* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/nimbleSCR.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 ‘nimbleSCR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘nimbleSCR’ version ‘0.2.1’ * 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 ‘nimbleSCR’ can be installed ... [39s/48s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/nimbleSCR-00install.html' for details. * checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: doc 4.0Mb extdata 1.8Mb * 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 ... [11s/14s] OK * checking whether the package can be loaded with stated dependencies ... [10s/13s] OK * checking whether the package can be unloaded cleanly ... [10s/14s] 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 ... [11s/12s] OK * checking whether startup messages can be suppressed ... [11s/12s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘methods’ 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 ... [33s/41s] OK * checking Rd files ... NOTE checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup? 58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited. | ^ checkRd: (-1) dcatState1Alive1Dead.Rd:58: Lost braces; missing escapes or markup? 58 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited. | ^ checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup? 59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3 | ^ checkRd: (-1) dcatState1Alive1Dead.Rd:59: Lost braces; missing escapes or markup? 59 | If z_{i,t} = 2, individual i can die and transition to z_{i,t+1}=3 with probability prob2To3, or survive with probability 1-prob2To3 | ^ checkRd: (-1) dcatState1Alive1Dead.Rd:60: Lost braces; missing escapes or markup? 60 | Individuals in dead states (z_{i,t} = 3 ) remain in that state with probability 1, the absorbing state. | ^ checkRd: (-1) dcatState1Alive1Dead.Rd:32: Lost braces; missing escapes or markup? 32 | \item{x}{Scalar, individual state z_{i,t+1}.} | ^ checkRd: (-1) dcatState1Alive1Dead.Rd:34: Lost braces; missing escapes or markup? 34 | \item{z}{Scalar, initial individual state z_{i,t}.} | ^ checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup? 68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited. | ^ checkRd: (-1) dcatState1Alive2Dead.Rd:68: Lost braces; missing escapes or markup? 68 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited. | ^ checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup? 69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. | ^ checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup? 69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. | ^ checkRd: (-1) dcatState1Alive2Dead.Rd:69: Lost braces; missing escapes or markup? 69 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=3 with probability prob2To3, or die from another cause with probability prob2To4 z_{i,t+1}=4. | ^ checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup? 71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1. | ^ checkRd: (-1) dcatState1Alive2Dead.Rd:71: Lost braces; missing escapes or markup? 71 | Individuals in dead states (z_{i,t} = 3 or 4) transition to z_{i,t+1} = 4, the absorbing state, with probability 1. | ^ checkRd: (-1) dcatState1Alive2Dead.Rd:36: Lost braces; missing escapes or markup? 36 | \item{x}{Scalar, individual state z_{i,t+1}.} | ^ checkRd: (-1) dcatState1Alive2Dead.Rd:38: Lost braces; missing escapes or markup? 38 | \item{z}{Scalar, initial individual state z_{i,t}.} | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup? 92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:92: Lost braces; missing escapes or markup? 92 | If z_{i,t} = 1, individual i can be recruited (transition to state 2) with probability prob1To2_t, so z_{i,t+1} ~ dcat(1- prob1To2_t, prob1To2_t, 0,0 , 0) where prob1To2_t represent the probability of an unborn individual to be recruited. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup? 93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup? 93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:93: Lost braces; missing escapes or markup? 93 | If z_{i,t} = 2, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob2To4, or die from another cause with probability prob2To5 z_{i,t+1}=5. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup? 94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:94: Lost braces; missing escapes or markup? 94 | If the individual does not die (1-(prob2To4+prob2To5)), it can either transition to the second state alive (z_{i,t+1}=3) with probability prob2To3 or remain in the first state alive (z_{i,t+1}=2) with probability (1-prob2To3). | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup? 95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup? 95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:95: Lost braces; missing escapes or markup? 95 | If z_{i,t} = 3, individual i can die from one cause of mortality (e.g. culling) and transition to z_{i,t+1}=4 with probability prob3To4, or die from another cause with probability prob3To5 z_{i,t+1}=5. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup? 97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:97: Lost braces; missing escapes or markup? 97 | Individuals in dead states (z_{i,t} = 4 or 5) transition to z_{i,t+1} = 5, the absorbing state, with probability 1. | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:48: Lost braces; missing escapes or markup? 48 | \item{x}{Scalar, individual state z_{i,t+1}.} | ^ checkRd: (-1) dcatState2Alive2Dead.Rd:50: Lost braces; missing escapes or markup? 50 | \item{z}{Scalar, initial individual state z_{i,t}.} | ^ checkRd: (-1) dpoisppLocalDetection_normal.Rd:148-152: Lost braces 148 | for(i in 1:nrow(x)){ | ^ checkRd: (-1) sampler_categorical_general.Rd:19: Lost braces 19 | The \code{categorical_general} sampler operates within \code{nimble}'s MCMC engine to perform Gibbs sampling for a single node, which must in essence follow a categorical distribution. However, the prior distribution need not be \code{nimble}'s \code{dcat} distribution, but rather can be any (potentially user-defined) distribution which has the same support as a standard categorical (\code{dcat}) distribution. Specifically: the distribution must define a discrete random variable, which can only attain values from the set {1, 2, 3, ..., \code{numCategories}}. | ^ * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [23s/26s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [435s/567s] OK * checking PDF version of manual ... [11s/18s] 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: 3 NOTEs