• using R version 4.4.2 Patched (2024-11-18 r87347)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-8) 14.2.0     GNU Fortran (Debian 14.2.0-8) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• 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 ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [3s/3s] OK
• checking whether startup messages can be suppressed ... [2s/3s] 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 ... [21s/26s] OK
• checking Rd files ... [1s/1s] 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 ... [10s/12s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [234s/295s] OK
• checking PDF version of manual ... [7s/9s] OK
• checking HTML version of manual ... [3s/5s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE