• using R version 4.4.3 (2025-02-28 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 13.3.0     GNU Fortran (GCC) 13.3.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• checking for file 'phyloregion/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'phyloregion' version '1.0.9'
• 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 hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'phyloregion' 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 ... [12s] OK
• checking whether the package can be loaded with stated dependencies ... [12s] OK
• checking whether the package can be unloaded cleanly ... [13s] OK
• checking whether the namespace can be loaded with stated dependencies ... [11s] OK
• checking whether the namespace can be unloaded cleanly ... [12s] OK
• checking loading without being on the library search path ... [12s] 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 ... [36s] OK
• checking Rd files ... [1s] OK
• checking Rd metadata ... 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 ... [2s] OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [38s] ERROR Running examples in 'phyloregion-Ex.R' failed The error most likely occurred in: > ### Name: rast2comm > ### Title: Convert raw input distribution data to community > ### Aliases: rast2comm polys2comm points2comm > > ### ** Examples > > > > library(terra) terra 1.8.86 > s <- vect(system.file("ex/nigeria.json", package="phyloregion")) > set.seed(1) > m <- as.data.frame(spatSample(s, 1000, method = "random"), + geom = "XY")[-1] > names(m) <- c("lon", "lat") > species <- paste0("sp", sample(1:100)) > m$taxon <- sample(species, size = nrow(m), replace = TRUE) > > pt <- points2comm(dat = m, res = 0.5) # This generates a list of two objects Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1) Warning: [crs<-] Cannot set raster SRS: empty srs Error: [project] output crs is not valid Execution halted
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [15s] OK   Running 'tinytest.R' [14s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [20s] ERROR Error(s) in re-building vignettes: --- re-building 'Benchmark.Rmd' using rmarkdown --- finished re-building 'Benchmark.Rmd' --- re-building 'ed.Rmd' using rmarkdown --- finished re-building 'ed.Rmd' --- re-building 'phyloregion-intro.Rmd' using rmarkdown Quitting from phyloregion-intro.Rmd:74-87 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! [project] output crs is not valid --- Backtrace:     ▆  1. └─phyloregion::points2comm(...)  2. ├─base::suppressWarnings(invisible(project(m, "epsg:4326")))  3. │ └─base::withCallingHandlers(...)  4. ├─terra::project(m, "epsg:4326")  5. └─terra::project(m, "epsg:4326")  6. └─terra (local) .local(x, ...)  7. └─terra:::messages(x, "project")  8. └─terra:::error(f, x@pntr$getError()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'phyloregion-intro.Rmd' failed with diagnostics: [project] output crs is not valid --- failed re-building 'phyloregion-intro.Rmd' SUMMARY: processing the following file failed:   'phyloregion-intro.Rmd' Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [19s] OK
• checking HTML version of manual ... [9s] OK
• DONE

Status: 2 ERRORs