Error(s) in re-building vignettes:
--- re-building ‘bym.Rnw’ using knitr


	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'



	*** max_correction = 25.01 >= 25.00, so 'vb.correction' is aborted
	*** Please (re-)consider your model, priors, confounding, etc.
	*** You can change the emergency value (current value=25.00) by 
	*** 	'control.inla=list(control.vb=list(emergency=...))'

--- finished re-building ‘bym.Rnw’

make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/diseasemapping.Rcheck/vign_test/diseasemapping/vignettes'
xelatex bym;
This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex)
 restricted \write18 enabled.
entering extended mode
(./bym.tex
LaTeX2e <2023-06-01> patch level 1
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Overfull \hbox (38.1448pt too wide) in paragraph at lines 94--94
[]    []\TU/lmtt/m/n/12 larynxRates[] []=[] []\TU/lmtt/b/n/12 structure[][]\TU/
lmtt/m/n/12 ([][]\TU/lmtt/b/n/12 c[][]\TU/lmtt/m/n/12 ([][]0[][],[] []0[][],[] 
[]0[][],[] []0[][],[] []1e-06[][],[] []6e-06[][],[] []2.3e-05[][],[] []4.5e-05[
][],[] []9.9e-05[][],[][] 

Overfull \hbox (24.59683pt too wide) in paragraph at lines 95--95
[]        []\TU/lmtt/m/n/12 0.000163[][],[] []0.000243[][],[] []0.000299[][],[]
 []0.000343[][],[] []0.000308[][],[] []0.000291[][],[] []0.000217[][],[] []0[][
],[][] 

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[]        []\TU/lmtt/m/n/12 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[][],[][] 

Overfull \hbox (55.66483pt too wide) in paragraph at lines 97--97
[]        []\TU/lmtt/m/n/12 7.5e-05[][],[] []5.5e-05[][],[] []4.1e-05[][],[] []
3e-05[][]),[] [].Names[] []=[] []\TU/lmtt/b/n/12 c[][]\TU/lmtt/m/n/12 ([][]"M_1
0"[][],[] []"M_15"[][],[] []"M_20"[][],[] []"M_25"[][],[][] 

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[]        []\TU/lmtt/m/n/12 "M_30"[][],[] []"M_35"[][],[] []"M_40"[][],[] []"M_
45"[][],[] []"M_50"[][],[] []"M_55"[][],[] []"M_60"[][],[] []"M_65"[][],[] []"M
_70"[][],[] []"M_75"[][],[][] 

Overfull \hbox (67.9048pt too wide) in paragraph at lines 99--99
[]        []\TU/lmtt/m/n/12 "M_80"[][],[] []"M_85"[][],[] []"F_10"[][],[] []"F_
15"[][],[] []"F_20"[][],[] []"F_25"[][],[] []"F_30"[][],[] []"F_35"[][],[] []"F
_40"[][],[] []"F_45"[][],[][] 
[1]
Overfull \hbox (44.62482pt too wide) in paragraph at lines 157--157
[][]\TU/lmtt/m/n/12 kBYM[] []=[] []\TU/lmtt/b/n/12 try[][]\TU/lmtt/m/n/12 ([][]
\TU/lmtt/b/n/12 bym[][]\TU/lmtt/m/n/12 ([][]formula[] []= observed[] []~[] []\T
U/lmtt/b/n/12 offset[][]\TU/lmtt/m/n/12 (logExpected)[] []+[] []poverty,[] []da
ta[] []= kentucky,[][] 

Overfull \hbox (80.98477pt too wide) in paragraph at lines 158--158
[]    []\TU/lmtt/m/n/12 prior[] []=[] []\TU/lmtt/b/n/12 list[][]\TU/lmtt/m/n/12
 ([][]sdSpatial[] []=[] []\TU/lmtt/b/n/12 c[][]\TU/lmtt/m/n/12 ([][]0.01[][],[]
 []0.2[][]),[] []sdIndep[] []=[] []\TU/lmtt/b/n/12 c[][]\TU/lmtt/m/n/12 ([][]0.
01[][],[] []0.2[][])),[] []region.id[] []=[] []"County"[][],[][] 

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[]\TU/lmtt/m/n/12 ## Warning in .local(formula, data, adjMat, region.id, ...): 
There are 1 regions

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[]\TU/lmtt/m/it/12 ## The legacy packages maptools, rgdal, and rgeos, underpinn
ing the sp package, 
[2]
! Argument of \caption@@@withoptargs has an extra }.
<inserted text> 
                \par 
l.209 ...dth=0.48\textwidth]{figure/priorPost-1} }
                                                  
? 
! Emergency stop.
<inserted text> 
                \par 
l.209 ...dth=0.48\textwidth]{figure/priorPost-1} }
                                                  
Output written on bym.pdf (2 pages).
Transcript written on bym.log.
make[1]: *** [Makefile:7: bym.pdf] Error 1
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/diseasemapping.Rcheck/vign_test/diseasemapping/vignettes'
Error in tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/diseasemapping.Rcheck/vign_test/diseasemapping",  : 
  running 'make' failed
Execution halted