* using log directory ‘/srv/hornik/tmp/CRAN/RPANDA.Rcheck’ * using R Under development (unstable) (2024-01-29 r85841) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘RPANDA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RPANDA’ version ‘2.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/6s] NOTE Maintainer: ‘Hélène Morlon ’ Possibly misspelled words in DESCRIPTION: Mazet (47:123) Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Found the following (possibly) invalid URLs: URL: https://travis-ci.org/hmorlon/PANDA (moved to https://app.travis-ci.com/hmorlon/PANDA) From: README.md Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * 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 ‘RPANDA’ can be installed ... [37s/37s] OK * used C compiler: ‘Debian clang version 17.0.6 (5)’ * 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 ... [7s/7s] OK * checking whether the package can be loaded with stated dependencies ... [7s/7s] OK * checking whether the package can be unloaded cleanly ... [7s/7s] OK * checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK * checking whether the namespace can be unloaded cleanly ... [7s/7s] OK * checking loading without being on the library search path ... [7s/7s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... NOTE Mismatches for apparent methods not registered: plot: function(x, ...) plot.with.trait: function(phylo, rate, scale, lwd, direction) plot: function(x, ...) plot.network: function(link, spec, trait.id, method, order, scale) plot: function(x, ...) plot.species: function(spec, trait.id, net, ...) plot: function(x, ...) plot.phylo.comb: function(phylo, data, sampling.fractions, shift.res, combi, backbone.option, main, col.sub, col.bck, lty.bck, tested_nodes, lad, leg, text.cex, pch.cex, ...) mean: function(x, ...) mean.rate: function(tree, rate) abs: function(x) abs.to.rel: function(tree, true.rate, lambda_0) See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [64s/64s] NOTE fit_bd_backbone_c: multiple local function definitions for ‘optimLH’ with different formal arguments simul.comb.shift: no visible global function definition for ‘txtProgressBar’ simul.comb.shift: no visible global function definition for ‘setTxtProgressBar’ Undefined global functions or variables: setTxtProgressBar txtProgressBar Consider adding importFrom("utils", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. Found if() conditions comparing class() to string: File ‘RPANDA/R/misc_functions.R’: if (class(class.object) == "try-error") ... File ‘RPANDA/R/misc_functions.R’: if (class(class.object) == "try-error") ... File ‘RPANDA/R/misc_functions.R’: if (class(class.object) == "try-error") ... File ‘RPANDA/R/misc_functions.R’: if (class(class.object) == "try-error") ... File ‘RPANDA/R/misc_functions.R’: if (class(trimmed.class.object) == "try-error") ... File ‘RPANDA/R/misc_functions.R’: if (class(trimmed.class.object) == "try-error") ... File ‘RPANDA/R/misc_functions.R’: if (class(class.by.class.object) == "try-error") ... File ‘RPANDA/R/misc_functions.R’: if (class(class.by.class.object) == "try-error") ... File ‘RPANDA/R/misc_functions.R’: if (class(trimmed.class.object) == "try-error") ... File ‘RPANDA/R/misc_functions.R’: if (class(trimmed.class.object) == "try-error") ... Use inherits() (or maybe is()) instead. * checking Rd files ... [1s/1s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'fit_t_comp.Rd': \examples lines wider than 100 characters: #Now fit models that estimate parameters separately according to different 'regimes', including biogeography MC.two_regime.geo.fit<-fit_t_comp(phylo, pPC1, model="MC", geography.object=geography.object, regime.map=regime.map) DDlin.two_regime.geo.fit<-fit_t_comp(phylo, pPC1,model="DDlin", geography.object=geography.object, regime.map=regime.map) DDexp.two_regime.geo.fit<-fit_t_comp(phylo, pPC1, model="DDexp", geography.object=geography.object, regime.map=regime.map) Rd file 'fit_t_comp_subgroup.Rd': \usage lines wider than 90 characters: fit_t_comp_subgroup(full.phylo, data, subgroup, subgroup.map, model=c("MC","DDexp","DDlin"), \examples lines wider than 100 characters: MC.fit_subgroup_geo<-fit_t_comp_subgroup(full.phylo=Canidae.phylo,ana.events=BGB.examples$Canidae.ana.events, DDexp.fit_subgroup_geo<-fit_t_comp_subgroup(full.phylo=Canidae.phylo,ana.events=BGB.examples$Canidae.ana.events, DDlin.fit_subgroup_geo<-fit_t_comp_subgroup(full.phylo=Canidae.phylo,ana.events=BGB.examples$Canidae.ana.events, DDexp.fit_subgroup_two.regime<-fit_t_comp_subgroup(full.phylo=Canidae.phylo,data=Canidae.A,subgroup="A", DDlin.fit_subgroup_two.regime<-fit_t_comp_subgroup(full.phylo=Canidae.phylo,data=Canidae.A,subgroup="A", These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘all_comb_models’ ‘extract.clade.ln’ ‘get.branching.nodes’ ‘get.node.ages’ ‘subtree’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE S3 methods shown with full name in Rd file 'plot.phylo.comb.Rd': ‘plot.phylo.comb’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [7s/7s] OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [61s/61s] WARNING Found the following significant warnings: Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. Warning: 'is.R' is deprecated. 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Examples with CPU (user + system) or elapsed time > 5s user system elapsed div.models 6.037 0.108 6.146 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [7s/7s] OK Running ‘test-all.R’ [7s/7s] * checking PDF version of manual ... [6s/6s] OK * checking HTML version of manual ... [3s/3s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 WARNINGs, 5 NOTEs