Last updated on 2018-05-28 06:46:33 CEST.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 0.2 | 7.48 | 177.28 | 184.76 | WARN | |
r-devel-linux-x86_64-debian-gcc | 0.2 | 6.85 | 153.67 | 160.52 | WARN | |
r-devel-linux-x86_64-fedora-clang | 0.2 | 235.19 | WARN | |||
r-devel-linux-x86_64-fedora-gcc | 0.2 | 238.45 | WARN | |||
r-devel-windows-ix86+x86_64 | 0.2 | 14.00 | 171.00 | 185.00 | OK | --no-vignettes |
r-patched-linux-x86_64 | 0.2 | 6.62 | 171.73 | 178.35 | WARN | |
r-patched-solaris-x86 | 0.2 | 928.50 | WARN | |||
r-release-linux-x86_64 | 0.2 | 6.75 | 170.68 | 177.43 | WARN | |
r-release-windows-ix86+x86_64 | 0.2 | 17.00 | 112.00 | 129.00 | OK | --no-vignettes |
r-release-osx-x86_64 | 0.2 | NOTE | ||||
r-oldrel-windows-ix86+x86_64 | 0.2 | 16.00 | 121.00 | 137.00 | OK | --no-vignettes |
r-oldrel-osx-x86_64 | 0.2 | NOTE |
Version: 0.2
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘INLA’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘INLA’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: parallel
Loading required package: sp
Loading required package: spacetime
Loading required package: DCluster
Loading required package: boot
Loading required package: spdep
Loading required package: Matrix
Loading required package: spData
To access larger datasets in this package, install the
spDataLarge package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`
Loading required package: MASS
Loading required package: lattice
Attaching package: 'lattice'
The following object is masked from 'package:boot':
melanoma
Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
make[1]: Entering directory '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
Babel <3.20> and hyphenation patterns for 84 language(s) loaded.
(/home/hornik/tmp/R.check/r-devel-clang/Work/build/share/texmf/tex/latex/jss.cl
s
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/share/texlive/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
No file DClusterm.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/var/lib
/texmf/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
LaTeX Warning: Reference `sec:GLM' on page 3 undefined on input line 191.
LaTeX Warning: Reference `sec:mixed' on page 3 undefined on input line 192.
LaTeX Warning: Reference `sec:zeroinfl' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:spacetime' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:disc' on page 3 undefined on input line 198.
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
LaTeX Warning: Reference `fig:NYmap' on page 4 undefined on input line 315.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
LaTeX Warning: Reference `sec:spacetime' on page 6 undefined on input line 422.
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
LaTeX Warning: Reference `fig:NYcl' on page 7 undefined on input line 517.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7]
(/home/hornik/tmp/R.check/r-devel-clang/Work/build/share/texmf/tex/latex/ts1aet
t.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
LaTeX Warning: Reference `fig:NYcl' on page 9 undefined on input line 607.
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
LaTeX Warning: Reference `fig:NYclmm' on page 12 undefined on input line 812.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: Reference `fig:NYclmm' on page 13 undefined on input line 865.
LaTeX Warning: Reference `subsec:ex:NY' on page 13 undefined on input line 867.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
LaTeX Warning: Reference `fig:Navarre' on page 13 undefined on input line 929.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 105
7.
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 106
8.
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
LaTeX Warning: Reference `eq:stcluster' on page 17 undefined on input line 1108
.
LaTeX Warning: Reference `sec:mixed' on page 17 undefined on input line 1109.
LaTeX Warning: Reference `sec:zeroinfl' on page 17 undefined on input line 1110
.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: Reference `fig:NMSMR' on page 18 undefined on input line 1141.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: Reference `fig:NMcluster' on page 22 undefined on input line 135
0.
LaTeX Warning: `!h' float specifier changed to `!ht'.
No file DClusterm.bbl.
Package natbib Warning: There were undefined citations.
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 23
[23 <./DClusterm-053.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 24 []
[24] (./DClusterm.aux)
Package rerunfilecheck Warning: File `DClusterm.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
(see the transcript file for additional information){/usr/share/texmf/fonts/enc
/dvips/cm-super/cm-super-ts1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips
/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbxsl10.pfb></usr/shar
e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texl
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/p
ublic/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/
amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmss10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy
8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/
texmf/fonts/type1/public/cm-super/sftt1095.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/zapfchan/uzcmi8a.pfb>
Output written on DClusterm.pdf (24 pages, 2313234 bytes).
Transcript written on DClusterm.log.
bibtex DClusterm
This is BibTeX, Version 0.99d (TeX Live 2018/Debian)
The top-level auxiliary file: DClusterm.aux
The style file: jss.bst
Database file #1: DClusterm.bib
Warning--there's a number but no volume in Moraga:2017
(There was 1 warning)
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
Babel <3.20> and hyphenation patterns for 84 language(s) loaded.
(/home/hornik/tmp/R.check/r-devel-clang/Work/build/share/texmf/tex/latex/jss.cl
s
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/share/texlive/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(./DClusterm.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./DClusterm.out) (./DClusterm.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/var/lib
/texmf/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7]
(/home/hornik/tmp/R.check/r-devel-clang/Work/build/share/texmf/tex/latex/ts1aet
t.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: `!h' float specifier changed to `!ht'.
(./DClusterm.bbl
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
! Package inputenc Error: Invalid UTF-8 byte sequence.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
...
l.13 All<e9>vi
us B (2018).
?
! Emergency stop.
...
l.13 All<e9>vi
us B (2018).
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on DClusterm.log.
Makefile:6: recipe for target 'DClusterm.pdf' failed
make[1]: *** [DClusterm.pdf] Error 1
make[1]: Leaving directory '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
Error in buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm") :
running ‘make’ failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: parallel
Loading required package: sp
Loading required package: spacetime
Loading required package: DCluster
Loading required package: boot
Loading required package: spdep
Loading required package: Matrix
Loading required package: spData
To access larger datasets in this package, install the
spDataLarge package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`
Loading required package: MASS
Loading required package: lattice
Attaching package: 'lattice'
The following object is masked from 'package:boot':
melanoma
Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
make[1]: Entering directory '/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
Babel <3.20> and hyphenation patterns for 84 language(s) loaded.
(/home/hornik/tmp/R.check/r-devel-gcc/Work/build/share/texmf/tex/latex/jss.cls
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/share/texlive/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
No file DClusterm.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/var/lib
/texmf/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
LaTeX Warning: Reference `sec:GLM' on page 3 undefined on input line 191.
LaTeX Warning: Reference `sec:mixed' on page 3 undefined on input line 192.
LaTeX Warning: Reference `sec:zeroinfl' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:spacetime' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:disc' on page 3 undefined on input line 198.
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
LaTeX Warning: Reference `fig:NYmap' on page 4 undefined on input line 315.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
LaTeX Warning: Reference `sec:spacetime' on page 6 undefined on input line 422.
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
LaTeX Warning: Reference `fig:NYcl' on page 7 undefined on input line 517.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7]
(/home/hornik/tmp/R.check/r-devel-gcc/Work/build/share/texmf/tex/latex/ts1aett.
fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
LaTeX Warning: Reference `fig:NYcl' on page 9 undefined on input line 607.
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
LaTeX Warning: Reference `fig:NYclmm' on page 12 undefined on input line 812.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: Reference `fig:NYclmm' on page 13 undefined on input line 865.
LaTeX Warning: Reference `subsec:ex:NY' on page 13 undefined on input line 867.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
LaTeX Warning: Reference `fig:Navarre' on page 13 undefined on input line 929.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 105
7.
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 106
8.
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
LaTeX Warning: Reference `eq:stcluster' on page 17 undefined on input line 1108
.
LaTeX Warning: Reference `sec:mixed' on page 17 undefined on input line 1109.
LaTeX Warning: Reference `sec:zeroinfl' on page 17 undefined on input line 1110
.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: Reference `fig:NMSMR' on page 18 undefined on input line 1141.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: Reference `fig:NMcluster' on page 22 undefined on input line 135
0.
LaTeX Warning: `!h' float specifier changed to `!ht'.
No file DClusterm.bbl.
Package natbib Warning: There were undefined citations.
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 23
[23 <./DClusterm-053.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 24 []
[24] (./DClusterm.aux)
Package rerunfilecheck Warning: File `DClusterm.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
(see the transcript file for additional information){/usr/share/texmf/fonts/enc
/dvips/cm-super/cm-super-ts1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips
/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbxsl10.pfb></usr/shar
e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texl
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/p
ublic/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/
amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmss10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy
8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/
texmf/fonts/type1/public/cm-super/sftt1095.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/zapfchan/uzcmi8a.pfb>
Output written on DClusterm.pdf (24 pages, 2313238 bytes).
Transcript written on DClusterm.log.
bibtex DClusterm
This is BibTeX, Version 0.99d (TeX Live 2018/Debian)
The top-level auxiliary file: DClusterm.aux
The style file: jss.bst
Database file #1: DClusterm.bib
Warning--there's a number but no volume in Moraga:2017
(There was 1 warning)
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
Babel <3.20> and hyphenation patterns for 84 language(s) loaded.
(/home/hornik/tmp/R.check/r-devel-gcc/Work/build/share/texmf/tex/latex/jss.cls
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/share/texlive/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(./DClusterm.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./DClusterm.out) (./DClusterm.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/var/lib
/texmf/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7]
(/home/hornik/tmp/R.check/r-devel-gcc/Work/build/share/texmf/tex/latex/ts1aett.
fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: `!h' float specifier changed to `!ht'.
(./DClusterm.bbl
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
! Package inputenc Error: Invalid UTF-8 byte sequence.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
...
l.13 All<e9>vi
us B (2018).
?
! Emergency stop.
...
l.13 All<e9>vi
us B (2018).
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on DClusterm.log.
Makefile:6: recipe for target 'DClusterm.pdf' failed
make[1]: *** [DClusterm.pdf] Error 1
make[1]: Leaving directory '/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
Error in buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm") :
running ‘make’ failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘RColorBrewer’ ‘gridExtra’ ‘latticeExtra’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2
Check: data for non-ASCII characters
Result: NOTE
Note: found 2 marked Latin-1 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: parallel
Loading required package: sp
Loading required package: spacetime
Loading required package: DCluster
Loading required package: boot
Loading required package: spdep
Loading required package: Matrix
Loading required package: spData
To access larger datasets in this package, install the
spDataLarge package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`
Loading required package: MASS
Loading required package: lattice
Attaching package: 'lattice'
The following object is masked from 'package:boot':
melanoma
Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
(/data/gannet/ripley/R/R-clang/share/texmf/tex/latex/jss.cls
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/size11.clo))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/ae.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/local/texlive/2018/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
No file DClusterm.aux.
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/usr/loc
al/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
LaTeX Warning: Reference `sec:GLM' on page 3 undefined on input line 191.
LaTeX Warning: Reference `sec:mixed' on page 3 undefined on input line 192.
LaTeX Warning: Reference `sec:zeroinfl' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:spacetime' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:disc' on page 3 undefined on input line 198.
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
LaTeX Warning: Reference `fig:NYmap' on page 4 undefined on input line 315.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
LaTeX Warning: Reference `sec:spacetime' on page 6 undefined on input line 422.
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
LaTeX Warning: Reference `fig:NYcl' on page 7 undefined on input line 517.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7] (/data/gannet/ripley/R/R-clang/share/texmf/tex/latex/ts1aett.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
LaTeX Warning: Reference `fig:NYcl' on page 9 undefined on input line 607.
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
LaTeX Warning: Reference `fig:NYclmm' on page 12 undefined on input line 812.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: Reference `fig:NYclmm' on page 13 undefined on input line 865.
LaTeX Warning: Reference `subsec:ex:NY' on page 13 undefined on input line 867.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
LaTeX Warning: Reference `fig:Navarre' on page 13 undefined on input line 929.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 105
7.
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 106
8.
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
LaTeX Warning: Reference `eq:stcluster' on page 17 undefined on input line 1108
.
LaTeX Warning: Reference `sec:mixed' on page 17 undefined on input line 1109.
LaTeX Warning: Reference `sec:zeroinfl' on page 17 undefined on input line 1110
.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: Reference `fig:NMSMR' on page 18 undefined on input line 1141.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: Reference `fig:NMcluster' on page 22 undefined on input line 135
0.
LaTeX Warning: `!h' float specifier changed to `!ht'.
No file DClusterm.bbl.
Package natbib Warning: There were undefined citations.
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 23
[23 <./DClusterm-053.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 24 []
[24] (./DClusterm.aux)
Package rerunfilecheck Warning: File `DClusterm.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
(see the transcript file for additional information){/usr/local/texlive/2018/te
xmf-dist/fonts/enc/dvips/cm-super/cm-super-ts1.enc}{/usr/local/texlive/2018/tex
mf-dist/fonts/enc/dvips/base/8r.enc}</usr/local/texlive/2018/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmb10.pfb></usr/local/texlive/2018/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmbx10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1
/public/amsfonts/cm/cmbxsl10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type
1/public/amsfonts/cm/cmex10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/
public/amsfonts/cm/cmmi8.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmr10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmr8.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/
amsfonts/cm/cmsl10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/a
msfonts/cm/cmsltt10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/
amsfonts/cm/cmss10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/a
msfonts/cm/cmsy10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/am
sfonts/cm/cmsy8.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/amsf
onts/cm/cmti10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmti12.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmtt10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/cm-supe
r/sftt1095.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw/zapfchan/uzc
mi8a.pfb>
Output written on DClusterm.pdf (24 pages, 2313196 bytes).
Transcript written on DClusterm.log.
bibtex DClusterm
This is BibTeX, Version 0.99d (TeX Live 2018)
The top-level auxiliary file: DClusterm.aux
The style file: jss.bst
Database file #1: DClusterm.bib
Warning--there's a number but no volume in Moraga:2017
(There was 1 warning)
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
(/data/gannet/ripley/R/R-clang/share/texmf/tex/latex/jss.cls
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/size11.clo))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/ae.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/local/texlive/2018/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(./DClusterm.aux) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./DClusterm.out) (./DClusterm.out)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/usr/loc
al/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7] (/data/gannet/ripley/R/R-clang/share/texmf/tex/latex/ts1aett.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: `!h' float specifier changed to `!ht'.
(./DClusterm.bbl
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
! Package inputenc Error: Invalid UTF-8 byte sequence.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
...
l.13 All<e9>vi
us B (2018).
?
! Emergency stop.
...
l.13 All<e9>vi
us B (2018).
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on DClusterm.log.
make[1]: *** [Makefile:8: DClusterm.pdf] Error 1
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
Error in buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/DClusterm.Rcheck/vign_test/DClusterm") :
running 'make' failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: parallel
Loading required package: sp
Loading required package: spacetime
Loading required package: DCluster
Loading required package: boot
Loading required package: spdep
Loading required package: Matrix
Loading required package: spData
To access larger datasets in this package, install the
spDataLarge package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`
Loading required package: MASS
Loading required package: lattice
Attaching package: 'lattice'
The following object is masked from 'package:boot':
melanoma
Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
(/data/gannet/ripley/R/R-devel/share/texmf/tex/latex/jss.cls
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/size11.clo))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/ae.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/local/texlive/2018/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
No file DClusterm.aux.
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/usr/loc
al/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
LaTeX Warning: Reference `sec:GLM' on page 3 undefined on input line 191.
LaTeX Warning: Reference `sec:mixed' on page 3 undefined on input line 192.
LaTeX Warning: Reference `sec:zeroinfl' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:spacetime' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:disc' on page 3 undefined on input line 198.
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
LaTeX Warning: Reference `fig:NYmap' on page 4 undefined on input line 315.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
LaTeX Warning: Reference `sec:spacetime' on page 6 undefined on input line 422.
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
LaTeX Warning: Reference `fig:NYcl' on page 7 undefined on input line 517.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7] (/data/gannet/ripley/R/R-devel/share/texmf/tex/latex/ts1aett.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
LaTeX Warning: Reference `fig:NYcl' on page 9 undefined on input line 607.
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
LaTeX Warning: Reference `fig:NYclmm' on page 12 undefined on input line 812.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: Reference `fig:NYclmm' on page 13 undefined on input line 865.
LaTeX Warning: Reference `subsec:ex:NY' on page 13 undefined on input line 867.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
LaTeX Warning: Reference `fig:Navarre' on page 13 undefined on input line 929.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 105
7.
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 106
8.
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
LaTeX Warning: Reference `eq:stcluster' on page 17 undefined on input line 1108
.
LaTeX Warning: Reference `sec:mixed' on page 17 undefined on input line 1109.
LaTeX Warning: Reference `sec:zeroinfl' on page 17 undefined on input line 1110
.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: Reference `fig:NMSMR' on page 18 undefined on input line 1141.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: Reference `fig:NMcluster' on page 22 undefined on input line 135
0.
LaTeX Warning: `!h' float specifier changed to `!ht'.
No file DClusterm.bbl.
Package natbib Warning: There were undefined citations.
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 23
[23 <./DClusterm-053.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 24 []
[24] (./DClusterm.aux)
Package rerunfilecheck Warning: File `DClusterm.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
(see the transcript file for additional information){/usr/local/texlive/2018/te
xmf-dist/fonts/enc/dvips/cm-super/cm-super-ts1.enc}{/usr/local/texlive/2018/tex
mf-dist/fonts/enc/dvips/base/8r.enc}</usr/local/texlive/2018/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmb10.pfb></usr/local/texlive/2018/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmbx10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1
/public/amsfonts/cm/cmbxsl10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type
1/public/amsfonts/cm/cmex10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/
public/amsfonts/cm/cmmi8.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmr10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmr8.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/
amsfonts/cm/cmsl10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/a
msfonts/cm/cmsltt10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/
amsfonts/cm/cmss10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/a
msfonts/cm/cmsy10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/am
sfonts/cm/cmsy8.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/amsf
onts/cm/cmti10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmti12.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmtt10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/cm-supe
r/sftt1095.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw/zapfchan/uzc
mi8a.pfb>
Output written on DClusterm.pdf (24 pages, 2313195 bytes).
Transcript written on DClusterm.log.
bibtex DClusterm
This is BibTeX, Version 0.99d (TeX Live 2018)
The top-level auxiliary file: DClusterm.aux
The style file: jss.bst
Database file #1: DClusterm.bib
Warning--there's a number but no volume in Moraga:2017
(There was 1 warning)
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
(/data/gannet/ripley/R/R-devel/share/texmf/tex/latex/jss.cls
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/size11.clo))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/ae.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/local/texlive/2018/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(./DClusterm.aux) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./DClusterm.out) (./DClusterm.out)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/usr/loc
al/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7] (/data/gannet/ripley/R/R-devel/share/texmf/tex/latex/ts1aett.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: `!h' float specifier changed to `!ht'.
(./DClusterm.bbl
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
! Package inputenc Error: Invalid UTF-8 byte sequence.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
...
l.13 All<e9>vi
us B (2018).
?
! Emergency stop.
...
l.13 All<e9>vi
us B (2018).
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on DClusterm.log.
make[1]: *** [Makefile:8: DClusterm.pdf] Error 1
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
Error in buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/DClusterm.Rcheck/vign_test/DClusterm") :
running 'make' failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: parallel
Loading required package: sp
Loading required package: spacetime
Loading required package: DCluster
Loading required package: boot
Loading required package: spdep
Loading required package: Matrix
Loading required package: spData
To access larger datasets in this package, install the
spDataLarge package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`
Loading required package: MASS
Loading required package: lattice
Attaching package: 'lattice'
The following object is masked from 'package:boot':
melanoma
Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
make[1]: Entering directory '/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
Babel <3.20> and hyphenation patterns for 84 language(s) loaded.
(/home/hornik/tmp/R.check/r-patched-gcc/Work/build/share/texmf/tex/latex/jss.cl
s
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/share/texlive/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
No file DClusterm.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/var/lib
/texmf/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
LaTeX Warning: Reference `sec:GLM' on page 3 undefined on input line 191.
LaTeX Warning: Reference `sec:mixed' on page 3 undefined on input line 192.
LaTeX Warning: Reference `sec:zeroinfl' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:spacetime' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:disc' on page 3 undefined on input line 198.
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
LaTeX Warning: Reference `fig:NYmap' on page 4 undefined on input line 315.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
LaTeX Warning: Reference `sec:spacetime' on page 6 undefined on input line 422.
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
LaTeX Warning: Reference `fig:NYcl' on page 7 undefined on input line 517.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7]
(/home/hornik/tmp/R.check/r-patched-gcc/Work/build/share/texmf/tex/latex/ts1aet
t.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
LaTeX Warning: Reference `fig:NYcl' on page 9 undefined on input line 607.
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
LaTeX Warning: Reference `fig:NYclmm' on page 12 undefined on input line 812.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: Reference `fig:NYclmm' on page 13 undefined on input line 865.
LaTeX Warning: Reference `subsec:ex:NY' on page 13 undefined on input line 867.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
LaTeX Warning: Reference `fig:Navarre' on page 13 undefined on input line 929.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 105
7.
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 106
8.
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
LaTeX Warning: Reference `eq:stcluster' on page 17 undefined on input line 1108
.
LaTeX Warning: Reference `sec:mixed' on page 17 undefined on input line 1109.
LaTeX Warning: Reference `sec:zeroinfl' on page 17 undefined on input line 1110
.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: Reference `fig:NMSMR' on page 18 undefined on input line 1141.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: Reference `fig:NMcluster' on page 22 undefined on input line 135
0.
LaTeX Warning: `!h' float specifier changed to `!ht'.
No file DClusterm.bbl.
Package natbib Warning: There were undefined citations.
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 23
[23 <./DClusterm-053.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 24 []
[24] (./DClusterm.aux)
Package rerunfilecheck Warning: File `DClusterm.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
(see the transcript file for additional information){/usr/share/texmf/fonts/enc
/dvips/cm-super/cm-super-ts1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips
/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbxsl10.pfb></usr/shar
e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texl
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/p
ublic/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/
amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmss10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy
8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/
texmf/fonts/type1/public/cm-super/sftt1095.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/zapfchan/uzcmi8a.pfb>
Output written on DClusterm.pdf (24 pages, 2313233 bytes).
Transcript written on DClusterm.log.
bibtex DClusterm
This is BibTeX, Version 0.99d (TeX Live 2018/Debian)
The top-level auxiliary file: DClusterm.aux
The style file: jss.bst
Database file #1: DClusterm.bib
Warning--there's a number but no volume in Moraga:2017
(There was 1 warning)
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
Babel <3.20> and hyphenation patterns for 84 language(s) loaded.
(/home/hornik/tmp/R.check/r-patched-gcc/Work/build/share/texmf/tex/latex/jss.cl
s
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/share/texlive/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(./DClusterm.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./DClusterm.out) (./DClusterm.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/var/lib
/texmf/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7]
(/home/hornik/tmp/R.check/r-patched-gcc/Work/build/share/texmf/tex/latex/ts1aet
t.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: `!h' float specifier changed to `!ht'.
(./DClusterm.bbl
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
! Package inputenc Error: Invalid UTF-8 byte sequence.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
...
l.13 All<e9>vi
us B (2018).
?
! Emergency stop.
...
l.13 All<e9>vi
us B (2018).
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on DClusterm.log.
Makefile:6: recipe for target 'DClusterm.pdf' failed
make[1]: *** [DClusterm.pdf] Error 1
make[1]: Leaving directory '/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
Error in buildVignettes(dir = "/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm") :
running ‘make’ failed
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: parallel
Loading required package: sp
Loading required package: spacetime
Loading required package: DCluster
Loading required package: boot
Loading required package: spdep
Loading required package: Matrix
Loading required package: spData
To access larger datasets in this package, install the
spDataLarge package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`
Loading required package: MASS
Loading required package: lattice
Attaching package: 'lattice'
The following object is masked from 'package:boot':
melanoma
Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
(/home/ripley/R/cc/share/texmf/tex/latex/jss.cls
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/size11.clo))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/ae.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/local/texlive/2018/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
No file DClusterm.aux.
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/usr/loc
al/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
LaTeX Warning: Reference `sec:GLM' on page 3 undefined on input line 191.
LaTeX Warning: Reference `sec:mixed' on page 3 undefined on input line 192.
LaTeX Warning: Reference `sec:zeroinfl' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:spacetime' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:disc' on page 3 undefined on input line 198.
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
LaTeX Warning: Reference `fig:NYmap' on page 4 undefined on input line 315.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
LaTeX Warning: Reference `sec:spacetime' on page 6 undefined on input line 422.
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
LaTeX Warning: Reference `fig:NYcl' on page 7 undefined on input line 517.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7] (/home/ripley/R/cc/share/texmf/tex/latex/ts1aett.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
LaTeX Warning: Reference `fig:NYcl' on page 9 undefined on input line 607.
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
LaTeX Warning: Reference `fig:NYclmm' on page 12 undefined on input line 812.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: Reference `fig:NYclmm' on page 13 undefined on input line 865.
LaTeX Warning: Reference `subsec:ex:NY' on page 13 undefined on input line 867.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
LaTeX Warning: Reference `fig:Navarre' on page 13 undefined on input line 929.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 105
7.
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 106
8.
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
LaTeX Warning: Reference `eq:stcluster' on page 17 undefined on input line 1108
.
LaTeX Warning: Reference `sec:mixed' on page 17 undefined on input line 1109.
LaTeX Warning: Reference `sec:zeroinfl' on page 17 undefined on input line 1110
.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: Reference `fig:NMSMR' on page 18 undefined on input line 1141.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: Reference `fig:NMcluster' on page 22 undefined on input line 135
0.
LaTeX Warning: `!h' float specifier changed to `!ht'.
No file DClusterm.bbl.
Package natbib Warning: There were undefined citations.
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 23
[23 <./DClusterm-053.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 24 []
[24] (./DClusterm.aux)
Package rerunfilecheck Warning: File `DClusterm.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
(see the transcript file for additional information){/usr/local/texlive/2018/te
xmf-dist/fonts/enc/dvips/cm-super/cm-super-ts1.enc}{/usr/local/texlive/2018/tex
mf-dist/fonts/enc/dvips/base/8r.enc}</usr/local/texlive/2018/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmb10.pfb></usr/local/texlive/2018/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmbx10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type
1/public/amsfonts/cm/cmbx12.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1
/public/amsfonts/cm/cmbxsl10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type
1/public/amsfonts/cm/cmex10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/
public/amsfonts/cm/cmmi8.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmr10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmr8.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/
amsfonts/cm/cmsl10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/a
msfonts/cm/cmsltt10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/
amsfonts/cm/cmss10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/a
msfonts/cm/cmsy10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/am
sfonts/cm/cmsy8.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/amsf
onts/cm/cmti10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmti12.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/amsfon
ts/cm/cmtt10.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/public/cm-supe
r/sftt1095.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw/zapfchan/uzc
mi8a.pfb>
Output written on DClusterm.pdf (24 pages, 2313197 bytes).
Transcript written on DClusterm.log.
bibtex DClusterm
This is BibTeX, Version 0.99d (TeX Live 2018)
The top-level auxiliary file: DClusterm.aux
The style file: jss.bst
Database file #1: DClusterm.bib
Warning--there's a number but no volume in Moraga:2017
(There was 1 warning)
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
(/home/ripley/R/cc/share/texmf/tex/latex/jss.cls
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/size11.clo))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/ae.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/local/texlive/2018/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(./DClusterm.aux) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./DClusterm.out) (./DClusterm.out)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/usr/loc
al/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/local/texlive/2018/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7] (/home/ripley/R/cc/share/texmf/tex/latex/ts1aett.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: `!h' float specifier changed to `!ht'.
(./DClusterm.bbl
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
! Package inputenc Error: Invalid UTF-8 byte sequence.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
...
l.13 All<e9>vi
us B (2018).
?
! Emergency stop.
...
l.13 All<e9>vi
us B (2018).
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on DClusterm.log.
*** Error code 1
make: Fatal error: Command failed for target `DClusterm.pdf'
Current working directory /home/ripley/R/packages/tests32/DClusterm.Rcheck/vign_test/DClusterm/vignettes
Error in buildVignettes(dir = "/home/ripley/R/packages/tests32/DClusterm.Rcheck/vign_test/DClusterm") :
running 'make' failed
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.2
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: parallel
Loading required package: sp
Loading required package: spacetime
Loading required package: DCluster
Loading required package: boot
Loading required package: spdep
Loading required package: Matrix
Loading required package: spData
To access larger datasets in this package, install the
spDataLarge package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`
Loading required package: MASS
Loading required package: lattice
Attaching package: 'lattice'
The following object is masked from 'package:boot':
melanoma
Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
make[1]: Entering directory '/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
Babel <3.20> and hyphenation patterns for 84 language(s) loaded.
(/home/hornik/tmp/R.check/r-release-gcc/Work/build/share/texmf/tex/latex/jss.cl
s
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/share/texlive/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
No file DClusterm.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/var/lib
/texmf/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
LaTeX Warning: Reference `sec:GLM' on page 3 undefined on input line 191.
LaTeX Warning: Reference `sec:mixed' on page 3 undefined on input line 192.
LaTeX Warning: Reference `sec:zeroinfl' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:spacetime' on page 3 undefined on input line 195.
LaTeX Warning: Reference `sec:disc' on page 3 undefined on input line 198.
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
LaTeX Warning: Reference `fig:NYmap' on page 4 undefined on input line 315.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
LaTeX Warning: Reference `sec:spacetime' on page 6 undefined on input line 422.
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
LaTeX Warning: Reference `fig:NYcl' on page 7 undefined on input line 517.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7]
(/home/hornik/tmp/R.check/r-release-gcc/Work/build/share/texmf/tex/latex/ts1aet
t.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
LaTeX Warning: Reference `fig:NYcl' on page 9 undefined on input line 607.
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
LaTeX Warning: Reference `fig:NYclmm' on page 12 undefined on input line 812.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: Reference `fig:NYclmm' on page 13 undefined on input line 865.
LaTeX Warning: Reference `subsec:ex:NY' on page 13 undefined on input line 867.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
LaTeX Warning: Reference `fig:Navarre' on page 13 undefined on input line 929.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 105
7.
LaTeX Warning: Reference `fig:Navarrecl' on page 17 undefined on input line 106
8.
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
LaTeX Warning: Reference `eq:stcluster' on page 17 undefined on input line 1108
.
LaTeX Warning: Reference `sec:mixed' on page 17 undefined on input line 1109.
LaTeX Warning: Reference `sec:zeroinfl' on page 17 undefined on input line 1110
.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: Reference `fig:NMSMR' on page 18 undefined on input line 1141.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: Reference `fig:NMcluster' on page 22 undefined on input line 135
0.
LaTeX Warning: `!h' float specifier changed to `!ht'.
No file DClusterm.bbl.
Package natbib Warning: There were undefined citations.
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Underfull \hbox (badness 10000) in paragraph at lines 1411--1411
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 23
[23 <./DClusterm-053.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 24 []
[24] (./DClusterm.aux)
Package rerunfilecheck Warning: File `DClusterm.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
)
(see the transcript file for additional information){/usr/share/texmf/fonts/enc
/dvips/cm-super/cm-super-ts1.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips
/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmb1
0.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmbxsl10.pfb></usr/shar
e/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmex10.pfb></usr/share/texl
ive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/p
ublic/amsfonts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/
amsfonts/cm/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsf
onts/cm/cmss10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy
8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/
share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/
texmf/fonts/type1/public/cm-super/sftt1095.pfb></usr/share/texlive/texmf-dist/f
onts/type1/urw/zapfchan/uzcmi8a.pfb>
Output written on DClusterm.pdf (24 pages, 2313234 bytes).
Transcript written on DClusterm.log.
bibtex DClusterm
This is BibTeX, Version 0.99d (TeX Live 2018/Debian)
The top-level auxiliary file: DClusterm.aux
The style file: jss.bst
Database file #1: DClusterm.bib
Warning--there's a number but no volume in Moraga:2017
(There was 1 warning)
pdflatex DClusterm
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./DClusterm.tex
LaTeX2e <2018-04-01> patch level 4
Babel <3.20> and hyphenation patterns for 84 language(s) loaded.
(/home/hornik/tmp/R.check/r-release-gcc/Work/build/share/texmf/tex/latex/jss.cl
s
Document Class: jss 2015/09/01 3.0 jss class by Achim Zeileis
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/ae/ae.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aer.fd)))
(/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix
<2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.dfu))))
(/usr/share/texlive/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 446.
) (/usr/share/texlive/texmf-dist/tex/generic/thumbpdf/thumbpdf.sty
Package thumbpdf Warning: Compressed PDF objects of PDF 1.5 are not supported.
Package thumbpdf Warning: Thumbnail data file `DClusterm.tpt' not found.
) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(./DClusterm.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./DClusterm.out) (./DClusterm.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pzc.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aess.fd)
Underfull \vbox (badness 7888) has occurred while \output is active [1{/var/lib
/texmf/fonts/map/pdftex/updmap/pdftex.map} <./jsslogo.jpg>]
Package natbib Warning: Citation `McCullaghNelder:1989' on page 2 undefined on
input line 120.
Package natbib Warning: Citation `Kulldorff:1997' on page 2 undefined on input
line 129.
Package natbib Warning: Citation `DCluster:2005' on page 2 undefined on input l
ine 149.
Package natbib Warning: Citation `SpatialEpi:2016' on page 2 undefined on input
line 152.
Package natbib Warning: Citation `rsatscan:2015' on page 2 undefined on input l
ine 154.
Package natbib Warning: Citation `scanstatistics:2018' on page 2 undefined on i
nput line 157.
Package natbib Warning: Citation `smerc:2015' on page 2 undefined on input line
165.
Package natbib Warning: Citation `AMOEBA:2014' on page 2 undefined on input lin
e 167.
Package natbib Warning: Citation `PReMiuM:2015' on page 2 undefined on input li
ne 170.
Package natbib Warning: Citation `SNscan:2016' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `Moraga:2017' on page 2 undefined on input lin
e 172.
Package natbib Warning: Citation `smacpod:2018' on page 2 undefined on input li
ne 176.
Package natbib Warning: Citation `Salmonetal:2016' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `Meyeretal:2017' on page 2 undefined on input
line 177.
Package natbib Warning: Citation `ClustGeo:2017' on page 2 undefined on input l
ine 179.
Package natbib Warning: Citation `R:2018' on page 2 undefined on input line 186
.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 2 []
[2]
Package natbib Warning: Citation `Jung:2009' on page 3 undefined on input line
221.
Package natbib Warning: Citation `ZhangLinCSDA:2009' on page 3 undefined on inp
ut line 221.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 3
[3]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 4 undefined o
n input line 293.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 4 undefined on i
nput line 293.
Package natbib Warning: Citation `Rueetal:2009' on page 4 undefined on input li
ne 296.
(/usr/share/texlive/texmf-dist/tex/latex/ae/t1aett.fd)
Package natbib Warning: Citation `Walletetal:1992' on page 4 undefined on input
line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 313.
Package natbib Warning: Citation `WallerGotway:2004' on page 4 undefined on inp
ut line 339.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 4 []
[4]
Package natbib Warning: Citation `Pebesma:2012' on page 5 undefined on input li
ne 369.
Package natbib Warning: Citation `RColorBrewer:2014' undefined on input line 37
3.
Underfull \vbox (badness 10000) has occurred while \output is active
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 5
[5 <./DClusterm-006.pdf>]
Package natbib Warning: Citation `Dunn:1958' on page 6 undefined on input line
431.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 6 []
[6]
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 7
[7]
(/home/hornik/tmp/R.check/r-release-gcc/Work/build/share/texmf/tex/latex/ts1aet
t.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd)
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 8 []
[8]
Package natbib Warning: Citation `gridExtra:2016' undefined on input line 616.
Package natbib Warning: Citation `latticeExtra:2016' undefined on input line 61
6.
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 9
[9 <./DClusterm-017.pdf>]
Package natbib Warning: Citation `BilanciaDemarinis:2014' on page 10 undefined
on input line 691.
Package natbib Warning: Citation `Dean:1992' on page 10 undefined on input line
709.
Package natbib Warning: Citation `DCluster:2005' on page 10 undefined on input
line 711.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 10 []
[10]
Package natbib Warning: Citation `lme4:2015' on page 11 undefined on input line
776.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 11
[11]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 12 []
[12]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 8
98.
Package natbib Warning: Citation `Ugarteetal:2006' on page 13 undefined on inpu
t line 928.
Package natbib Warning: Citation `Ugarteetal:2004' on page 13 undefined on inpu
t line 931.
Package natbib Warning: Citation `RD:2010' on page 13 undefined on input line 9
34.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 13
[13]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 14 []
[14 <./DClusterm-029.pdf>]
Package natbib Warning: Citation `Ugarteetal:2004' on page 15 undefined on inpu
t line 976.
Package natbib Warning: Citation `pscl:2008' on page 15 undefined on input line
978.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 15
[15 <./DClusterm-031.pdf>]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 16 []
[16]
Overfull \hbox (9.0599pt too wide) in paragraph at lines 1059--1069
[]\T1/aer/m/n/10.95 An in-dex for the ar-eas in each of the de-tected clus-ters
can be ob-tained with func-tion \T1/aett/m/n/10.95 knbinary()\T1/aer/m/n/10.95
.
LaTeX Warning: `!h' float specifier changed to `!ht'.
Package natbib Warning: Citation `Jung:2009' on page 17 undefined on input line
1096.
Package natbib Warning: Citation `GomezRubioetal:2018' on page 17 undefined on
input line 1098.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 17
[17]
LaTeX Warning: `!h' float specifier changed to `!ht'.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 18 []
[18 <./DClusterm-039.pdf>]
Underfull \vbox (badness 6708) has occurred while \output is active
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 19
[19 <./DClusterm-042.pdf>]
Package natbib Warning: Citation `sp:2005' on page 20 undefined on input line 1
249.
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 20 []
[20]
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
[] \T1/aer/m/n/10.95 21
[21]
LaTeX Warning: `!h' float specifier changed to `!ht'.
(./DClusterm.bbl
Overfull \hbox (10.94998pt too wide) has occurred while \output is active
\T1/aer/m/n/10.95 22 []
[22]
! Package inputenc Error: Invalid UTF-8 byte sequence.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
...
l.13 All<e9>vi
us B (2018).
?
! Emergency stop.
...
l.13 All<e9>vi
us B (2018).
! ==> Fatal error occurred, no output PDF file produced!
Transcript written on DClusterm.log.
Makefile:6: recipe for target 'DClusterm.pdf' failed
make[1]: *** [DClusterm.pdf] Error 1
make[1]: Leaving directory '/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm/vignettes'
Error in buildVignettes(dir = "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DClusterm.Rcheck/vign_test/DClusterm") :
running ‘make’ failed
Execution halted
Flavor: r-release-linux-x86_64