* using log directory '/home/kingaa/projects/Rpkg/subplex/revdep/geiger.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 'geiger/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geiger' version '2.0.10'
* 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 'geiger' can be installed ... [45s/53s] OK
* checking installed package size ... OK
* 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 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 ... [59s/92s] NOTE
.adjustjump: local variable ‘fdesc’ assigned but may not be used
.adjustjump: local variable ‘origjumps’ assigned but may not be used
.adjustshift: local variable ‘root.des’ assigned but may not be used
.cache.tree: local variable ‘mm’ assigned but may not be used
.cache.y.nodes: local variable ‘rr’ assigned but may not be used
.check.gbm: local variable ‘modzz’ assigned but may not be used
.coda: local variable ‘nvar’ assigned but may not be used
.constrain.m: local variable ‘npar’ assigned but may not be used
.constrain.m: local variable ‘upar’ assigned but may not be used
.delta.cache: local variable ‘mm’ assigned but may not be used
.delta.phylo: local variable ‘mm’ assigned but may not be used
.drop.tip: local variable ‘NEWROOT’ assigned but may not be used
.drop.tip: local variable ‘Nedge’ assigned but may not be used
.drop.tip: local variable ‘Nnode’ assigned but may not be used
.drop.tip: local variable ‘ROOT’ assigned but may not be used
.drop.tip: local variable ‘idx.old’ assigned but may not be used
.edger: local variable ‘vv’ assigned but may not be used
.fix.rjmcmc.matrix: local variable ‘nm’ assigned but may not be used
.jumps.edgewise: local variable ‘jj’ assigned but may not be used
.jumps.plot: local variable ‘j.var’ assigned but may not be used
.jumps.plot: local variable ‘legend.seq’ assigned but may not be used
.lambda.phylo: local variable ‘Tmax’ assigned but may not be used
.laser.getlambda: local variable ‘Lfunc_phy’ assigned but may not be
  used
.laser.gettipdata: local variable ‘tmp’ assigned but may not be used
.lik.partition.medusa: local variable ‘f’ assigned but may not be used
.lik.partition.medusa: local variable ‘pend.n.0’ assigned but may not
  be used
.lrate.phylo: local variable ‘vv’ assigned but may not be used
.make.bm.relaxed.direct: local variable ‘vv’ assigned but may not be
  used
.make.ode.deSolve: local variable ‘INTONE’ assigned but may not be used
.make.ode.deSolve: local variable ‘INTTWO’ assigned but may not be used
.make.ode.deSolve: local variable ‘INTZERO’ assigned but may not be
  used
.make.ode.deSolve: local variable ‘elag’ assigned but may not be used
.make.ode.deSolve: local variable ‘flist’ assigned but may not be used
.make.ode.deSolve: local variable ‘jacfunc’ assigned but may not be
  used
.make.ode.deSolve: local variable ‘jactype’ assigned but may not be
  used
.make.ode.deSolve: local variable ‘liw’ assigned but may not be used
.make.ode.deSolve: local variable ‘lrw’ assigned but may not be used
.make.ode.deSolve: local variable ‘np’ assigned but may not be used
.make.pars.mkn: local variable ‘qmat’ assigned but may not be used
.make.pij.mkn: local variable ‘method’ assigned but may not be used
.nrate.phylo: local variable ‘mm’ assigned but may not be used
.oldestyle.gfit.continuous: local variable ‘oddoldemodels’ assigned but
  may not be used
.oldestyle.gfit.discrete: local variable ‘nms’ assigned but may not be
  used
.oldestyle.gfit.discrete: local variable ‘numberize’ assigned but may
  not be used
.parlog.rjmcmc: local variable ‘pT’ assigned but may not be used
.parlog.rjmcmc: local variable ‘parmbase’ assigned but may not be used
.paths.cache: local variable ‘left’ assigned but may not be used
.paths.cache: local variable ‘right’ assigned but may not be used
.read.ests.rjmcmc: local variable ‘base’ assigned but may not be used
.read.ests.rjmcmc: local variable ‘log’ assigned but may not be used
.read.ests.rjmcmc: local variable ‘mod’ assigned but may not be used
.replace.tip.with.subtree: local variable ‘N’ assigned but may not be
  used
.replace.tip.with.subtree: local variable ‘a_length’ assigned but may
  not be used
.rootfunc.mkn: local variable ‘k’ assigned but may not be used
.shifts.plot: local variable ‘nodes’ assigned but may not be used
.shifts.plot: local variable ‘xee’ assigned but may not be used
.simple.yule.medusa: local variable ‘par’ assigned but may not be used
.slater.branchingtimesfossil: local variable ‘phy2’ assigned but may
  not be used
.slater.initiate: local variable ‘p.out’ assigned but may not be used
.slater.mrca: local variable ‘bb’ assigned but may not be used
.splitormerge: local variable ‘new.values’ assigned but may not be used
.startingpt.bm : .rates.simulation: local variable ‘nm’ assigned but
  may not be used
.startingpt.bm: local variable ‘j’ assigned but may not be used
.subset.auteurRAW : <anonymous>: local variable ‘ngen’ assigned but may
  not be used
.traceplot : <anonymous>: local variable ‘xxx’ assigned but may not be
  used
.traceplot: local variable ‘xs’ assigned but may not be used
.traceplot: local variable ‘ys’ assigned but may not be used
aov.phylo: local variable ‘group’ assigned but may not be used
bf: local variable ‘ordres’ assigned but may not be used
bm.lik : ll.bm.direct : .xxSE: local variable ‘vv’ assigned but may not
  be used
bm.lik : ll.bm.direct: local variable ‘adjSE’ assigned but may not be
  used
calibrate.mecca: local variable ‘cmeans’ assigned but may not be used
calibrate.mecca: local variable ‘cvar’ assigned but may not be used
calibrate.mecca: local variable ‘mecca.env’ assigned but may not be
  used
calibrate.mecca: local variable ‘mecca.lm’ assigned but may not be used
calibrate.rjmcmc: local variable ‘acc’ assigned but may not be used
calibrate.rjmcmc: local variable ‘model’ assigned but may not be used
calibrate.rjmcmc: local variable ‘wid’ assigned but may not be used
dtt: local variable ‘mean.sims’ assigned but may not be used
edges.phylo : .hash_proppart: local variable ‘nn’ assigned but may not
  be used
ex.jumpsimulator: local variable ‘edges’ assigned but may not be used
exemplar.phylo: local variable ‘ff’ assigned but may not be used
fitContinuousMCMC: local variable ‘foo’ assigned but may not be used
fitDiscrete: local variable ‘constr’ assigned but may not be used
glomogram.phylo: local variable ‘nn’ assigned but may not be used
hashes.phylo : <anonymous>: local variable ‘ss’ assigned but may not be
  used
heights.phylo: local variable ‘labs’ assigned but may not be used
lookup.phylo: local variable ‘genuslevel_tree’ assigned but may not be
  used
lookup.phylo: local variable ‘original_taxonomy’ assigned but may not
  be used
mecca: local variable ‘k’ assigned but may not be used
medusa : medusa_runner : summarizeZ: local variable ‘opt.model’
  assigned but may not be used
medusa : medusa_runner: local variable ‘z.orig’ assigned but may not be
  used
nodelabel.phylo: local variable ‘orig’ assigned but may not be used
nodelabel.phylo: local variable ‘true_missed’ assigned but may not be
  used
nodelabel.phylo: local variable ‘unmatched’ assigned but may not be
  used
ou.lik : fx_exporter : lik: local variable ‘rtmx’ assigned but may not
  be used
ou.lik: local variable ‘model’ assigned but may not be used
rc: local variable ‘pp’ assigned but may not be used
rjmcmc.bm: local variable ‘jumpsedgewise’ assigned but may not be used
rjmcmc.bm: local variable ‘lnLikelihoodRatio’ assigned but may not be
  used
stem.limits: local variable ‘alpha’ assigned but may not be used
write.pathd8: local variable ‘taxon’ assigned but may not be used
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [8s/14s] OK
** found \donttest examples: check also with --run-donttest
* 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 NOTE
