• using R Under development (unstable) (2026-07-26 r90304)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 22.1.8 (1+b2)     Debian flang version 22.1.8 (1+b2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-07-27 20:10:05 UTC
• checking for file ‘TreeTools/DESCRIPTION’ ... OK
• this is package ‘TreeTools’ version ‘2.4.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [3s/4s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘TreeTools’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 22.1.8 (1+b2)’
• checking C++ specification ... INFO   specified C++17
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [30s/39s] NOTE Found calls to structure() using deprecated special names:   TreeTools/tests/testthat/test-AddTip.R (.Dim: 1)   TreeTools/tests/testthat/test-DropTip.R (.Dim: 3)   TreeTools/tests/testthat/test-ImposeConstraint.R (.Dim: 1, .Dimnames: 1)   TreeTools/tests/testthat/test-ReadTntTree.R (.Dim: 1, .Dimnames: 1)   TreeTools/tests/testthat/test-Splits.R (.Dim: 8)   TreeTools/tests/testthat/test-TotalCopheneticIndex.R (.Dim: 1)   TreeTools/tests/testthat/test-consensus.R (.Dim: 1)   TreeTools/tests/testthat/test-parsers.R (.Dim: 1, .Dimnames: 1, .Label: 1)   TreeTools/tests/testthat/test-phylo.R (.Dim: 1)   TreeTools/tests/testthat/test-tree_numbering.R (.Dim: 5)   TreeTools/tests/testthat/test-tree_properties.R (.Dim: 1)   TreeTools/tests/testthat/test-tree_rearrange.R (.Dim: 11)   TreeTools/tests/testthat/test-tree_shape.R (.Dim: 1)   TreeTools/tests/testthat/test-tree_write.R (.Dim: 1) '.Dim' should be changed to 'dim'. '.Dimnames' should be changed to 'dimnames'. '.Label' should be changed to 'levels'.
• checking Rd files ... [3s/4s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/6s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [85s/102s] OK   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [85s/101s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [6s/9s] OK
• checking PDF version of manual ... [12s/16s] OK
• checking HTML version of manual ... [8s/11s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE