* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/jointNmix.Rcheck’
* using R Under development (unstable) (2024-04-05 r86344)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘jointNmix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘jointNmix’ version ‘1.0’
* 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 ‘jointNmix’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/jointNmix-00install.html' for details.
* 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 ... [9s/11s] OK
* checking Rd files ... NOTE
checkRd: (-1) jointNmix.Rd:30: Lost braces; missing escapes or markup?
    30 | The function fits a bivariate extension to Royle's (2004) N-mixture model to data on the abundance of two species collected at R sites over T time occasions. The model for observation on site i at time t for species 1 can be specified as \deqn{Y_{1it}|N_{1i} ~ Bin(N_{1i},p_{1it})}\deqn{N_{1i} ~ a count distribution with mean \lambda_{1i}.} The model for species 2 is \deqn{Y_{2it}|N_{1i},N_{2i} ~ Bin(N_{2i},p_{2it})}\deqn{N_{2i}|N_{1i} ~ a count distribution with mean \psi+\lambda_{2i}N_{1i}.} Here, users may define a Poisson or negative binomial distribution for the latent abundances N_{1i} and N_{2i}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) jointNmix.Rd:30: Lost braces; missing escapes or markup?
    30 | The function fits a bivariate extension to Royle's (2004) N-mixture model to data on the abundance of two species collected at R sites over T time occasions. The model for observation on site i at time t for species 1 can be specified as \deqn{Y_{1it}|N_{1i} ~ Bin(N_{1i},p_{1it})}\deqn{N_{1i} ~ a count distribution with mean \lambda_{1i}.} The model for species 2 is \deqn{Y_{2it}|N_{1i},N_{2i} ~ Bin(N_{2i},p_{2it})}\deqn{N_{2i}|N_{1i} ~ a count distribution with mean \psi+\lambda_{2i}N_{1i}.} Here, users may define a Poisson or negative binomial distribution for the latent abundances N_{1i} and N_{2i}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ^
* 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 examples ... OK
* checking PDF version of manual ... [7s/11s] 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