Error(s) in re-building vignettes:
--- re-building 'glrnb.Rnw' using Sweave
Loading required package: sp
Loading required package: xtable
Warning: replacing previous import 'spatstat.utils::RelevantNA' by 'spatstat.sparse::RelevantNA' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::grokIndexVector' by 'spatstat.sparse::grokIndexVector' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::fullIndexSequence' by 'spatstat.sparse::fullIndexSequence' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::positiveIndex' by 'spatstat.sparse::positiveIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::replacementIndex' by 'spatstat.sparse::replacementIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantEmpty' by 'spatstat.sparse::RelevantEmpty' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::isRelevantZero' by 'spatstat.sparse::isRelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::logicalIndex' by 'spatstat.sparse::logicalIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantZero' by 'spatstat.sparse::RelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::strictIndexSequence' by 'spatstat.sparse::strictIndexSequence' when loading 'spatstat.geom'
This is surveillance 1.19.0. For overview type 'help(surveillance)'.
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting glm.nb model with alpha=0.22596692307607
glrnb: Fitting glm.nb model with alpha=0.22596692307607
glrnb: Fitting glm.nb model with alpha=0.22596692307607
glrnb: Fitting glm.nb model with alpha=0.22596692307607
glrnb: Fitting glm.nb model with alpha=0.22596692307607
glrnb: Fitting glm.nb model with alpha=0.22596692307607
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
glrnb: Fitting Poisson model because alpha == 0
--- finished re-building 'glrnb.Rnw'

--- re-building 'hhh4.Rnw' using Sweave
Loading required package: sp
Loading required package: xtable
Warning: replacing previous import 'spatstat.utils::RelevantNA' by 'spatstat.sparse::RelevantNA' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::grokIndexVector' by 'spatstat.sparse::grokIndexVector' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::fullIndexSequence' by 'spatstat.sparse::fullIndexSequence' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::positiveIndex' by 'spatstat.sparse::positiveIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::replacementIndex' by 'spatstat.sparse::replacementIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantEmpty' by 'spatstat.sparse::RelevantEmpty' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::isRelevantZero' by 'spatstat.sparse::isRelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::logicalIndex' by 'spatstat.sparse::logicalIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantZero' by 'spatstat.sparse::RelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::strictIndexSequence' by 'spatstat.sparse::strictIndexSequence' when loading 'spatstat.geom'
This is surveillance 1.19.0. For overview type 'help(surveillance)'.
Doing computations: FALSE
--- finished re-building 'hhh4.Rnw'

--- re-building 'monitoringCounts.Rnw' using Sweave
Loading required package: sp
Loading required package: xtable
Warning: replacing previous import 'spatstat.utils::RelevantNA' by 'spatstat.sparse::RelevantNA' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::grokIndexVector' by 'spatstat.sparse::grokIndexVector' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::fullIndexSequence' by 'spatstat.sparse::fullIndexSequence' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::positiveIndex' by 'spatstat.sparse::positiveIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::replacementIndex' by 'spatstat.sparse::replacementIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantEmpty' by 'spatstat.sparse::RelevantEmpty' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::isRelevantZero' by 'spatstat.sparse::isRelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::logicalIndex' by 'spatstat.sparse::logicalIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantZero' by 'spatstat.sparse::RelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::strictIndexSequence' by 'spatstat.sparse::strictIndexSequence' when loading 'spatstat.geom'
This is surveillance 1.19.0. For overview type 'help(surveillance)'.
Loading required package: splines
Loading required package: gamlss.data

Attaching package: 'gamlss.data'

The following object is masked from 'package:datasets':

    sleep

Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.3-1  ********** 
For more on GAMLSS look at https://www.gamlss.com/
Type gamlssNews() to see new features/changes/bug fixes.

Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
--- finished re-building 'monitoringCounts.Rnw'

--- re-building 'surveillance.Rnw' using Sweave
Loading required package: sp
Loading required package: xtable
Warning: replacing previous import 'spatstat.utils::RelevantNA' by 'spatstat.sparse::RelevantNA' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::grokIndexVector' by 'spatstat.sparse::grokIndexVector' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::fullIndexSequence' by 'spatstat.sparse::fullIndexSequence' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::positiveIndex' by 'spatstat.sparse::positiveIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::replacementIndex' by 'spatstat.sparse::replacementIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantEmpty' by 'spatstat.sparse::RelevantEmpty' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::isRelevantZero' by 'spatstat.sparse::isRelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::logicalIndex' by 'spatstat.sparse::logicalIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantZero' by 'spatstat.sparse::RelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::strictIndexSequence' by 'spatstat.sparse::strictIndexSequence' when loading 'spatstat.geom'
This is surveillance 1.19.0. For overview type 'help(surveillance)'.
Doing computations: FALSE
--- finished re-building 'surveillance.Rnw'

--- re-building 'hhh4_spacetime.Rnw' using knitr
Loading required package: sp
Loading required package: xtable
Warning: replacing previous import 'spatstat.utils::RelevantNA' by 'spatstat.sparse::RelevantNA' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::grokIndexVector' by 'spatstat.sparse::grokIndexVector' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::fullIndexSequence' by 'spatstat.sparse::fullIndexSequence' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::positiveIndex' by 'spatstat.sparse::positiveIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::replacementIndex' by 'spatstat.sparse::replacementIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantEmpty' by 'spatstat.sparse::RelevantEmpty' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::isRelevantZero' by 'spatstat.sparse::isRelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::logicalIndex' by 'spatstat.sparse::logicalIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantZero' by 'spatstat.sparse::RelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::strictIndexSequence' by 'spatstat.sparse::strictIndexSequence' when loading 'spatstat.geom'
This is surveillance 1.19.0. For overview type 'help(surveillance)'.
Doing computations: FALSE
Loading required namespace: spdep
Failed with error:  'there is no package called 'spdep''
Quitting from lines 264-266 (hhh4_spacetime.Rnw) 
Error: processing vignette 'hhh4_spacetime.Rnw' failed with diagnostics:
package "spdep" is required to derive adjacencies from SpatialPolygons
--- failed re-building 'hhh4_spacetime.Rnw'

--- re-building 'twinSIR.Rnw' using knitr
Loading required package: sp
Loading required package: xtable
Warning: replacing previous import 'spatstat.utils::RelevantNA' by 'spatstat.sparse::RelevantNA' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::grokIndexVector' by 'spatstat.sparse::grokIndexVector' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::fullIndexSequence' by 'spatstat.sparse::fullIndexSequence' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::positiveIndex' by 'spatstat.sparse::positiveIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::replacementIndex' by 'spatstat.sparse::replacementIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantEmpty' by 'spatstat.sparse::RelevantEmpty' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::isRelevantZero' by 'spatstat.sparse::isRelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::logicalIndex' by 'spatstat.sparse::logicalIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantZero' by 'spatstat.sparse::RelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::strictIndexSequence' by 'spatstat.sparse::strictIndexSequence' when loading 'spatstat.geom'
This is surveillance 1.19.0. For overview type 'help(surveillance)'.
Doing computations: FALSE
Warning in `[.epidata`(x, 1:5, , drop = FALSE) :
  dropped class "epidata": subsetting blocks not allowed
Initialized 1 log-baseline interval:  0.00 92.55
Initial parameter vector:  1 1 1 1 0
Computing OSAIC weights for 4 epidemic covariates based on 1000 simulations ...
Initialized 1 log-baseline interval:  0.00 92.55
Initial parameter vector:  1 1 1 1 1 1 0
Computing OSAIC weights for 4 epidemic covariates based on 1000 simulations ...
--- finished re-building 'twinSIR.Rnw'

--- re-building 'twinstim.Rnw' using knitr
Loading required package: sp
Loading required package: xtable
Warning: replacing previous import 'spatstat.utils::RelevantNA' by 'spatstat.sparse::RelevantNA' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::grokIndexVector' by 'spatstat.sparse::grokIndexVector' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::fullIndexSequence' by 'spatstat.sparse::fullIndexSequence' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::positiveIndex' by 'spatstat.sparse::positiveIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::replacementIndex' by 'spatstat.sparse::replacementIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantEmpty' by 'spatstat.sparse::RelevantEmpty' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::isRelevantZero' by 'spatstat.sparse::isRelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::logicalIndex' by 'spatstat.sparse::logicalIndex' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::RelevantZero' by 'spatstat.sparse::RelevantZero' when loading 'spatstat.geom'
Warning: replacing previous import 'spatstat.utils::strictIndexSequence' by 'spatstat.sparse::strictIndexSequence' when loading 'spatstat.geom'
This is surveillance 1.19.0. For overview type 'help(surveillance)'.
Doing computations: FALSE
Warning in wkt(obj) : CRS object has no comment
Warning in wkt(obj) : CRS object has no comment
Warning in wkt(obj) : CRS object has no comment
Warning in wkt(obj) : CRS object has no comment
Warning in wkt(obj) : CRS object has no comment
Warning in wkt(obj) : CRS object has no comment
Warning in wkt(obj) : CRS object has no comment
Warning in wkt(obj) : CRS object has no comment
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded datum Unknown based on GRS80 ellipsoid in Proj4 definition
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded datum Unknown based on GRS80 ellipsoid in Proj4 definition
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded datum Unknown based on GRS80 ellipsoid in Proj4 definition
Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) :
  Discarded datum Unknown based on GRS80 ellipsoid in Proj4 definition
Loading required namespace: spdep
Failed with error:  'there is no package called 'spdep''
Quitting from lines 688-692 (twinstim.Rnw) 
Error: processing vignette 'twinstim.Rnw' failed with diagnostics:
package "spdep" is required to derive adjacencies from SpatialPolygons
--- failed re-building 'twinstim.Rnw'

SUMMARY: processing the following files failed:
  'hhh4_spacetime.Rnw' 'twinstim.Rnw'

Error: Vignette re-building failed.
Execution halted