- using R Under development (unstable) (2024-07-25 r86925)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.3.0-3) 13.3.0
GNU Fortran (Debian 13.3.0-3) 13.3.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘phangorn/DESCRIPTION’ ... OK
- this is package ‘phangorn’ version ‘2.11.1’
- 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 ‘phangorn’ can be installed ... OK
See the install log for details.
- used C compiler: ‘gcc-13 (Debian 13.3.0-3) 13.3.0’
- used C++ compiler: ‘g++-13 (Debian 13.3.0-3) 13.3.0’
- checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
- 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 ... [2s/4s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/5s] OK
- checking whether the package can be unloaded cleanly ... [2s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
- checking loading without being on the library search path ... [2s/4s] 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 ... [70s/123s] OK
- checking Rd files ... [1s/2s] 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:
add.tips.Rd: bind.tree
addConfidences.Rd: plot.phylo
add_ci.Rd: plot.phylo
add_edge_length.Rd: node.depth.edgelength, consensus
as.phyDat.Rd: read.dna, read.nexus.data
as.splits.Rd: prop.part
baseFreq.Rd: base.freq
bootstrap.pml.Rd: plot.phylo, nodelabels
cladePar.Rd: plot.phylo
coalSpeciesTree.Rd: speciesTree
densiTree.Rd: plot.phylo
dna2codon.Rd: trans
image.phyDat.Rd: image.DNAbin, image.AAbin
maxCladeCred.Rd: consensus, prop.part
phyDat.Rd: DNAbin, as.DNAbin, read.dna, read.nexus.data
plotBS.Rd: plot.phylo, nodelabels, consensus
pml.Rd: plot.phylo
pml_bb.Rd: rtt
read.nexus.splits.Rd: prop.part
upgma.Rd: as.phylo, fastme
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/1s] 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 line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... 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 ... [30s/48s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
superTree 6.401 0.032 10.513
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [1s/1s] OK
Running ‘tinytest.R’ [0s/0s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [191s/353s] OK
- checking PDF version of manual ... [10s/18s] OK
- checking HTML version of manual ... [4s/7s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 NOTEs