* using log directory '/home/kingaa/projects/Rpkg/subplex/revdep/diversitree.Rcheck'
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'diversitree/DESCRIPTION' ... OK
* this is package 'diversitree' version '0.9-16'
* 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 serialization versions ... OK
* checking whether package 'diversitree' can be installed ... [74s/96s] OK
* checking installed package size ... NOTE
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... WARNING
A complete check needs the 'checkbashisms' script.
See section 'Configure and cleanup' in the 'Writing R Extensions'
manual.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [47s/70s] NOTE
add.profile.outline: local variable ‘dx’ assigned but may not be used
all.branches.list: local variable ‘n.tip’ assigned but may not be used
all.branches.matrix: local variable ‘n.tip’ assigned but may not be
  used
caching.integer: local variable ‘ret’ assigned but may not be used
clades.from.polytomies: local variable ‘is.node’ assigned but may not
  be used
constrain.i: local variable ‘pars.out’ assigned but may not be used
constrain.i2: local variable ‘argnames.constrained’ assigned but may
  not be used
constrain.i2: local variable ‘pars.out’ assigned but may not be used
drop.tip.fixed: local variable ‘Nnode’ assigned but may not be used
drop.tip.fixed: local variable ‘tr’ assigned but may not be used
expand.pars.quasse: local variable ‘x’ assigned but may not be used
expm.expokit.sparse.pars: local variable ‘nz’ assigned but may not be
  used
fftR.propagate.x: local variable ‘f’ assigned but may not be used
make.all.branches.bm.contrasts: local variable ‘states’ assigned but
  may not be used
make.all.branches.pgls.pruning.phylo: local variable ‘y’ assigned but
  may not be used
make.all.branches.rescale.contrasts: local variable ‘states’ assigned
  but may not be used
make.asr.marginal.bisse.t: local variable ‘cache’ assigned but may not
  be used
make.asr.marginal.dtlik.t: local variable ‘cache’ assigned but may not
  be used
make.asr.marginal.mkn: local variable ‘states.idx’ assigned but may not
  be used
make.asr.marginal.musse.t: local variable ‘cache’ assigned but may not
  be used
make.branches.quasse: local variable ‘branches’ assigned but may not be
  used
make.branches.quasse.fftC: local variable ‘tc’ assigned but may not be
  used
make.branches.quasse.fftR: local variable ‘tc’ assigned but may not be
  used
make.branches.quasse.mol: local variable ‘tc’ assigned but may not be
  used
make.branches.td : <anonymous>: local variable ‘out’ assigned but may
  not be used
make.cache.mkn.multitrait: local variable ‘k’ assigned but may not be
  used
make.cache.mkn.multitrait: local variable ‘types’ assigned but may not
  be used
make.cache.quasse: local variable ‘n.args’ assigned but may not be used
make.caching.branches: local variable ‘prev.pars’ assigned but may not
  be used
make.derivs.mkn.meristic: local variable ‘dydt’ assigned but may not be
  used
make.initial.conditions.classe: local variable ‘d’ assigned but may not
  be used
make.initial.conditions.classe: local variable
  ‘initial.conditions.classe’ assigned but may not be used
make.initial.conditions.quasse: local variable ‘eps’ assigned but may
  not be used
make.pars.classe: local variable ‘np’ assigned but may not be used
make.pars.classe: local variable ‘qmat’ assigned but may not be used
make.pars.mkn: local variable ‘qmat’ assigned but may not be used
make.pars.mkn.multitrait: local variable ‘f.pars’ assigned but may not
  be used
make.pars.mkn.multitrait: local variable ‘n.trait’ assigned but may not
  be used
make.pars.musse: local variable ‘qmat’ assigned but may not be used
make.pars.musse.multitrait: local variable ‘k’ assigned but may not be
  used
make.pars.musse.multitrait: local variable ‘n.trait’ assigned but may
  not be used
make.quasse.split: local variable ‘n.part’ assigned but may not be used
make.rescale.phylo.eb: local variable ‘t.max’ assigned but may not be
  used
make.rootfunc.quasse: local variable ‘root.idx’ assigned but may not be
  used
make.sim.character: local variable ‘y’ assigned but may not be used
make.tree.bisse.C.core: local variable ‘info’ assigned but may not be
  used
make.tree.bisse.R.core: local variable ‘info’ assigned but may not be
  used
minimise.int1d: local variable ‘factor’ assigned but may not be used
minimise.int1d: local variable ‘step’ assigned but may not be used
plot.history: local variable ‘cols.seg’ assigned but may not be used
pp.clades.phylogram: local variable ‘n’ assigned but may not be used
pp.coords.phylogram: local variable ‘phy.p’ assigned but may not be
  used
rootfunc.mkn: local variable ‘k’ assigned but may not be used
split.group: local variable ‘descendants.idx’ assigned but may not be
  used
starting.point.classe: local variable ‘d’ assigned but may not be used
tree.musse.multitrait: local variable ‘np’ assigned but may not be used

Found if() conditions comparing class() to string:
File ‘diversitree/R/clade-tree.R’: if (class(class) != "character") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... 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 line endings in shell scripts ... 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 examples ... [33s/15s] OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
make.bisse.split 4.385  9.669   2.493
make.bisse       3.292  6.737   1.903
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
