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

Last updated on 2026-04-17 11:54:28 CEST.

Package	ERROR	WARN	NOTE	OK
CongreveLamsdell2016	1			13
ips				14
motmot			4	4
PlotTools				14
Quartet				14
Rogue			2	12
TBRDist			1	13
Ternary			3	11
TotalCopheneticIndex			2	12
TreeDist			3	11
TreeSearch			3	11
TreeTools		2	1	11

Package CongreveLamsdell2016

Current CRAN status: ERROR: 1, OK: 13

Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'Compare-methods.Rmd' using rmarkdown ! Package pdftex.def Error: File `2ab5bf26133c512d4676a9541eb7d6b9443f6235.pdf' not found: using draft setting. Error: processing vignette 'Compare-methods.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/CongreveLamsdell2016.Rcheck/vign_test/CongreveLamsdell2016/vignettes/Compare-methods.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Compare-methods.log for more info. --- failed re-building 'Compare-methods.Rmd' --- re-building 'Compare-node-supports.Rmd' using rmarkdown ! Package pdftex.def Error: File `1e97b62ea13fd520f0a88e63b2e57992dac88a96.pdf' not found: using draft setting. Error: processing vignette 'Compare-node-supports.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/CongreveLamsdell2016.Rcheck/vign_test/CongreveLamsdell2016/vignettes/Compare-node-supports.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Compare-node-supports.log for more info. --- failed re-building 'Compare-node-supports.Rmd' --- re-building 'Conduct-analyses.Rmd' using rmarkdown --- finished re-building 'Conduct-analyses.Rmd' SUMMARY: processing the following files failed: 'Compare-methods.Rmd' 'Compare-node-supports.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-windows-x86_64

Package ips

Current CRAN status: OK: 14

Package motmot

Current CRAN status: NOTE: 4, OK: 4

Version: 2.1.3
Check: C++ specification
Result: NOTE Specified C++11: please drop specification unless essential Flavors: r-devel-macos-arm64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64

Version: 2.1.3
Check: Rd files
Result: NOTE checkRd: (-1) transformPhylo.MCMC.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.MCMC.Rd:83: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.MCMC.Rd:84: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.MCMC.Rd:85: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.MCMC.Rd:86: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.MCMC.Rd:87: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:119: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:120: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:121: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:122: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:123: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:124: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:125: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:126: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:127: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:128: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:129: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:130: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:131: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:132: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ML.Rd:133: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.Rd:97: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.Rd:98: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.Rd:99: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.Rd:100: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:100: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:101: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:102: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:103: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:104: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:105: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:106: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:107: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:108: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:109: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:110: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:113: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformPhylo.ll.Rd:114: Lost braces in \itemize; meant \describe ? Flavors: r-devel-macos-arm64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64

Package PlotTools

Current CRAN status: OK: 14

Package Quartet

Current CRAN status: OK: 14

Package Rogue

Current CRAN status: NOTE: 2, OK: 12

Version: 2.2.0
Check: dependencies in R code
Result: NOTE Namespace in Imports field not imported from: ‘matrixStats’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Package TBRDist

Current CRAN status: NOTE: 1, OK: 13

Version: 2.0.0
Check: installed package size
Result: NOTE installed size is 9.7Mb sub-directories of 1Mb or more: libs 9.6Mb Flavor: r-oldrel-macos-x86_64

Package Ternary

Current CRAN status: NOTE: 3, OK: 11

Version: 2.3.6
Check: installed package size
Result: NOTE installed size is 6.4Mb sub-directories of 1Mb or more: doc 5.4Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package TotalCopheneticIndex

Current CRAN status: NOTE: 2, OK: 12

Version: 2.0.1
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Martin R. Smith <martin.smith@durham.ac.uk>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Package TreeDist

Current CRAN status: NOTE: 3, OK: 11

Version: 2.12.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘TreeDistData’ Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 2.12.0
Check: installed package size
Result: NOTE installed size is 6.7Mb sub-directories of 1Mb or more: doc 1.1Mb libs 4.8Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package TreeSearch

Current CRAN status: NOTE: 3, OK: 11

Version: 1.7.0
Check: installed package size
Result: NOTE installed size is 6.3Mb sub-directories of 1Mb or more: datasets 1.6Mb doc 1.3Mb libs 1.7Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package TreeTools

Current CRAN status: WARN: 2, NOTE: 1, OK: 11

Version: 2.2.0
Check: Rd files
Result: WARN 2026-03-23 09:58:03.478 R[70648:465865] XType: Using static font registry. Flavor: r-release-macos-arm64

Version: 2.2.0
Check: installed package size
Result: NOTE installed size is 7.6Mb sub-directories of 1Mb or more: R 1.1Mb libs 5.5Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 2.2.0
Check: Rd files
Result: WARN 2026-03-20 23:16:39.163 R[26288:198695] XType: Using static font registry. Flavor: r-oldrel-macos-arm64