* using log directory 'd:/Rcompile/CRANpkg/local/4.4/nimbleSCR.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'nimbleSCR' can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-windows-x86_64/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 ... [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 ... [3s] 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 ... [20s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [258s] OK
* checking PDF version of manual ... [23s] OK
* checking HTML version of manual ... [10s] OK
* DONE
Status: 2 NOTEs