* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/R0.Rcheck’
* using R Under development (unstable) (2025-02-15 r87725)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 20.1.0-rc2
    flang version 20.1.0-rc2
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘R0/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R0’ version ‘1.3-1’
* 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 ‘R0’ can be installed ... [7s/13s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/R0-00install.html' for details.
* checking installed package size ... OK
* checking package 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 ... [16s/24s] OK
* checking Rd files ... NOTE
checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... INFO
Undeclared package ‘epitools’ in Rd xrefs
* 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 examples ... [10s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [16s/25s] OK
  Running ‘check.incid.R’
  Running ‘est.GT.R’
  Running ‘est.R0.AR.R’
  Running ‘est.R0.EG.R’
  Running ‘est.R0.ML.R’
  Running ‘est.R0.SB.R’
  Running ‘est.R0.TD.R’
  Running ‘estimate.R.R’
  Running ‘generation.time.R’
  Running ‘sensitivity.analysis.R’ [8s/12s]
  Running ‘sim.epid.R’
  Running ‘smooth.Rt.R’
* checking PDF version of manual ... [12s/20s] 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