* using log directory ‘/srv/hornik/tmp/CRAN/nichetools.Rcheck’ * using R Under development (unstable) (2024-03-22 r86169) * 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 ‘nichetools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘nichetools’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/4s] NOTE Maintainer: ‘Benjamin L. Hlina ’ New submission Possibly misspelled words in DESCRIPTION: nicheROVER (3:33, 7:48, 9:18) Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Found the following (possibly) invalid URLs: URL: From: inst/doc/how_to_use_nichetools.html Message: Empty URL URL: https://codecov.io/gh/benjaminhlina/nichetools (moved to https://app.codecov.io/gh/benjaminhlina/nichetools) From: README.md Status: 301 Message: Moved Permanently URL: https://cran.r-project.org/web/packages/data.table/index.html From: inst/doc/how_to_use_nichetools.html Status: 200 Message: OK CRAN URL not in canonical form URL: https://cran.r-project.org/web/packages/nicheROVER/index.html From: man/extract_mu.Rd man/extract_niche_size.Rd man/extract_overlap.Rd man/extract_sigma.Rd man/mu_est_long.Rd man/niw_fish_post.Rd man/over_stat.Rd man/sigma_est_wide.Rd inst/doc/how_to_use_nichetools.html README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://github.com/benjaminhlina/nichetool/actions/workflows/R-CMD-check.yaml (moved to https://github.com/benjaminhlina/nichetools/actions/workflows/R-CMD-check.yaml) From: README.md Status: 301 Message: Moved Permanently The canonical URL of the CRAN page for a package is https://CRAN.R-project.org/package=pkgname For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Title field should be in title case. Current version is: ‘Complementary package to nicheROVER’ In title case that is: ‘Complementary Package to nicheROVER’ The Description field should not start with the package name, 'This package' or similar. * 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 ‘nichetools’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking whether startup messages can be suppressed ... [0s/0s] 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 ... [3s/3s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) nichetools-package.Rd:9: Lost braces; missing escapes or markup? 9 | This package is complementary to {nicheROVER} as it allows the user to extract Bayesian estimates from data objects created by package {nicheROVER}. | ^ checkRd: (-1) nichetools-package.Rd:9: Lost braces; missing escapes or markup? 9 | This package is complementary to {nicheROVER} as it allows the user to extract Bayesian estimates from data objects created by package {nicheROVER}. | ^ * 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 ... [0s/0s] 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 ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [40s/40s] OK Running ‘testthat.R’ [40s/40s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [12s/12s] OK * checking PDF version of manual ... [4s/4s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character μ (U+03BC) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ! LaTeX Error: Unicode character Σ (U+03A3) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘nichetools-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING, 3 NOTEs