* using log directory 'd:/Rcompile/CRANpkg/local64/2.11/glmmBUGS.Rcheck'
* using R version 2.11.1 Patched (2010-07-29 r52657)
* using session charset: ISO8859-1
* checking for file 'glmmBUGS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'glmmBUGS' version '1.7'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'glmmBUGS' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 ... NOTE
restoreParams: no visible binding for global variable 'VforNoV'
* checking Rd files ... NOTE
prepare_Rd: addSpatial.Rd:69: Dropping empty section \keyword
prepare_Rd: addSpatial.Rd:32: Dropping empty section \seealso
prepare_Rd: binToBinom.Rd:16-17: Dropping empty section \details
prepare_Rd: binToBinom.Rd:26-27: Dropping empty section \note
prepare_Rd: binToBinom.Rd:24: Dropping empty section \references
prepare_Rd: binToBinom.Rd:28: Dropping empty section \seealso
prepare_Rd: checkChain.Rd:22: Dropping empty section \note
prepare_Rd: checkChain.Rd:20: Dropping empty section \references
prepare_Rd: cholInvArray.Rd:57: Dropping empty section \keyword
prepare_Rd: cholInvArray.Rd:28-29: Dropping empty section \note
prepare_Rd: cholInvArray.Rd:27: Dropping empty section \author
prepare_Rd: cholInvArray.Rd:26: Dropping empty section \references
prepare_Rd: cholInvArray.Rd:30: Dropping empty section \seealso
prepare_Rd: getRaggedSeq.Rd:15-17: Dropping empty section \details
prepare_Rd: getRaggedSeq.Rd:23-24: Dropping empty section \note
prepare_Rd: getRaggedSeq.Rd:21: Dropping empty section \references
prepare_Rd: getRaggedSeq.Rd:26-27: Dropping empty section \examples
prepare_Rd: glmmPQLstrings.Rd:30: Dropping empty section \note
prepare_Rd: glmmPQLstrings.Rd:28: Dropping empty section \references
prepare_Rd: muscleResult.Rd:15-17: Dropping empty section \source
prepare_Rd: muscleResult.Rd:18-20: Dropping empty section \references
prepare_Rd: popDataAdjMat.Rd:9-10: Dropping empty section \format
prepare_Rd: popDataAdjMat.Rd:16-18: Dropping empty section \source
prepare_Rd: popDataAdjMat.Rd:19-21: Dropping empty section \references
prepare_Rd: restoreParams.Rd:17-18: Dropping empty section \details
prepare_Rd: restoreParams.Rd:33: Dropping empty section \references
prepare_Rd: restoreParams.Rd:42-44: Dropping empty section \examples
prepare_Rd: startingFunction.Rd:27: Dropping empty section \note
prepare_Rd: startingFunction.Rd:25: Dropping empty section \references
prepare_Rd: summaryChain.Rd:16-18: Dropping empty section \details
prepare_Rd: summaryChain.Rd:27-28: Dropping empty section \note
prepare_Rd: summaryChain.Rd:25: Dropping empty section \references
prepare_Rd: winBugsRaggedArray.Rd:39: Dropping empty section \note
prepare_Rd: writeBugsModel.Rd:59-61: Dropping empty section \note
prepare_Rd: writeBugsModel.Rd:65-67: Dropping empty section \seealso
* 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 data for non-ASCII characters ... OK
* checking examples ... ERROR
Running examples in 'glmmBUGS-Ex.R' failed.
The error most likely occurred in:

> ### * glmmBUGS
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: glmmBUGS
> ### Title: A function to run Generalised Linear Mixed Models in Bugs
> ### Aliases: glmmBUGS
> 
> ### ** Examples
>  
> library(nlme)
> data(Muscle)
> 
> muscleRagged = glmmBUGS(conc ~ length, data=Muscle, effects="Strip", family="gaussian")
iteration 1
iteration 2
> startingValues = muscleRagged$startingValues
> 
> ## Not run: 
> ##D source("getInits.R")
> ##D require(BRugs)
> ##D require(R2WinBUGS)  
> ##D muscleResult = bugs(muscleRagged$ragged, getInits, parameters.to.save = names(getInits()),
> ##D                 model.file="model.bug", n.chain=3, n.iter=1000, n.burnin=100, n.thin=10,
> ##D                              program="openbugs") 
> ## End(Not run)
>  
> data(muscleResult)
> 
> muscleParams = restoreParams(muscleResult, muscleRagged$ragged)  
> summaryChain(muscleParams)
$scalars
               mean       pval        sd        0.5%       2.5%       5%
intercept -1.265539 0.04074074 0.7010067 -2.94760500 -2.6941250 -2.45860
SDStrip    1.038826 0.00000000 0.4235040  0.04037235  0.1175025  0.17223
              50%       95%    97.5%    99.5%
intercept -1.2835 -0.086362 0.109909 0.362193
SDStrip    1.0560  1.653100 1.749325 2.007425

$betas
                  mean pval         sd      0.5%     2.5%     5%     50%
observations 0.2042404    0 0.02727729 0.1301215 0.152845 0.1569 0.20535
                 95%   97.5%     99.5%
observations 0.24732 0.25496 0.2655375

$RStrip
           mean       pval        sd       0.5%       2.5%        5%       50%
S01  1.54992198 0.03333333 0.8868596 -0.1768250 -0.0246500  0.057724  1.544250
S02  0.88417575 0.10740741 0.6983241 -0.9088650 -0.4244050 -0.155650  0.899500
S03 -0.23390863 0.34814815 0.5914435 -1.9491715 -1.4687375 -1.262370 -0.190000
S04  0.45283408 0.25925926 0.6843783 -1.1793696 -0.9058150 -0.669500  0.413550
S05  0.60819344 0.24444444 0.7703025 -1.0634295 -0.6081000 -0.483135  0.533250
S06  0.31592178 0.35925926 0.7376788 -1.3591490 -0.8759830 -0.731970  0.223750
S07 -0.70460736 0.20740741 0.8126383 -3.1227065 -2.6569750 -2.265800 -0.547250
S08 -0.25441374 0.35555556 0.7577606 -2.3061895 -1.7302175 -1.537680 -0.196500
S09 -0.38743685 0.28148148 0.7355054 -2.6393470 -1.6964750 -1.560860 -0.329050
S10 -0.68585621 0.21111111 0.8439765 -3.0587025 -2.5834400 -2.250790 -0.690900
S11 -0.71912356 0.18518519 0.7478093 -2.7717245 -2.2527500 -1.901530 -0.714300
S12 -0.71231756 0.18148148 0.7869166 -2.8318810 -2.2392250 -1.950660 -0.678975
S13 -0.31868543 0.34814815 0.8149412 -2.7769955 -2.0222575 -1.699450 -0.256350
S14 -0.48697259 0.28148148 0.8044144 -2.9784650 -2.2049950 -1.932700 -0.387950
S15 -0.97838181 0.10740741 0.8504277 -3.2020285 -2.7934550 -2.502000 -0.857500
S16  0.84256284 0.12592593 0.6946001 -0.5053900 -0.2942450 -0.152550  0.836100
S17  0.64807114 0.19259259 0.7215709 -0.7991797 -0.5750000 -0.310640  0.548200
S18  1.07191081 0.08888889 0.8276582 -0.8455955 -0.3352975 -0.115320  1.016500
S19 -0.59925374 0.20000000 0.7733523 -2.6562050 -2.2800750 -1.992600 -0.499850
S20 -0.06239375 0.48148148 0.7080924 -1.6509095 -1.5234050 -1.339950 -0.019600
S21  0.06676470 0.45925926 0.6311687 -1.5596288 -1.1945400 -0.964500  0.050350
          95%     97.5%     99.5%
S01 2.9949900 3.2311500 3.5329890
S02 1.9720450 2.2462605 2.6260415
S03 0.7350450 0.8952500 1.1674910
S04 1.5997700 1.7665375 2.0766735
S05 2.1246900 2.3195575 2.5335875
S06 1.5991900 1.9545075 2.5328225
S07 0.3115500 0.5566500 0.9338500
S08 1.0257300 1.3488825 1.9590830
S09 0.7478450 1.0226500 1.7744205
S10 0.6188800 0.8003152 1.0993755
S11 0.3735000 0.6804675 0.9901384
S12 0.4988500 0.6529947 1.0567460
S13 0.9844800 1.3630475 1.5559440
S14 0.6935000 0.8611075 1.4026265
S15 0.1796335 0.3359150 0.5011000
S16 2.0183800 2.0802900 2.3114275
S17 1.9229700 2.1993862 2.6873200
S18 2.4969750 2.6700415 3.4282300
S19 0.6090200 0.7528225 1.1546985
S20 1.0645500 1.2481600 2.0552690
S21 1.1254000 1.2890550 1.9970190

$FittedRStrip
          mean       pval        sd      0.5%      2.5%       5%      50%
S01  0.2843833 0.35555556 0.9352313 -1.792905 -1.385450 -1.23780  0.31130
S02 -0.3813629 0.35555556 0.8957498 -2.529095 -2.017550 -1.75560 -0.31270
S03 -1.4994473 0.02592593 0.7867285 -3.470145 -3.112875 -2.82725 -1.46700
S04 -0.8127046 0.12962963 0.7189631 -2.589780 -2.174950 -1.99675 -0.84455
S05 -0.6573452 0.19259259 0.7658188 -2.335315 -1.995350 -1.79865 -0.62335
S06 -0.9496169 0.09259259 0.7858372 -2.968710 -2.660275 -2.35600 -0.92520
S07 -1.9701460 0.04074074 1.1473757 -5.392215 -4.274800 -4.05355 -1.83900
S08 -1.5199524 0.04814815 0.8693870 -3.685370 -3.237650 -2.97615 -1.44250
S09 -1.6529755 0.03333333 0.9538261 -4.157025 -3.608650 -3.31420 -1.60650
S10 -1.9513948 0.04074074 1.0556197 -5.075270 -4.124600 -3.53905 -1.92500
S11 -1.9846622 0.01111111 0.9322485 -4.258000 -3.833750 -3.46500 -1.93450
S12 -1.9778562 0.02962963 1.1309717 -4.446620 -4.105350 -3.89935 -1.82350
S13 -1.5842241 0.06296296 1.0543192 -4.128115 -3.705625 -3.53825 -1.57350
S14 -1.7525112 0.05185185 1.0703809 -5.199205 -3.855150 -3.55950 -1.69900
S15 -2.2439204 0.01851852 1.1667545 -4.950170 -4.571850 -4.28945 -2.22900
S16 -0.4229758 0.31111111 0.8814157 -2.722620 -2.170275 -1.91445 -0.37980
S17 -0.6174675 0.28518519 0.9230020 -3.132810 -2.621875 -2.11805 -0.60655
S18 -0.1936278 0.38888889 0.8546320 -2.075205 -1.859850 -1.49365 -0.22885
S19 -1.8647924 0.05555556 1.1403275 -4.461565 -4.224875 -3.80615 -1.78400
S20 -1.3279324 0.09259259 1.0079839 -4.004515 -3.344100 -3.01325 -1.32000
S21 -1.1987739 0.08518519 0.9083019 -3.594535 -3.242025 -2.80675 -1.22700
           95%       97.5%     99.5%
S01  1.8397500  2.09522500 2.2832800
S02  1.0476000  1.36715000 2.1566450
S03 -0.1134550 -0.00046025 0.4915020
S04  0.3144900  0.57624250 0.9059075
S05  0.6854700  0.84702500 1.3936200
S06  0.2206050  0.40609750 0.7693275
S07 -0.0912150  0.15297500 0.5283185
S08 -0.0385945  0.16038500 0.4286980
S09 -0.0973070  0.12896750 0.8124975
S10 -0.0973375  0.04467425 0.5151385
S11 -0.5521200 -0.16512250 0.2273673
S12 -0.1306650  0.03379175 0.4698875
S13  0.0957815  0.49388000 1.1230440
S14 -0.0419790  0.27019250 0.4259840
S15 -0.3269450 -0.07050375 0.1745775
S16  1.0624500  1.39042500 1.7414450
S17  0.7634650  0.99061750 1.5403200
S18  1.3081000  1.40712500 1.8402850
S19  0.1248135  0.32123000 0.8894485
S20  0.2558300  0.42157000 1.5143000
S21  0.2581700  0.53922250 0.9853340

> checkChain(muscleParams)
> 
> 
> 
> # a spatial example
> ## Not run: 
> ##D library(diseasemapping)
> ##D 
> ##D data(popdata)
> ##D data(casedata)
> ##D 
> ##D model = getRates(casedata, popdata, ~age*sex)
> ##D ontario = getSMR(popdata, model, casedata)
> ##D ontario = ontario@data[,c("CSDUID","observed","logExpected")]
> ##D 
> ##D library(spdep)
> ##D popDataAdjMat = poly2nb(popdata,row.names=as.character(popdata[["CSDUID"]]))
> ## End(Not run)
> 
> data(popDataAdjMat)
> data(ontario)
> 
> forBugs = glmmBUGS(formula=observed + logExpected ~ 1,
+   effects="CSDUID",   family="poisson", spatial=popDataAdjMat,
+   data=ontario)
iteration 1
iteration 2
iteration 3
iteration 4
iteration 5
iteration 6
iteration 7
iteration 8
iteration 9
iteration 10
> 
> startingValues = forBugs$startingValues
> 
> source("getInits.R")
> 
> ## Not run: 
> ##D library(R2WinBUGS)
> ##D ontarioResult = bugs(forBugs$ragged, getInits, 
> ##D   parameters.to.save = names(getInits()),
> ##D     model.file="model.bug", n.chain=3, n.iter=50, n.burnin=10, n.thin=2,
> ##D       program="winbugs", debug=T)
> ## End(Not run)
> 
> data(ontarioResult)
> 
> ontarioParams = restoreParams(ontarioResult, forBugs$ragged)
> 
> ontarioSummary = summaryChain(ontarioParams)
> 
> # posterior probability of having 10x excess risk
> postProb = apply(ontarioParams$FittedRateCSDUID, 3, function(x) mean(x>10))
Error in apply(ontarioParams$FittedRateCSDUID, 3, function(x) mean(x >  : 
  dim(X) must have a positive length
Execution halted