* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/autoMFA.Rcheck’
* using R Under development (unstable) (2025-02-27 r87835)
* 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 ‘autoMFA/DESCRIPTION’ ... OK
* this is package ‘autoMFA’ version ‘1.0.0’
* 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 ‘autoMFA’ can be installed ... [13s/48s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/autoMFA-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 ... NOTE
Namespace in Imports field not imported from: ‘usethis’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [36s/114s] OK
* checking Rd files ... NOTE
checkRd: (-1) AMFA.Rd:37: Lost braces; missing escapes or markup?
37 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.Rd:37: Lost braces; missing escapes or markup?
37 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.Rd:37: Lost braces; missing escapes or markup?
37 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.Rd:37: Lost braces; missing escapes or markup?
37 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.Rd:37: Lost braces; missing escapes or markup?
37 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.Rd:37: Lost braces; missing escapes or markup?
37 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.Rd:45-52: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) AMFA.inc.Rd:30: Lost braces; missing escapes or markup?
30 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.inc.Rd:30: Lost braces; missing escapes or markup?
30 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.inc.Rd:30: Lost braces; missing escapes or markup?
30 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.inc.Rd:30: Lost braces; missing escapes or markup?
30 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.inc.Rd:30: Lost braces; missing escapes or markup?
30 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.inc.Rd:30: Lost braces; missing escapes or markup?
30 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) AMFA.inc.Rd:42-49: Lost braces in \itemize; \value handles \item{}{} directly
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checkRd: (-1) MFA_ECM.Rd:43: Lost braces; missing escapes or markup?
43 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) MFA_ECM.Rd:43: Lost braces; missing escapes or markup?
43 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) MFA_ECM.Rd:43: Lost braces; missing escapes or markup?
43 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) MFA_ECM.Rd:43: Lost braces; missing escapes or markup?
43 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) MFA_ECM.Rd:43: Lost braces; missing escapes or markup?
43 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) MFA_ECM.Rd:43: Lost braces; missing escapes or markup?
43 | \item{conv_measure}{The convergence criterion of the ECM algorithm. The default \code{'diff'} stops the ECM iterations if |l^{(k+1)} - l^{(k)}| < \code{tol} where l^{(k)} is the log-likelihood at the \emph{k}th ECM iteration. If \code{'ratio'}, then the convergence of the ECM iterations is measured using |(l^{(k+1)} - l^{(k)})/l^{(k+1)}|.}
| ^
checkRd: (-1) MFA_ECM.Rd:51-58: Lost braces in \itemize; \value handles \item{}{} directly
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* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [32s/108s] OK
* checking PDF version of manual ... [7s/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