- using R Under development (unstable) (2024-11-09 r87314)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.2.0-6) 14.2.0
GNU Fortran (Debian 14.2.0-6) 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/3s] 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/2s] 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 ... [16s/21s] OK
- checking Rd files ... [0s/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 ... [3s/3s] OK
- checking PDF version of manual ... [5s/8s] OK
- checking HTML version of manual ... [2s/3s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 NOTE