- using R version 4.4.0 alpha (2024-03-31 r86238)
- using platform: aarch64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- 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 ... [9s/9s] OK
See the install log 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/3s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the package can be unloaded cleanly ... [2s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [2s/2s] OK
- checking whether startup messages can be suppressed ... [2s/2s] 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 ... [5s/5s] OK
- checking Rd files ... [0s/0s] 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 ... [6s/6s] OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [114s/118s] OK
- checking PDF version of manual ... [5s/5s] OK
- DONE
Status: 2 NOTEs
- using check arguments '--no-clean-on-error '