• using R Under development (unstable) (2025-11-13 r89017)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.5     flang version 21.1.5
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘phyloraster/DESCRIPTION’ ... OK
• this is package ‘phyloraster’ version ‘2.2.0’
• 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 ‘phyloraster’ can be installed ... OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... 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 ... 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 ... [8s/16s] OK
• 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 LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [103s/359s] ERROR   Running ‘testthat.R’ [102s/358s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(phyloraster)   >   > test_check("phyloraster")   Saving _problems/test-delta-grid-81.R   Saving _problems/test-geo.phylo-144.R   Saving _problems/test-geo.phylo-167.R   Saving _problems/test-rast-ed-ses-121.R   Saving _problems/test-rast.pd.ses-120.R   Saving _problems/test-rast.pe.ses-102.R   Saving _problems/test-shp2rast-79.R   Saving _problems/test-shp2rast-101.R   [ FAIL 8 | WARN 0 | SKIP 0 | PASS 84 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-delta-grid.R:80:3'): Raster is saved when filename is provided ──   Error in `expect(phyloraster::delta.grid(riq.pres, riq.fut, filename = temp), ok = T)`: `failure_message` must be a character vector, not a <SpatRaster> object.   Backtrace:       ▆    1. └─testthat::expect(failure_message = phyloraster::delta.grid(riq.pres, riq.fut, filename = temp)) at test-delta-grid.R:80:3    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-geo.phylo.R:144:3'): arguments are calculated when is missing and the             tree is provided ──   Error in `expect(geo.phylo(data$x, tree), ok = T)`: `failure_message` must be a character vector, not a <SpatRaster> object.   Backtrace:       ▆    1. └─testthat::expect(failure_message = geo.phylo(data$x, tree)) at test-geo.phylo.R:144:3    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-geo.phylo.R:163:3'): names are reordened in the function geo.phylo ──   Error in `expect(geo.phylo(data$x, tree, inv.R = inv.R, edge.path = data$edge.path[sample(1:nrow(data$edge.path)), ], branch.length = data$branch.length, n.descen = data$n.descendants), ok = T)`: `failure_message` must be a character vector, not a <SpatRaster> object.   Backtrace:       ▆    1. └─testthat::expect(failure_message = geo.phylo(...)) at test-geo.phylo.R:163:3    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-rast-ed-ses.R:116:3'): function compute branch lenght when tree is supplied ──   Error in `expect(rast.ed.ses(x = x, tree = tree, spat_alg = "bootspat_str", spat_alg_args = list(rprob = NULL, rich = NULL, fr_prob = NULL), aleats = 5), ok = T)`: `failure_message` must be a character vector, not a <SpatRaster> object.   Backtrace:       ▆    1. └─testthat::expect(failure_message = rast.ed.ses(...)) at test-rast-ed-ses.R:116:3    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-rast.pd.ses.R:115:3'): function compute branch lenght when tree is supplied ──   Error in `expect(rast.pd.ses(x = x, tree = tree, spat_alg = "bootspat_str", spat_alg_args = list(rprob = NULL, rich = NULL, fr_prob = NULL), aleats = 5), ok = T)`: `failure_message` must be a character vector, not a <SpatRaster> object.   Backtrace:       ▆    1. └─testthat::expect(failure_message = rast.pd.ses(...)) at test-rast.pd.ses.R:115:3    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-rast.pe.ses.R:96:3'): function compute branch lenght when tree is supplied ──   Error in `expect(rast.pe.ses(x = x, tree = tree, spat_alg = "bootspat_str", metric = "pe", spat_alg_args = list(rprob = NULL, rich = NULL, fr_prob = NULL), aleats = 5), ok = T)`: `failure_message` must be a character vector, not a <SpatRaster> object.   Backtrace:       ▆    1. └─testthat::expect(failure_message = rast.pe.ses(...)) at test-rast.pe.ses.R:96:3    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-shp2rast.R:77:3'): function runs ok when a mask is applied ─────   Error in `expect(phyloraster::shp2rast(shp, y = coun.rast, sps.col = "BINOMIAL", ymask = TRUE, background = 0), ok = T)`: `failure_message` must be a character vector, not a <SpatRaster> object.   Backtrace:       ▆    1. └─testthat::expect(failure_message = phyloraster::shp2rast(...)) at test-shp2rast.R:77:3    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)   ── Error ('test-shp2rast.R:100:3'): Raster is saved when filename is provided ──   Error in `expect(shp2rast(shp, y = coun.rast, sps.col = "BINOMIAL", background = 0, filename = temp), ok = T)`: `failure_message` must be a character vector, not a <SpatRaster> object.   Backtrace:       ▆    1. └─testthat::expect(failure_message = shp2rast(...)) at test-shp2rast.R:100:3    2. └─testthat:::check_character(failure_message)    3. └─testthat:::stop_input_type(...)    4. └─rlang::abort(message, ..., call = call, arg = arg)      [ FAIL 8 | WARN 0 | SKIP 0 | PASS 84 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [125s/415s] OK
• checking PDF version of manual ... [9s/23s] OK
• checking HTML version of manual ... [5s/10s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR