* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/aghq.Rcheck’
* using R Under development (unstable) (2025-02-25 r87824)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘aghq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘aghq’ version ‘0.4.1’
* 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 ‘aghq’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/aghq-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
* checking loading without being on the library search path ... [1s/2s] 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 ... [10s/13s] OK
* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) aghq.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aghq.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aghq.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aghq.Rd:61-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aghq.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aghq.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aghq.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aghq.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aghq.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) aghq.Rd:79-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:86-91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:92-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aghq.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) default_control.Rd:23-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_marglaplace.Rd:23-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_marglaplace.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_marglaplace.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_marglaplace.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_marglaplace.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_marglaplace.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_tmb.Rd:23-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_tmb.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_tmb.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_tmb.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_tmb.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_control_tmb.Rd:31-33: Lost braces
    31 | \item \code{negate}: {default \code{TRUE}. Assumes that your \code{TMB} function
       |                      ^
checkRd: (-1) laplace_approximation.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) laplace_approximation.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) laplace_approximation.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) laplace_approximation.Rd:42-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) laplace_approximation.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) laplace_approximation.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) laplace_approximation.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) laplace_approximation.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) laplace_approximation.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace.Rd:53-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace_tmb.Rd:58-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace_tmb.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace_tmb.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace_tmb.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) marginal_laplace_tmb.Rd:65-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) normalize_logpost.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normalize_logpost.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normalize_logpost.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) optimize_theta.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimize_theta.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimize_theta.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimize_theta.Rd:29-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimize_theta.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimize_theta.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimize_theta.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimize_theta.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimize_theta.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) optimize_theta.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) optimize_theta.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) optimize_theta.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) optimize_theta.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample_marginal.Rd:60-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample_marginal.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sample_marginal.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.aghq.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.aghq.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.aghq.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.aghq.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.aghq.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.aghq.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary.aghq.Rd:24-26: Lost braces in \itemize; \value handles \item{}{} directly
* 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 examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [20s/22s] OK
  Running ‘testthat.R’ [20s/22s]
* checking PDF version of manual ... [7s/9s] OK
* checking HTML version of manual ... [2s/3s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE