Skip to content

Commit 98f23fe

Browse files
eddelbuetteleddelbuettel
committed
Updated vignette infrastructure
1 parent a532793 commit 98f23fe

File tree

4 files changed

+603
-531
lines changed

4 files changed

+603
-531
lines changed

‎vignettes/rmd/Makefile‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -7,19 +7,19 @@ rmdvignettes := $(rmdsources:.Rmd=.pdf)
77
%.pdf: %.Rmd
88
Rscript -e 'rmarkdown::render("$<")'
99
Rscript -e 'tools::compactPDF("$@", gs_quality="ebook")'
10-
cp -vax $@ ../pdf
10+
cp -vax $@ ..
1111

1212
all: ${rmdvignettes} RcppArmadillo-intro.pdf
1313

14-
RcppArmadillo-intro.tex: RcppArmadillo-intro.Rnw
14+
RcppArmadillo-intro.pdf: RcppArmadillo-intro.Rnw
1515
Rscript -e 'Sweave("$<")'
16-
17-
RcppArmadillo-intro.pdf: RcppArmadillo-intro.tex
18-
Rscript -e 'tools::texi2pdf("$<", texi2dvi="pdflatex")'
19-
Rscript -e 'tools::texi2pdf("$<", texi2dvi="pdflatex")'
16+
pdflatex RcppArmadillo-intro.tex
17+
bibtex RcppArmadillo-intro.aux
18+
pdflatex RcppArmadillo-intro.tex
19+
pdflatex RcppArmadillo-intro.tex
2020
Rscript -e 'tools::compactPDF("$@", gs_quality="ebook")'
21-
cp -vax $@ ../pdf
21+
cp -vax $@ ..
2222

2323
clean:
24-
@rm -rf *.aux *.log *.out *.tex *.spl Rcpp*.pdf \
25-
RcppArmadillo*_cache pinp.cls jss.bst
24+
@rm -rf *.aux *.log *.out *.tex *.spl *.bbl *.blg Rcpp*.pdf \
25+
RcppArmadillo*_cache pinp.cls jss.bst auto/

‎vignettes/rmd/RcppArmadillo-intro.Rnw‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -76,8 +76,8 @@ prettyDate <- format(Sys.Date(), "%B %e, %Y")
7676

7777
\title{RcppArmadillo: Accelerating R \\with High-Performance C++ Linear Algebra\footnote{
7878
This vignette corresponds to a
79-
\href{http://dx.doi.org/10.1016/j.csda.2013.02.005}{paper published} in
80-
\href{http://www.journals.elsevier.com/computational-statistics-and-data-analysis/}{Computational Statistics and Data Analysis}.
79+
\href{https://dx.doi.org/10.1016/j.csda.2013.02.005}{paper published} in
80+
\href{https://www.journals.elsevier.com/computational-statistics-and-data-analysis/}{Computational Statistics and Data Analysis}.
8181
Currently still identical to the paper, this vignette version may over time receive minor updates.
8282
For citations, please use \citet{Eddelbuettel+Sanderson:2014:RcppArmadillo} as provided by \code{citation("RcppArmadillo")}.
8383
%
@@ -92,7 +92,7 @@ prettyDate <- format(Sys.Date(), "%B %e, %Y")
9292
%\cortext[cor]{Corresponding author. Email: \url{edd@debian.org}.}% Postal address: 711 Monroe Avenue,
9393
%River Forest, IL 60305, USA. } %he \pkg{RcppArmadillo} package is available
9494
%with the electronic version of this article, as well as via every CRAN mirror.}
95-
\address[de]{Debian Project, \url{http://www.debian.org}}
95+
\address[de]{Debian Project, \url{https://www.debian.org}}
9696

9797
\author[cs1,cs2]{Conrad Sanderson}
9898
%\ead[cs1]{nowhere} % CS i'd prefer to leave out my email address
@@ -269,7 +269,7 @@ now-common multi-core platforms~\citep{Kurzak_2010}.
269269
\bottomrule
270270
\end{tabular}
271271
\caption{Selected \pkg{Armadillo} functions with brief descriptions; see
272-
\texttt{http://arma.sf.net/docs.html} for more complete
272+
\texttt{https://arma.sf.net/docs.html} for more complete
273273
documentation. Several optional additional arguments have been omitted
274274
here for brevity.\label{tab:arma}}
275275
\end{table}
@@ -478,7 +478,7 @@ All of these steps involve only matrix multiplication and inversions, making
478478
the algorithm very suitable for an implementation in any language which
479479
can use matrix expressions. An example for \proglang{Matlab} is provided on
480480
the Mathworks website\footnote{See
481-
\url{http://www.mathworks.com/products/matlab-coder/demos.html?file=/products/demos/shipping/coder/coderdemo_kalman_filter.html}.}
481+
\url{https://www.mathworks.com/products/matlab-coder/demos.html?file=/products/demos/shipping/coder/coderdemo_kalman_filter.html}.}
482482
and shown in Listing~\ref{code:matlabkalman}.
483483

484484
\lstset{
@@ -894,7 +894,7 @@ of applied researchers deploying computational methods in statistical
894894
computing and data analysis.
895895
As of early-2013, about 30 \proglang{R} packages on CRAN deploy
896896
\pkg{RcppArmadillo}\footnote{See
897-
\url{http://cran.r-project.org/package=RcppArmadillo} for more details.},
897+
\url{https://cran.r-project.org/package=RcppArmadillo} for more details.},
898898
showing both the usefulness of \proglang{Armadillo} and its acceptance by
899899
the \proglang{R} community.
900900

‎vignettes/rmd/RcppArmadillo.bib‎

Lines changed: 79 additions & 63 deletions
Original file line numberDiff line numberDiff line change
@@ -73,8 +73,8 @@ @Book{Chambers:2008:SoDA
7373
@Manual{CRAN:Matrix,
7474
title = {\pkg{Matrix}: Sparse and Dense Matrix Classes and Methods},
7575
author = {Douglas Bates and Martin Maechler and Mikael Jagan},
76-
year = {2024},
77-
note = {R package version 1.7-1},
76+
year = {2026},
77+
note = {R package version 1.7-5},
7878
doi = DOI # "Matrix",
7979
url = CRAN # "package=Matrix"
8080
}
@@ -90,116 +90,125 @@ @Manual{CRAN:RandomFields
9090
@Manual{CRAN:RDieHarder,
9191
title = {RDieHarder: R interface to the DieHarder RNG test suite},
9292
author = {Dirk Eddelbuettel},
93-
year = 2012,
94-
note = {R package version 0.1.2},
93+
year = 2025,
94+
note = {R package version 0.2.7},
9595
url = CRAN # "package=RDieHarder"
9696
}
9797

9898
@Manual{CRAN:RInside,
9999
title = {RInside: C++ classes to embed R in C++ applications},
100100
author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
101-
year = 2012,
102-
note = {R package version 0.2.6},
101+
year = 2025,
102+
note = {R package version 0.2.19},
103103
url = CRAN # "package=RInside"
104104
}
105105

106106
@Manual{CRAN:RProtoBuf,
107107
title = {RProtoBuf: R Interface to the Protocol Buffers API},
108-
author = {Romain Fran\c{c}ois and Dirk Eddelbuettel},
109-
year = 2011,
110-
note = {R package version 0.2.3},
111-
url = CRAN # "package=RProtoBuf"
108+
author = {Romain Fran\c{c}ois and Dirk Eddelbuettel and Murray Stokely and Jeroen Ooms},
109+
year = 2025,
110+
note = {R package version 0.4.24},
111+
oldurl = CRAN # "package=RProtoBuf",
112+
doi = DOI # "RProtoBuf"
112113
}
113114

114115
@Manual{CRAN:RQuantLib,
115-
title = {RQuantLib: {R} interface to the {QuantLib} library},
116-
author = {Dirk Eddelbuettel and Khanh Nguyen},
117-
year = 2011,
118-
note = {R package version 0.3.8},
119-
url = CRAN # "package=RQuantLib"
116+
title = {RQuantLib: {R} Interface to the {QuantLib} Library},
117+
author = {Dirk Eddelbuettel and Khanh Nguyen and Terry Leitch},
118+
year = 2025,
119+
note = {R package version 0.4.26},
120+
oldurl = CRAN # "package=RQuantLib",
121+
doi = DOI # "RQuantLib"
120122
}
121123

122124
@Manual{CRAN:Rcpp,
123-
title = {Rcpp: Seamless R and C++ Integration},
124-
author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
125-
year = 2012,
126-
note = {R package version 0.10.2},
127-
url = CRAN # "package=Rcpp"
125+
title = {{Rcpp}: Seamless {R} and {C++} Integration},
126+
author = {Dirk Eddelbuettel and Romain Fran\c{c}ois and JJ
127+
Allaire and Kevin Ushey and Qiang Kou and
128+
Nathan Russel and John Chambers and Douglas Bates},
129+
year = 2026,
130+
note = {{R} package version 1.1.1},
131+
oldurl = CRAN # "package=Rcpp",
132+
doi = DOI # "Rcpp"
128133
}
129134

130135
@Manual{CRAN:RcppArmadillo,
131136
title = {\pkg{RcppArmadillo}: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library},
132-
author = {Dirk Eddelbuettel and Romain Francois and Doug Bates and Binxiang Ni and Conrad Sanderson},
133-
year = {2024},
134-
note = {R package version 14.2.2-1},
137+
author = {Dirk Eddelbuettel and Romain Fran\c{c}ois and Doug Bates and Binxiang Ni and Conrad Sanderson},
138+
year = {2026},
139+
note = {{R} package version 15.2.4-1},
135140
doi = DOI # "RcppArmadillo",
136-
url = CRAN # "package=RcppArmadillo"
141+
oldurl = CRAN # "package=RcppArmadillo"
137142
}
138143

139144
@Manual{CRAN:RcppBDT,
140145
title = {RcppBDT: Rcpp binding for the Boost Date\_Time library},
141146
author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
142-
year = 2011,
143-
note = {R package version 0.1.0},
147+
year = 2026,
148+
note = {R package version 0.2.8},
144149
url = CRAN # "package=RcppBDT"
145150
}
146151

147152
@Manual{CRAN:RcppClassic,
148153
title = {RcppClassic: Deprecated 'classic' Rcpp API},
149154
author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
150-
year = 2011,
151-
note = {R package version 0.9.1},
155+
year = 2026,
156+
note = {R package version 0.9.14},
152157
url = CRAN # "package=RcppClassic"
153158
}
154159

155160
@Manual{CRAN:RcppDE,
156161
title = {RcppDE: Global optimization by differential evolution in C++},
157162
author = {Dirk Eddelbuettel},
158-
year = 2012,
159-
note = {R package version 0.1.1},
163+
year = 2026,
164+
note = {R package version 0.1.9},
160165
url = CRAN # "package=RcppDE"
161166
}
162167

163168
@Manual{CRAN:RcppEigen,
164-
title = {RcppEigen: Rcpp integration for the Eigen templated linear
165-
algebra library},
166-
author = {Douglas Bates and Romain Fran\c{c}ois and Dirk Eddelbuettel},
167-
year = 2012,
168-
note = {R package version 0.2.0},
169-
url = CRAN # "package=RcppEigen"
169+
title = {RcppEigen: Rcpp Integration for the Eigen Templated Linear
170+
Algebra Library},
171+
author = {Douglas Bates and Dirk Eddelbuettel and Romain Fran\c{c}ois and Yixuan Qiu},
172+
year = 2024,
173+
note = {{R} package version 0.3.4.0.2},
174+
oldurl = CRAN # "package=RcppEigen",
175+
doi = DOI # "RcppEigen"
170176
}
171177

172178
@Manual{CRAN:RcppExamples,
173179
title = {RcppExamples: Examples using {Rcpp} to interface {R}
174180
and {C++}},
175181
author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
176-
year = 2011,
177-
note = {R package version 0.1.3},
178-
url = CRAN # "package=RcppExamples"
182+
year = 2025,
183+
note = {R package version 0.1.10},
184+
oldurl = CRAN # "package=RcppExamples",
185+
doi = DOI # "RcppExamples"
179186
}
180187

181188
@Manual{CRAN:RcppGSL,
182-
title = {RcppGSL: Rcpp integration for GNU GSL vectors and matrices},
183-
author = {Romain Fran\c{c}ois and Dirk Eddelbuettel},
184-
year = 2010,
185-
note = {R package version 0.1.0},
186-
url = CRAN # "package=RcppGSL"
189+
title = {RcppGSL: Rcpp Integration for GNU GSL Vectors and Matrices},
190+
author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
191+
year = 2026,
192+
note = {R package version 0.3.14},
193+
oldurl = CRAN # "package=RcppGSL",
194+
doi = DOI # "RcppGSL"
187195
}
188196

189197
@Manual{CRAN:Rserve,
190198
title = {Rserve: Binary R server},
191199
author = {Simon Urbanek},
192-
year = 2012,
193-
note = {R package version 0.6-8},
200+
year = 2026,
201+
note = {R package version 1.8-19},
194202
url = CRAN # "package=Rserve"
195203
}
196204

197205
@Manual{CRAN:rbenchmark,
198-
title = {rbenchmark: Benchmarking routine for R},
199-
author = {Wacek Kusnierczyk},
200-
year = 2010,
201-
note = {R package version 0.3},
202-
url = CRAN # "package=rbenchmark"
206+
title = {rbenchmark: Benchmarking routine for R},
207+
author = {Wacek Kusnierczyk},
208+
year = {2012},
209+
note = {R package version 1.0.0},
210+
url = {https://CRAN.R-project.org/package=rbenchmark},
211+
doi = {10.32614/CRAN.package.rbenchmark},
203212
}
204213

205214
@Manual{CRAN:rdyncall,
@@ -236,13 +245,14 @@ @Manual{CRAN:highlight
236245
}
237246

238247
@Manual{CRAN:inline,
239-
title = {inline: Inline C, C++, Fortran function calls from
240-
R},
241-
author = {Oleg Sklyar and Duncan Murdoch and Mike Smith and
242-
Dirk Eddelbuettel and Romain Fran\c{c}ois},
243-
year = 2012,
244-
note = {R package version 0.3.10},
245-
url = CRAN # "package=inline"
248+
title = {inline: Functions to Inline C, C++, Fortran Function
249+
Calls from R},
250+
author = {Oleg Sklyar and Dirk Eddelbuettel and Romain
251+
Francois},
252+
year = {2025},
253+
note = {{R} package version 0.3.21},
254+
oldurl = {https://CRAN.R-project.org/package=inline},
255+
doi = {10.32614/CRAN.package.inline},
246256
}
247257

248258
@Manual{CRAN:minqa,
@@ -272,7 +282,7 @@ @Article{Eddelbuettel+Sanderson:2014:RcppArmadillo
272282
month = {March},
273283
pages = {1054--1063},
274284
doi = {10.1016/j.csda.2013.02.005},
275-
url = {http://dx.doi.org/10.1016/j.csda.2013.02.005}
285+
oldurl = {http://dx.doi.org/10.1016/j.csda.2013.02.005}
276286
}
277287

278288
@Article{Eddelbuettel+Francois:2011:Rcpp,
@@ -284,6 +294,7 @@ @Article{Eddelbuettel+Francois:2011:Rcpp
284294
number = 8,
285295
pages = {1--18},
286296
url = {http://www.jstatsoft.org/v40/i08/},
297+
doi = {10.18637/jss.v040.i08}
287298
}
288299

289300
@Book{Eddelbuettel:2013:Rcpp,
@@ -292,7 +303,8 @@ @Book{Eddelbuettel:2013:Rcpp
292303
publisher = {Springer},
293304
year = 2013,
294305
address = {New York},
295-
isbn = {978-1-4614-6867-7}
306+
isbn = {978-1-4614-6867-7},
307+
doi = {10.1007/978-1-4614-6868-4}
296308
}
297309

298310
@Article{Gropp+Lusk+Doss+Skjellum:1996:MPI,
@@ -431,6 +443,7 @@ @manual{R:Internals
431443
year = 2012,
432444
title = "R internals",
433445
note = {{ISBN} 3-900051-14-3},
446+
doi = "10.32614/R.manuals",
434447
url = manuals # "R-ints.html"
435448
}
436449

@@ -440,9 +453,10 @@ @manual{R:Main
440453
author = RCoreTeam,
441454
organization = RFoundation,
442455
address = {Vienna, Austria},
443-
year = 2012,
456+
year = 2026,
444457
note = {{ISBN} 3-900051-07-0},
445-
url = {http://www.R-project.org/},
458+
doi = "10.32614/R.manuals",
459+
oldurl = {http://www.R-project.org/},
446460
}
447461

448462
@manual{R:Language,
@@ -452,6 +466,7 @@ @manual{R:Language
452466
year = 2012,
453467
title = "R language",
454468
note = {{ISBN} 3-900051-13-5},
469+
doi = "10.32614/R.manuals",
455470
url = manuals # "R-lang.html"
456471
}
457472

@@ -536,7 +551,8 @@ @article{Tusell:2010:Kalman
536551
number = 2,
537552
pages = "1--27",
538553
year = 2011,
539-
URL = "http://www.jstatsoft.org/v39/i02"
554+
oldurl = "http://www.jstatsoft.org/v39/i02",
555+
doi = {10.18637/jss.v039.i02}
540556
}
541557

542558
@InProceedings{Urbanek:2003:Rserve,

0 commit comments

Comments
 (0)