* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/lcpm.Rcheck’
* using R Under development (unstable) (2024-04-24 r86484)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 18.1.4
    flang-new version 18.1.4
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘lcpm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lcpm’ version ‘0.1.1’
* 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 ‘lcpm’ can be installed ... [11s/14s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/lcpm-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 ... [17s/22s] OK
* checking Rd files ... NOTE
checkRd: (-1) lcpm.Rd:52: Lost braces; missing escapes or markup?
    52 | \code{lcpm} provides the maximum likelihood estimate for ordinal outcomes (J>2 categories) and a Generalized Linear Model (GLM) with the log link without the assumption of proportionality. That is, lcpm determines the MLE for log[P(y <= j)]= cut_j + X beta_j subject to [cut_{j-1} + X beta_{j-1} <= cut_j + X beta_j] and [cut_j + X beta_j <=0]. This implementation uses \code{\link{constrOptim}}  to determine the MLE and so the results account for the restricted parameter space.
       |                                                                                                                                                                                                                                                                                    ^
checkRd: (-1) lcpm.Rd:52: Lost braces; missing escapes or markup?
    52 | \code{lcpm} provides the maximum likelihood estimate for ordinal outcomes (J>2 categories) and a Generalized Linear Model (GLM) with the log link without the assumption of proportionality. That is, lcpm determines the MLE for log[P(y <= j)]= cut_j + X beta_j subject to [cut_{j-1} + X beta_{j-1} <= cut_j + X beta_j] and [cut_j + X beta_j <=0]. This implementation uses \code{\link{constrOptim}}  to determine the MLE and so the results account for the restricted parameter space.
       |                                                                                                                                                                                                                                                                                                   ^
checkRd: (-1) ppm.Rd:51: Lost braces; missing escapes or markup?
    51 | \code{ppm} provides the maximum likelihood estimate for ordinal outcomes (J>2 categories) and a Generalized Linear Model with the log link with the assumption of proportionality. That is, ppm determines the MLE for log[P(y <= j)]= cut_j + X beta subject to [cut_{j-1} <= cut_j ] and [cut_j + X beta <=0]. This implementation uses \code{\link{constrOptim}} to determine the MLE and so the results should correctly account for the restricted parameter space. A proposed test for proportionality is included in \code{\link{lcpm}}.
       |                                                                                                                                                                                                                                                                       ^
* 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 LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* checking examples ... [9s/13s] OK
* checking PDF version of manual ... [9s/14s] 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: 2 NOTEs