* using log directory 'd:/Rcompile/CRANpkg/local/4.6/nimbleSCR.Rcheck' * using R version 4.6.1 (2026-06-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-08-12 19:13:38 UTC * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'nimbleSCR' can be installed ... OK * checking installed package size ... INFO 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 ... [2s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [2s] OK * checking loading without being on the library search path ... [2s] OK * checking whether startup messages can be suppressed ... [2s] 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 ... [11s] OK * checking Rd files ... [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 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 ... [18s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [241s] OK * checking PDF version of manual ... [22s] OK * checking HTML version of manual ... [13s] OK * DONE Status: 1 NOTE Check process probably crashed or hung up for 20 minutes ... killed Most likely this happened in the example checks (?), if not, ignore the following last lines of example output: [,1] [,2] [1,] 1.0229784 1.0766023 [2,] 1.1629290 1.0910405 [3,] 0.9911378 0.9002532 [4,] 0.9856483 1.0372425 [5,] 1.0976146 1.0615326 [6,] 0.9666666 1.0530347 [7,] 1.0488740 0.9931434 [8,] 0.8815279 1.0368812 [9,] 0.9736894 0.8786530 [10,] 0.9949093 1.1091924 > > > > > ### *