony.Rd:52: missing link ‘phylo’ Rd warning: MaximizeParsimony.Rd:112: missing link ‘ImposeConstraint’ Rd warning: MorphyTreeLength.Rd:26: missing link ‘RenumberTips’ Rd warning: MorphyTreeLength.Rd:33: missing link ‘phylo’ Rd warning: MorphyTreeLength.Rd:36: missing link ‘phylo’ Rd warning: NNI.Rd:27: missing link ‘phylo’ Rd warning: NNI.Rd:40: missing link ‘phylo’ Rd warning: NNI.Rd:43: missing link ‘phylo’ Rd warning: PlotCharacter.Rd:25: missing link ‘phylo’ Rd warning: Ratchet.Rd:106: missing link ‘phylo’ Rd warning: RearrangeEdges.Rd:22: missing link ‘phylo’ Rd warning: RearrangeEdges.Rd:25: missing link ‘phylo’ Rd warning: SPR.Rd:42: missing link ‘phylo’ Rd warning: SPR.Rd:49: missing link ‘phylo’ Rd warning: SPR.Rd:52: missing link ‘phylo’ Rd warning: SPR.Rd:55: missing link ‘phylo’ Rd warning: SiteConcordance.Rd:23: missing link ‘phylo’ Rd warning: StopUnlessBifurcating.Rd:11: missing link ‘phylo’ Rd warning: SuccessiveApproximations.Rd:25: missing link ‘phylo’ Rd warning: TBR.Rd:40: missing link ‘phylo’ Rd warning: TBR.Rd:54: missing link ‘phylo’ Rd warning: TBR.Rd:57: missing link ‘phylo’ Rd warning: TBRWarning.Rd:15: missing link ‘phylo’ Rd warning: TBRWarning.Rd:18: missing link ‘phylo’ Rd warning: TaxonInfluence.Rd:29: missing link ‘ClusteringInfoDistance’ Rd warning: TaxonInfluence.Rd:35: missing link ‘write.nexus’ Rd warning: TaxonInfluence.Rd:39: missing link ‘path_sanitize’ Rd warning: TreeSearch.Rd:86: missing link ‘phylo’ Rd warning: cSPR.Rd:10: missing link ‘phylo’ Rd warning: dot-NonDuplicateRoot.Rd:11: missing link ‘phylo’ Rd warning: dot-NonDuplicateRoot.Rd:14: missing link ‘phylo’ Rd warning: dot-NonDuplicateRoot.Rd:17: missing link ‘phylo’ Rd warning: inapplicable.datasets.Rd:149: missing link ‘read.nexus.data’ See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TreeSearch.Rcheck/00install.out’ for details. * used C compiler: ‘gcc-14 (Debian 14.2.0-17) 14.2.0’ * used C++ compiler: ‘g++-14 (Debian 14.2.0-17) 14.2.0’ Flavor: r-patched-linux-x86_64

Version: 1.5.1
Check: installed package size
Result: NOTE installed size is 5.9Mb sub-directories of 1Mb or more: datasets 1.6Mb doc 1.3Mb libs 1.4Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package TreeTools

Current CRAN status: NOTE: 4, OK: 11

Version: 1.13.0
Check: installed package size
Result: NOTE installed size is 6.1Mb sub-directories of 1Mb or more: R 1.1Mb libs 3.9Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64