* using log directory 'd:/Rcompile/CRANpkg/local/2.7/glmmBUGS.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'glmmBUGS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'glmmBUGS' version '1.2'
* 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 name space can be loaded with stated dependencies ... 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating glmmBUGS-Ex.R ... 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$startingValues
> source("getInits.R")
> 
> library(R2WinBUGS)
> muscleResult = bugs(muscleRagged$ragged, getInits, parameters.to.save = names(getInits()), model.file="model.bug", n.chain=3, n.iter=1000, n.burnin=100, n.thin=10, program="openbugs")
model is syntactically correct
data loaded
model compiled
Initializing chain 1: initial values loaded but this or another chain contain uninitialized variables
Initializing chain 2: initial values loaded but this or another chain contain uninitialized variables
Initializing chain 3: initial values loaded but this or another chain contain uninitialized variables
initial values generated, model initialized
100 updates took 0 s
deviance set
monitor set for variable 'intercept'
monitor set for variable 'betaobservations'
monitor set for variable 'SDStrip'
monitor set for variable 'RStrip'
monitor set for variable 'deviance'
900 updates took 0 s
> 
> muscleParams = restoreParams(muscleResult, muscleRagged$ragged)  
> summaryChain(muscleParams)
$scalars
               mean       pval        sd       0.5%      2.5%         5%
intercept -1.172094 0.01111111 0.5834867 -2.5750658 -2.262985 -2.1353708
SDStrip    1.136957 0.00000000 0.3252613  0.4325006  0.552333  0.6187835
                50%        95%      97.5%      99.5%
intercept -1.152160 -0.2595845 -0.0737769 0.08646553
SDStrip    1.127405  1.7080604  1.8072246 1.99810786

$RStrip
           mean       pval        sd       0.5%        2.5%          5%
S01  1.70253692 0.01111111 0.7613378 -0.1496897  0.21991365  0.42938361
S02  1.04823427 0.06666667 0.7015787 -0.5831565 -0.14303703 -0.08905091
S03 -0.25642979 0.32222222 0.6405082 -1.8755769 -1.46939095 -1.28808424
S04  0.35530703 0.29259259 0.6995264 -1.4178252 -1.07357136 -0.82289293
S05  0.55675241 0.21111111 0.6954633 -1.0401278 -0.74634441 -0.62213908
S06  0.34021640 0.31481481 0.7507220 -1.4254813 -1.08087345 -0.94220735
S07 -0.81191208 0.14814815 0.8473101 -3.3153907 -2.67411426 -2.32280378
S08 -0.25554903 0.38518519 0.8210138 -2.6681706 -1.93064650 -1.60579274
S09 -0.52722820 0.27037037 0.8623066 -2.6252519 -2.15018541 -1.85861155
S10 -0.80175192 0.14814815 0.7992036 -2.4005725 -2.27125510 -2.14682657
S11 -0.81748053 0.14074074 0.7555969 -2.8033378 -2.50433877 -2.09969947
S12 -0.80009846 0.18148148 0.8516853 -2.9360018 -2.54360055 -2.34636179
S13 -0.34254925 0.35925926 0.8169705 -2.3598730 -2.00879839 -1.68671404
S14 -0.61742296 0.22592593 0.7582032 -2.4339963 -2.05001504 -1.96328784
S15 -1.14731433 0.07777778 0.8408582 -3.2192678 -2.92357924 -2.62037207
S16  0.87784181 0.08518519 0.6846724 -0.7587540 -0.36737796 -0.20891160
S17  0.73194313 0.13333333 0.6682084 -0.7895606 -0.62000762 -0.37601266
S18  1.21914394 0.03703704 0.7729721 -0.4316341 -0.09450317  0.09690723
S19 -0.67851512 0.19259259 0.7785018 -2.7462395 -2.07621840 -1.89540332
S20 -0.04221947 0.49629630 0.7137264 -1.9617747 -1.39913600 -1.24137535
S21  0.11765900 0.41851852 0.6768016 -1.8469394 -1.24807530 -0.95077683
            50%       95%     97.5%     99.5%
S01  1.71680512 2.9836935 3.1183461 3.3211153
S02  0.99798729 2.1907267 2.4097927 2.6552428
S03 -0.27111655 0.8303644 0.9951611 1.3463429
S04  0.37114651 1.5454978 1.6851804 1.9825557
S05  0.52780019 1.7502594 1.9018744 2.4411472
S06  0.31076152 1.5940641 1.8383743 2.6233481
S07 -0.79270858 0.5370239 0.9020836 1.0621990
S08 -0.19237426 0.9884308 1.2776485 1.6926731
S09 -0.54200363 0.9695904 1.1153716 1.3033329
S10 -0.77621353 0.5642829 0.7511976 1.1874203
S11 -0.74223274 0.4194015 0.5304346 0.8343408
S12 -0.70804012 0.5814630 0.8262465 1.0221379
S13 -0.27712993 0.9635678 1.1027982 1.6804125
S14 -0.65836599 0.5010307 0.7102948 1.3086008
S15 -1.11230636 0.1376393 0.3391471 0.7174522
S16  0.78352135 2.0037911 2.2012463 2.5079278
S17  0.70877247 1.7509873 1.9017458 2.3299371
S18  1.17322931 2.4901825 2.8260278 3.4538525
S19 -0.65055680 0.5535095 0.6999781 1.6760172
S20 -0.01215231 1.0353547 1.2974664 1.8965897
S21  0.09689446 1.1698568 1.3843671 1.5694197

$betas
                  mean pval         sd      0.5%      2.5%        5%       50%
observations 0.2008372    0 0.02473386 0.1409717 0.1538117 0.1630345 0.2025770
                  95%     97.5%     99.5%
observations 0.239556 0.2526695 0.2644519

> 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(model, popdata, casedata)
> ##D ontario = ontario@data[,c("CSDUID","Observed","logExpected")]
> ##D popDataAdjMat = poly2nb(ontario,row.names=as.character(ontario[["CDSUID"]]))
> ## 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$startingValues
> 
> source("getInits.R")
> 
> ## Not run: 
> ##D ontarioResult = bugs(forBugs$ragged, getInits, parameters.to.save = names(getInits()),
> ##D     model.file="model.bug", n.chain=3, n.iter=100, n.burnin=10, n.thin=2,
> ##D       program="openbugs", debug=T)
> ## End(Not run)
> 
> data(ontarioResult)
> 
> ontarioParams = restoreParams(ontarioResult, forBugs$ragged)
Error in dimnames(result[[D]])[[3]] = thenames[as.integer(theID)] : 
  length of 'dimnames' [2] must match that of 'dims' [3]
Calls: restoreParams
Execution halted