* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BoolNet.Rcheck’
* using R Under development (unstable) (2025-02-23 r87804)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘BoolNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BoolNet’ version ‘2.1.9’
* 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
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* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘BoolNet’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/BoolNet-00install.html' for details.
* used C compiler: ‘Debian clang version 19.1.7 (1+b1)’
* checking package directory ... OK
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* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
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* checking code files for non-ASCII characters ... OK
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* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) getPathToAttractor.Rd:23: Lost braces; missing escapes or markup?
    23 |   Specifies whether the actual attractor states are included in the resulting table or not. If \code{includeAttractorStates = "all"} (which is the default behaviour), the sequence ends when the attractor was traversed once. If \code{includeAttractorStates = "first"}, only the first state of attractor is added to the sequence. This corresponds to the behaviour prior to \pkg{BoolNet} version 1.5. If {includeAttractorStates = "none"}, the sequence ends with the last non-attractor state. In this case, the sequence can be empty if the start state is an attractor state.
       |                                                                                                                                                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) plotSequence.Rd:42: Lost braces; missing escapes or markup?
    42 |   Specifies whether the actual attractor states are included in the plot or not (see also \code{\link{getPathToAttractor}}). If \code{includeAttractorStates = "all"} (which is the default behaviour), the sequence ends when the attractor was traversed once. If \code{includeAttractorStates = "first"}, only the first state of attractor is added to the sequence. If {includeAttractorStates = "none"}, the sequence ends with the last non-attractor state. 
       |                                                                                                                                                                                                                                                                                                                                                                             ^
checkRd: (-1) sequenceToLaTeX.Rd:37: Lost braces; missing escapes or markup?
    37 |   Specifies whether the actual attractor states are included in the table or not (see also \code{\link{getPathToAttractor}}). If \code{includeAttractorStates = "all"} (which is the default behaviour), the sequence ends when the attractor was traversed once. If \code{includeAttractorStates = "first"}, only the first state of attractor is added to the sequence. If {includeAttractorStates = "none"}, the sequence ends with the last non-attractor state. 
       |                                                                                                                                                                                                                                                                                                                                                                              ^
checkRd: (-1) simulateSymbolicModel.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulateSymbolicModel.Rd:66-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulateSymbolicModel.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testNetworkProperties.Rd:131: Lost braces; missing escapes or markup?
   131 | If {perturb="functions"} or \code{perturb="transitions"} and \code{accumulate=FALSE}, the function returns a vector of percentages of original attractors found in each of the perturbed copies of the original network. If \code{accumulate=TRUE}, the function returns the overall percentage of original attractors found in all perturbed copies.
       |    ^
checkRd: (-1) testNetworkProperties.Rd:140: Lost braces
   140 | code{params} can hold parameters \code{numSamples, flipBits} corresponding to the parameters of \code{\link{perturbTrajectories}} that define how many initial states are drawn and how many bits are flipped.
       |     ^
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* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE