* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/NetworkExtinction.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 ‘NetworkExtinction/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NetworkExtinction’ version ‘1.0.3’
* 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 ‘NetworkExtinction’ can be installed ... [12s/18s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/NetworkExtinction-00install.html' for details.
* checking installed package size ... OK
* 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 ... [17s/22s] OK
* checking Rd files ... NOTE
checkRd: (-1) ExtinctionOrder.Rd:35: Lost braces
    35 | \item{RewiringDist}{a numeric matrix of NxN dimension (N... number of nodes in Network). Contains, for example, phylogenetic or functional trait distances between nodes in Network which are used by the Rewiring argument to calculate rewiring probabilities. If Rewiring == function(x){x}, this matrix is expected to contain probabilities of a connection being present between species-pairs.}
       |                                                                                                                                                                                                                                                                                            ^
checkRd: (-1) RandomExtinctions.Rd:52: Lost braces
    52 | \item{RewiringDist}{a numeric matrix of NxN dimension (N... number of nodes in Network). Contains, for example, phylogenetic or functional trait distances between nodes in Network which are used by the Rewiring argument to calculate rewiring probabilities. If Rewiring == function(x){x}, this matrix is expected to contain probabilities of a connection being present between species-pairs.}
       |                                                                                                                                                                                                                                                                                            ^
checkRd: (-1) RandomExtinctions.Rd:71-72: Lost braces
    71 | primary removals. For example, if a network has five species {A,B,
       |                                                              ^
checkRd: (-1) RandomExtinctions.Rd:72: Lost braces; missing escapes or markup?
    72 | ,D,E} and a pre-defined "random" order of removal {C,A,B,E,D} with
       |                                                   ^
checkRd: (-1) RandomExtinctions.Rd:77: Lost braces; missing escapes or markup?
    77 | vector, i.e., {C,A,B}."
       |               ^
checkRd: (-1) SimulateExtinctions.Rd:38: Lost braces
    38 | \item{RewiringDist}{a numeric matrix of NxN dimension (N... number of nodes in Network). Contains, for example, phylogenetic or functional trait distances between nodes in Network which are used by the Rewiring argument to calculate rewiring probabilities. If Rewiring == function(x){x}, this matrix is expected to contain probabilities of a connection being present between species-pairs.}
       |                                                                                                                                                                                                                                                                                            ^
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
  Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [39s/47s] OK
* checking PDF version of manual ... [7s/13s] 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