* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/diseasemapping.Rcheck’
* using R Under development (unstable) (2022-03-19 r81944)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘diseasemapping/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘diseasemapping’ version ‘1.5.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘geostatsp’
* 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 ‘diseasemapping’ can be installed ... [11s/27s] OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... 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 ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘rgeos’
  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 ... [15s/37s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘geostatsp’ in Rd xrefs
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/65s] ERROR
Running examples in ‘diseasemapping-Ex.R’ failed
The error most likely occurred in:

> ### Name: bym-methods
> ### Title: Fit the BYM model
> ### Aliases: bym bym-methods bym,formula,ANY,ANY,missing-method
> ###   bym,formula,ANY,missing,missing-method
> ###   bym,formula,SpatialPolygonsDataFrame,NULL,character-method
> ###   bym,formula,SpatialPolygonsDataFrame,missing,character-method
> ###   bym,formula,SpatialPolygonsDataFrame,nb,character-method
> ###   bym,formula,data.frame,nb,character-method
> ### Keywords: Bayesian inference disease mapping
> 
> ### ** Examples
> 
> 
> data('kentucky')
> 
> # must have an internet connection to do the following
> ## Not run: 
> ##D 	larynxRates= cancerRates("USA", year=1998:2002,site="Larynx")
> ##D 	dput(larynxRates)
> ## End(Not run)
> 
> larynxRates = structure(c(0, 0, 0, 0, 0, 0, 1e-06, 6e-06, 2.3e-05, 4.5e-05, 
+ 9.9e-05, 0.000163, 0.000243, 0.000299, 0.000343, 0.000308, 0.000291, 
+ 0.000217, 0, 0, 0, 0, 0, 1e-06, 1e-06, 3e-06, 8e-06, 1.3e-05, 
+ 2.3e-05, 3.5e-05, 5.8e-05, 6.8e-05, 7.5e-05, 5.5e-05, 4.1e-05, 
+ 3e-05), .Names = c("M_0", "M_5", "M_10", "M_15", "M_20", "M_25", 
+ "M_30", "M_35", "M_40", "M_45", "M_50", "M_55", "M_60", "M_65", 
+ "M_70", "M_75", "M_80", "M_85", "F_0", "F_5", "F_10", "F_15", 
+ "F_20", "F_25", "F_30", "F_35", "F_40", "F_45", "F_50", "F_55", 
+ "F_60", "F_65", "F_70", "F_75", "F_80", "F_85"), 
+ site = "Larynx", area = "USA, SEER", year = "1998-2002")
> 
> # get rid of under 10's
> larynxRates = larynxRates[-grep("_(0|5)$",names(larynxRates))]
> 
> kentucky = getSMR(kentucky, larynxRates, larynx, regionCode="County")
> 
> if( require("spdep", quietly=TRUE)) {
+ 
+ kBYM = bym(observed ~ offset(logExpected) + poverty, kentucky, 
+ 	 priorCI = list(sdSpatial=c(0.1, 5), sdIndep=c(0.1, 5)),
+ 	 control.mode=list(theta=c(3.52, 3.35),restart=TRUE))
+ 
+ 	kBYM$par$summary
+ 	
+ 	if(requireNamespace('geostatsp', quietly=TRUE))
+ 		kBYM$data$exc1 = geostatsp::excProb(
+ 			kBYM$inla$marginals.fitted.bym, log(1.2)
+ 			)
+ }  else {
+ 	kBYM = list()
+ }
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Linking to GEOS 3.9.0, GDAL 3.2.2, PROJ 7.2.1; sf_use_s2() is TRUE
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
INLA
 --- call from context --- 
FUN(X[[i]], ...)
 --- call from argument --- 
is.null(x) || is.na(x)
 --- R stacktrace ---
where 1: FUN(X[[i]], ...)
where 2: lapply(X = X, FUN = FUN, ...)
where 3: sapply(marginals.random, function(x) (is.null(x) || is.na(x)))
where 4: inla.collect.random(results.dir, debug)
where 5: inla.collect.results(results.dir, only.hyperparam = only.hyperparam, 
    file.log = file.log, file.log2 = file.log2)
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, classes, parentenv, handlers)
where 9: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call, nlines = 1L)
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 10: try(inla.collect.results(results.dir, only.hyperparam = only.hyperparam, 
    file.log = file.log, file.log2 = file.log2), silent = FALSE)
where 11: INLA::inla(formula, data = data, family = family, lincomb = inlaLincombs, 
    ...)
where 12: .local(formula, data, adjMat, region.id, ...)
where 13: bym(formula = formula, data = data@data, adjMat = adjMat, region.id = region.id, 
    ...)
where 14: bym(formula = formula, data = data@data, adjMat = adjMat, region.id = region.id, 
    ...)
where 15: eval(call, parent.frame())
where 16: eval(call, parent.frame())
where 17: methods::callGeneric(formula = formula, data = data@data, adjMat = adjMat, 
    region.id = region.id, ...)
where 18: bym(formula = formula, data = data, adjMat = adjMatNB, region.id = region.id, 
    ...)
where 19: bym(formula = formula, data = data, adjMat = adjMatNB, region.id = region.id, 
    ...)
where 20: eval(call, parent.frame())
where 21: eval(call, parent.frame())
where 22: methods::callGeneric(formula = formula, data = data, adjMat = adjMatNB, 
    region.id = region.id, ...)
where 23: bym(formula, data, adjMat, region.idX, ...)
where 24: bym(formula, data, adjMat, region.idX, ...)
where 25: eval(call, parent.frame())
where 26: eval(call, parent.frame())
where 27: methods::callGeneric(formula, data, adjMat, region.idX, ...)
where 28: bym(observed ~ offset(logExpected) + poverty, kentucky, priorCI = list(sdSpatial = c(0.1, 
    5), sdIndep = c(0.1, 5)), control.mode = list(theta = c(3.52, 
    3.35), restart = TRUE))
where 29: bym(observed ~ offset(logExpected) + poverty, kentucky, priorCI = list(sdSpatial = c(0.1, 
    5), sdIndep = c(0.1, 5)), control.mode = list(theta = c(3.52, 
    3.35), restart = TRUE))

 --- value of length: 240 type: logical ---
  index.1   index.2   index.3   index.4   index.5   index.6   index.7   index.8 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.9  index.10  index.11  index.12  index.13  index.14  index.15  index.16 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.17  index.18  index.19  index.20  index.21  index.22  index.23  index.24 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.25  index.26  index.27  index.28  index.29  index.30  index.31  index.32 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.33  index.34  index.35  index.36  index.37  index.38  index.39  index.40 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.41  index.42  index.43  index.44  index.45  index.46  index.47  index.48 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.49  index.50  index.51  index.52  index.53  index.54  index.55  index.56 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.57  index.58  index.59  index.60  index.61  index.62  index.63  index.64 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.65  index.66  index.67  index.68  index.69  index.70  index.71  index.72 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.73  index.74  index.75  index.76  index.77  index.78  index.79  index.80 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.81  index.82  index.83  index.84  index.85  index.86  index.87  index.88 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.89  index.90  index.91  index.92  index.93  index.94  index.95  index.96 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 index.97  index.98  index.99 index.100 index.101 index.102 index.103 index.104 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.105 index.106 index.107 index.108 index.109 index.110 index.111 index.112 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.113 index.114 index.115 index.116 index.117 index.118 index.119 index.120 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.121 index.122 index.123 index.124 index.125 index.126 index.127 index.128 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.129 index.130 index.131 index.132 index.133 index.134 index.135 index.136 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.137 index.138 index.139 index.140 index.141 index.142 index.143 index.144 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.145 index.146 index.147 index.148 index.149 index.150 index.151 index.152 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.153 index.154 index.155 index.156 index.157 index.158 index.159 index.160 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.161 index.162 index.163 index.164 index.165 index.166 index.167 index.168 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.169 index.170 index.171 index.172 index.173 index.174 index.175 index.176 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.177 index.178 index.179 index.180 index.181 index.182 index.183 index.184 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.185 index.186 index.187 index.188 index.189 index.190 index.191 index.192 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.193 index.194 index.195 index.196 index.197 index.198 index.199 index.200 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.201 index.202 index.203 index.204 index.205 index.206 index.207 index.208 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.209 index.210 index.211 index.212 index.213 index.214 index.215 index.216 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.217 index.218 index.219 index.220 index.221 index.222 index.223 index.224 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.225 index.226 index.227 index.228 index.229 index.230 index.231 index.232 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
index.233 index.234 index.235 index.236 index.237 index.238 index.239 index.240 
    FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
 --- function from context --- 
function (x) 
(is.null(x) || is.na(x))
<bytecode: 0xe317230>
<environment: 0xe30b578>
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘bym.R’ [25s/59s]
  Running ‘cancerRates.R’ [14s/37s]
  Running ‘getRates.R’
  Running ‘getSMR.R’ [16s/41s]
 [60s/148s] ERROR
Running the tests in ‘tests/bym.R’ failed.
Complete output:
  > havePackages = c(
  +   'INLA' = requireNamespace('INLA', quietly=TRUE),
  +   "spdep" = requireNamespace('spdep', quietly=TRUE)
  + )
  > 
  > print(havePackages)
   INLA spdep 
   TRUE  TRUE 
  > 
  > library('diseasemapping')
  > data('kentucky')
  > 
  > 
  > 
  > 
  > 
  > 
  > if(FALSE) {
  + 	# must have an internet connection to do the following
  + 	larynxRates= cancerRates("USA", year=1998:2002,site="Larynx")
  + 	# get rid of under 10's
  + 	larynxRates = larynxRates[-grep("_(0|5)$",names(larynxRates))]
  + 	dput(larynxRates)
  + } else {
  + 	larynxRates = structure(c(0, 0, 0, 0, 1e-06, 6e-06, 2.3e-05, 4.5e-05, 9.9e-05, 
  + 					0.000163, 0.000243, 0.000299, 0.000343, 0.000308, 0.000291, 0.000217, 
  + 					0, 0, 0, 1e-06, 1e-06, 3e-06, 8e-06, 1.3e-05, 2.3e-05, 3.5e-05, 
  + 					5.8e-05, 6.8e-05, 7.5e-05, 5.5e-05, 4.1e-05, 3e-05), .Names = c("M_10", 
  + 					"M_15", "M_20", "M_25", "M_30", "M_35", "M_40", "M_45", "M_50", 
  + 					"M_55", "M_60", "M_65", "M_70", "M_75", "M_80", "M_85", "F_10", 
  + 					"F_15", "F_20", "F_25", "F_30", "F_35", "F_40", "F_45", "F_50", 
  + 					"F_55", "F_60", "F_65", "F_70", "F_75", "F_80", "F_85"))
  + 	
  + }
  > 
  > kentucky = getSMR(kentucky, larynxRates, larynx,
  + 		regionCode="County")
  > 
  > if(all(havePackages)){
  + 
  +   kBYM = bym(
  + 			formula = observed ~ offset(logExpected) + poverty,
  +       data=kentucky@data,
  + 			adjMat = spdep::poly2nb(kentucky, row.names=kentucky$County),
  +       priorCI = list(sdSpatial=c(0.1, 5), sdIndep=c(0.1, 5)),
  + 			region.id="County",
  + 			control.predictor=list(compute=TRUE)
  +   )
  + 	kBYM$parameters$summary
  + 
  + 	pdf("priorPostKentucky.pdf")
  + 	plot(kBYM$parameters$sdSpatial$posterior, type='l', 
  + 			xlim=c(0,max(kBYM$parameters$sdSpatial$priorCI)))
  + 	lines(kBYM$parameters$sdSpatial$prior, col='blue')
  + 	legend('topright', lty=1, col=c('black','blue'), legend=c('posterior','prior'))
  + 	dev.off()
  + 
  + 	
  + 	
  + 
  + 
  + # also try no covariate or prior
  + 
  + kBYM = bym(
  + 		formula = observed ~ offset(logExpected),
  + 		data=kentucky)
  + 
  + 
  + if(require('geostatsp', quietly=TRUE)) {
  +  	kBYM$data$exc1 = geostatsp::excProb(kBYM$inla$marginals.fitted.bym, log(1.2))
  + } else {
  + 	kBYM$data$exc1 = rep(NA, length(kBYM$data))
  + }
  + 
  + kBYM$par$summary
  + 
  + if(require('mapmisc', quietly=TRUE)) {
  + 
  + colFit = colourScale(kBYM$data$fitted.exp,
  + 		breaks=6, dec=3)
  + 	
  + plot(kBYM$data, col=colFit$plot)
  + legendBreaks('topleft', colFit)
  + 
  + colExc = colourScale(kBYM$data$exc1 ,
  + 		style='fixed',
  + 		breaks=c(0, 0.2, 0.8,0.9, 1), 
  + 		col=rainbow, rev=TRUE
  + 	)
  + 
  + 	plot(kBYM$data, col=colExc$plot)
  + 	legendBreaks('topleft', colExc)
  +  		
  + }
  + # and try passing a data frame and adjacency matrix
  + 
  + 	
  + adjMat = spdep::poly2nb(kentucky, row.names =as.character(kentucky$County) )
  + kBYM = bym(data=kentucky@data, formula=observed ~ offset(logExpected) + poverty,
  + 		adjMat = adjMat, region.id="County",
  + 		priorCI = list(sdSpatial=c(0.1, 5), sdIndep=c(0.1, 5)))
  + 
  + kBYM$par$summary
  + 
  + # subtract a few regions
  + 
  + kBYM = bym(
  +     formula=observed ~ offset(logExpected) + poverty,
  +     data=kentucky@data[-(1:4),],  
  +  	  adjMat = adjMat, region.id="County",
  + 		priorCI = list(sdSpatial=c(0.1, 5), sdIndep=c(0.1, 5)))
  +  
  + 
  + kBYM$par$summary
  + 
  + # intercept only, no offset
  + 
  + 
  + kBYM = bym(data=kentucky,  formula=observed ~ 1,
  + 		priorCI = list(sdSpatial=c(0.1, 5), sdIndep=c(0.1, 5)))
  + 
  + kBYM$par$summary
  + 
  + 
  + if(require('mapmisc', quietly=TRUE)) {
  + 	
  + 	colFit = colourScale(kBYM$data$fitted.exp,
  + 			breaks=6, dec=1)
  + 	
  + 	plot(kBYM$data, col=colFit$plot)
  + 	legendBreaks('topleft', colFit)
  + 	
  + }
  + 
  +  
  + 
  + # give spdf but some regions have no data
  + # but keep the 'county' column as is
  + kentucky@data[1:2,-grep("County", names(kentucky))] = NA 
  + 
  + kBYM = bym(observed ~ offset(logExpected) + poverty,
  + 		kentucky, 
  + 		region.id="County",
  + 		priorCI = list(sdSpatial=c(0.1, 5), sdIndep=c(0.1, 5)))
  + 
  +  
  + kBYM$par$summary
  + 
  + 
  + # missing value in a categorical variable
  + 
  + pCuts = quantile(kentucky$poverty, na.rm=TRUE)
  + kentucky$povertyFac = cut(kentucky$poverty, 
  + 		breaks = pCuts,
  + 		labels = letters[seq(1,length(pCuts)-1)])
  + kentucky$povertyFac[c(2,34,100)] = NA
  + 
  + kBYM = bym(
  + 		formula = observed ~ offset(logExpected) + povertyFac,
  + 		data = kentucky, 
  + 		region.id="County",
  + 		priorCI = list(sdSpatial=c(0.1, 5), sdIndep=c(0.1, 5))
  + )
  + 
  + 
  + kBYM$par$summary
  + }
   ----------- FAILURE REPORT -------------- 
   --- failure: length > 1 in coercion to logical ---
   --- srcref --- 
  : 
   --- package (from environment) --- 
  INLA
   --- call from context --- 
  FUN(X[[i]], ...)
   --- call from argument --- 
  is.null(x) || is.na(x)
   --- R stacktrace ---
  where 1: FUN(X[[i]], ...)
  where 2: lapply(X = X, FUN = FUN, ...)
  where 3: sapply(marginals.random, function(x) (is.null(x) || is.na(x)))
  where 4: inla.collect.random(results.dir, debug)
  where 5: inla.collect.results(results.dir, only.hyperparam = only.hyperparam, 
      file.log = file.log, file.log2 = file.log2)
  where 6: doTryCatch(return(expr), name, parentenv, handler)
  where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 8: tryCatchList(expr, classes, parentenv, handlers)
  where 9: tryCatch(expr, error = function(e) {
      call <- conditionCall(e)
      if (!is.null(call)) {
          if (identical(call[[1L]], quote(doTryCatch))) 
              call <- sys.call(-4L)
          dcall <- deparse(call, nlines = 1L)
          prefix <- paste("Error in", dcall, ": ")
          LONG <- 75L
          sm <- strsplit(conditionMessage(e), "\n")[[1L]]
          w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
          if (is.na(w)) 
              w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                  type = "b")
          if (w > LONG) 
              prefix <- paste0(prefix, "\n  ")
      }
      else prefix <- "Error : "
      msg <- paste0(prefix, conditionMessage(e), "\n")
      .Internal(seterrmessage(msg[1L]))
      if (!silent && isTRUE(getOption("show.error.messages"))) {
          cat(msg, file = outFile)
          .Internal(printDeferredWarnings())
      }
      invisible(structure(msg, class = "try-error", condition = e))
  })
  where 10: try(inla.collect.results(results.dir, only.hyperparam = only.hyperparam, 
      file.log = file.log, file.log2 = file.log2), silent = FALSE)
  where 11: INLA::inla(formula, data = data, family = family, lincomb = inlaLincombs, 
      ...)
  where 12: .local(formula, data, adjMat, region.id, ...)
  where 13: bym(formula = observed ~ offset(logExpected) + poverty, data = kentucky@data, 
      adjMat = spdep::poly2nb(kentucky, row.names = kentucky$County), 
      priorCI = list(sdSpatial = c(0.1, 5), sdIndep = c(0.1, 5)), 
      region.id = "County", control.predictor = list(compute = TRUE))
  where 14: bym(formula = observed ~ offset(logExpected) + poverty, data = kentucky@data, 
      adjMat = spdep::poly2nb(kentucky, row.names = kentucky$County), 
      priorCI = list(sdSpatial = c(0.1, 5), sdIndep = c(0.1, 5)), 
      region.id = "County", control.predictor = list(compute = TRUE))
  
   --- value of length: 240 type: logical ---
    index.1   index.2   index.3   index.4   index.5   index.6   index.7   index.8 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
    index.9  index.10  index.11  index.12  index.13  index.14  index.15  index.16 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.17  index.18  index.19  index.20  index.21  index.22  index.23  index.24 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.25  index.26  index.27  index.28  index.29  index.30  index.31  index.32 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.33  index.34  index.35  index.36  index.37  index.38  index.39  index.40 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.41  index.42  index.43  index.44  index.45  index.46  index.47  index.48 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.49  index.50  index.51  index.52  index.53  index.54  index.55  index.56 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.57  index.58  index.59  index.60  index.61  index.62  index.63  index.64 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.65  index.66  index.67  index.68  index.69  index.70  index.71  index.72 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.73  index.74  index.75  index.76  index.77  index.78  index.79  index.80 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.81  index.82  index.83  index.84  index.85  index.86  index.87  index.88 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.89  index.90  index.91  index.92  index.93  index.94  index.95  index.96 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   index.97  index.98  index.99 index.100 index.101 index.102 index.103 index.104 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.105 index.106 index.107 index.108 index.109 index.110 index.111 index.112 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.113 index.114 index.115 index.116 index.117 index.118 index.119 index.120 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.121 index.122 index.123 index.124 index.125 index.126 index.127 index.128 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.129 index.130 index.131 index.132 index.133 index.134 index.135 index.136 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.137 index.138 index.139 index.140 index.141 index.142 index.143 index.144 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.145 index.146 index.147 index.148 index.149 index.150 index.151 index.152 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.153 index.154 index.155 index.156 index.157 index.158 index.159 index.160 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.161 index.162 index.163 index.164 index.165 index.166 index.167 index.168 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.169 index.170 index.171 index.172 index.173 index.174 index.175 index.176 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.177 index.178 index.179 index.180 index.181 index.182 index.183 index.184 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.185 index.186 index.187 index.188 index.189 index.190 index.191 index.192 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.193 index.194 index.195 index.196 index.197 index.198 index.199 index.200 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.201 index.202 index.203 index.204 index.205 index.206 index.207 index.208 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.209 index.210 index.211 index.212 index.213 index.214 index.215 index.216 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.217 index.218 index.219 index.220 index.221 index.222 index.223 index.224 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.225 index.226 index.227 index.228 index.229 index.230 index.231 index.232 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
  index.233 index.234 index.235 index.236 index.237 index.238 index.239 index.240 
      FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE     FALSE 
   --- function from context --- 
  function (x) 
  (is.null(x) || is.na(x))
  <bytecode: 0x154bfe08>
  <environment: 0x154c3688>
   --- function search by body ---
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [29s/67s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/diseasemapping.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 8:38.93, 192.98 + 16.46