• using R Under development (unstable) (2024-12-19 r87451)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-8) 14.2.0     GNU Fortran (Debian 14.2.0-8) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘ips/DESCRIPTION’ ... OK
• this is package ‘ips’ version ‘0.0.12’
• package encoding: UTF-8
• 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 ‘ips’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/3s] 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 ... [18s/21s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   DNAbin2index.Rd: DNAbin   EmptyCells.Rd: DNAbin   code.simple.gaps.Rd: DNAbin   collapseUnsupportedEdges.Rd: phylo   combMyTree.Rd: phylo   del.miss.Rd: DNAbin   deleteGaps.Rd: DNAbin   fixNodes.Rd: phylo, read.nexus   forceEqualTipHeights.Rd: is.ultrametric, chronos   index2DNAbin.Rd: DNAbin   ips-package.Rd: ladderize, rotate   ips.16S.Rd: DNAbin   ips.28S.Rd: DNAbin   ips.cox1.Rd: DNAbin   mafft.Rd: phylo   mafft.merge.Rd: DNAbin, AAbin, phylo   mrbayes.Rd: DNAbin   multistate.Rd: ace   neighboringPairs.Rd: mst   ntip.Rd: phylo   pathd8.Rd: phylo   phylo2mafft.Rd: phylo   phylo2mst.Rd: phylo   pis.Rd: DNAbin   raxml.Rd: DNAbin, phylo   raxml.partitions.Rd: DNAbin, cbind.DNAbin   rbeauti.Rd: DNAbin   read.Rd: cbind.DNAbin   sister.Rd: phylo   splitIntoClades.Rd: phylo   terminalSisters.Rd: phylo   tipHeights.Rd: phylo, branching.times   traitRate.Rd: phylo, DNAbin, read.tree   write.fas.Rd: DNAbin Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• 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 data for ASCII and uncompressed saves ... OK
• checking examples ... [2s/3s] OK
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE