* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/MSwM.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 ‘MSwM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSwM’ version ‘1.5’
* 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 ‘MSwM’ can be installed ... [15s/16s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/MSwM-00install.html' for details.
* checking package directory ... 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 ... 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 ... [15s/18s] OK
* checking Rd files ... NOTE
checkRd: (-1) msmFit.Rd:30: Lost braces
    30 |         -\code{trace}{: A logical value. If it is TRUE, tracing information on the progress of the optimization is produced.}
       |                      ^
checkRd: (-1) msmFit.Rd:32: Lost braces
    32 |         -\code{maxiter}{: The maximum number of iterations in the EM method. Default is 100.}
       |                        ^
checkRd: (-1) msmFit.Rd:34: Lost braces
    34 |         -\code{tol}{: Tolerance. The algorithm stops if it is unable to reduce the value by a factor of \code{tol} at a step. Default is 1e-8.}
       |                    ^
checkRd: (-1) msmFit.Rd:36: Lost braces
    36 |         -\code{maxiterOuter}{: The number of short runs of the EM method to stablish the initial values. Default is 5}
       |                             ^
checkRd: (-1) msmFit.Rd:38: Lost braces
    38 |         -\code{maxiterInner}{: The number of iterations in the EM method in each short run to stablish the initial values. Default is 10}
       |                             ^
checkRd: (-1) msmFit.Rd:40: Lost braces
    40 |         -\code{parallelization}{: A logical value. Whether the process is done by using parallelization or not. Default is TRUE.}
       |                                ^
checkRd: (-1) plotDiag.Rd:33: Lost braces
    33 | - \code{1}{: represents the plot of residuals against fitted values. }
       |           ^
checkRd: (-1) plotDiag.Rd:35: Lost braces
    35 | - \code{2}{: represents the Normal Q-Q plot. }
       |           ^
checkRd: (-1) plotDiag.Rd:37: Lost braces
    37 | - \code{3}{: represents the ACF/PACF of residuals and ACF/PACF of square residuals. }
       |           ^
checkRd: (-1) plotProb.Rd:29: Lost braces
    29 | -\code{1}{: represents the plots that contains, for each regime, its smoothed and filtered probabilities.}.
       |          ^
checkRd: (-1) plotProb.Rd:31: Lost braces
    31 | -\code{2:(number of regimes +1)}{: represents plot of the regime minus one with the response variable against the smoothed probabilities.}
       |                                 ^
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [29s/40s] OK
* checking PDF version of manual ... [8s/12s] 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