geobosh / rdpack Goto Github PK

The attached zip file contains an RStudio notebook file illustrating the error.

If I remove the url field from the bibtex entry, get_bibentries works without a problem, so it looks to me like there is a parsing problem with URLs (perhaps when % encoded characters are present?)

test.zip

Hi Dr. Boshnakov (@GeoBosh),

Thank you for creating such a wonderful package. I'm currently trying to
use Rdpack in the roxygen2 comments for a function in an R package I'm writing.
I encounter an error in using the package (I'm a first time user of this package).
Here is the branch with errors for your reference. Here is the R CMD check warning message.

Error Details

I am encountering the following error when trying to view the rendered documentation:

> Rdpack::viewRd("./man/comp_sandwich_qr_var.Rd", type = "html")
Warning messages:
1: In safe_cite(keys, bibs, textual = textual, before = before, after = after,  :
  possibly non-existing or duplicated key(s) in bib file from package 'Rdpack':
    white1980usinglsapproxunknownregfuncs

2: In safe_cite(keys, bibs, textual = textual, before = before, after = after,  :
  possibly non-existing or duplicated key(s) in bib file from package 'Rdpack':
    white1980heteroskedasticconsistentcovest

3: In safe_cite(key, bibs, textual = textual, bibpunct = bibpunct,  :
  possibly non-existing or duplicated key(s) in bib file from package 'Rdpack':
    buja2019modelsasapproximationspart1

4: In safe_cite(key, bibs, textual = textual, bibpunct = bibpunct,  :
  possibly non-existing or duplicated key(s) in bib file from package 'Rdpack':
    buja2019modelsasapproximationspart2

5: In safe_cite(keys, bibs, textual = textual, before = before, after = after,  :
  possibly non-existing or duplicated key(s) in bib file from package 'Rdpack':
    white1980usinglsapproxunknownregfuncs

6: In safe_cite(keys, bibs, textual = textual, before = before, after = after,  :
  possibly non-existing or duplicated key(s) in bib file from package 'Rdpack':
    white1980heteroskedasticconsistentcovest

7: In safe_cite(key, bibs, textual = textual, bibpunct = bibpunct,  :
  possibly non-existing or duplicated key(s) in bib file from package 'Rdpack':
    buja2019modelsasapproximationspart1

8: In safe_cite(key, bibs, textual = textual, bibpunct = bibpunct,  :
  possibly non-existing or duplicated key(s) in bib file from package 'Rdpack':
    buja2019modelsasapproximationspart2

Session Info

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] maar_0.1.0     testthat_3.0.0

loaded via a namespace (and not attached):
 [1] pkgload_1.1.0     tidyr_1.1.2       Rdpack_2.1       
 [4] assertthat_0.2.1  profmem_0.5.0     vipor_0.4.5      
 [7] yaml_2.2.1        remotes_2.2.0     sessioninfo_1.1.1
[10] pillar_1.4.6      backports_1.2.0   lattice_0.20-41  
[13] glue_1.4.1.9000   digest_0.6.27     rbibutils_2.0    
[16] colorspace_2.0-0  sandwich_3.0-0    htmltools_0.5.0  
[19] Matrix_1.2-18     pkgconfig_2.0.3   devtools_2.3.0   
[22] broom_0.7.2       bench_1.1.1       purrr_0.3.4      
[25] scales_1.1.1      processx_3.4.4    tibble_3.0.4     
[28] generics_0.1.0    farver_2.0.3      ggplot2_3.3.2    
[31] usethis_1.6.1     ellipsis_0.3.1    withr_2.3.0      
[34] cli_2.1.0         magrittr_1.5      crayon_1.3.4     
[37] memoise_1.1.0     evaluate_0.14     ps_1.4.0         
[40] fs_1.5.0          fansi_0.4.1       MASS_7.3-51.6    
[43] xml2_1.3.2        beeswarm_0.2.3    pkgbuild_1.1.0   
[46] tools_4.0.2       prettyunits_1.1.1 gbRd_0.4-11      
[49] lifecycle_0.2.0   stringr_1.4.0     munsell_0.5.0    
[52] callr_3.5.1       compiler_4.0.2    rlang_0.4.8      
[55] grid_4.0.2        rstudioapi_0.13   rmarkdown_2.5    
[58] gtable_0.3.0      roxygen2_7.1.1    R6_2.5.0         
[61] zoo_1.8-8         knitr_1.30        dplyr_1.0.2      
[64] utf8_1.1.4        commonmark_1.7    rprojroot_2.0.2  
[67] desc_1.2.0        stringi_1.5.3     ggbeeswarm_0.6.0 
[70] Rcpp_1.0.5        vctrs_0.3.4       tidyselect_1.1.0 
[73] xfun_0.19 

Setup

I've done the following to ensure that Rdpack is setup correctly in our R pacakge.

1. Added Rdpack to imports as follows:

   CLICK ME

   Imports: 
       magrittr,
       rlang (>= 0.1.2),
       broom,
       Matrix,
       sandwich,
       bench,
       Rdpack
   Suggests: 
       spelling,
       testthat,
       roxygen2,
       covr
   RdMacros: Rdpack
   

2. Created a inst/REFERENCES.bib file which contains the following contents:

   CLICK ME

   @article{buja2019modelsasapproximationspart1,
     author	= {Buja, Andreas and Brown, Lawrence and Berk, Richard and
   		  George, Edward and Pitkin, Emil and Traskin, Mikhail and
   		  Zhang, Kai and Zhao, Linda},
     title		= {Models as approximations {I}: consequences illustrated
   		  with linear regression},
     journal	= {Statist. Sci.},
     fjournal	= {Statistical Science. A Review Journal of the Institute of
   		  Mathematical Statistics},
     volume	= {34},
     year		= {2019},
     number	= {4},
     pages		= {523--544},
     issn		= {0883-4237},
     mrclass	= {62J05 (62F12 62F35 62H12 62J02)},
     mrnumber	= {4048582},
     doi		= {10.1214/18-STS693}
   }
   
   @article{buja2019modelsasapproximationspart2,
     author	= {Buja, Andreas and Brown, Lawrence and Kuchibhotla, Arun
   		  Kumar and Berk, Richard and George, Edward and Zhao,
   		  Linda},
     title		= {Models as approximations {II}: {A} model-free theory of
   		  parametric regression},
     journal	= {Statist. Sci.},
     fjournal	= {Statistical Science. A Review Journal of the Institute of
   		  Mathematical Statistics},
     volume	= {34},
     year		= {2019},
     number	= {4},
     pages		= {545--565},
     issn		= {0883-4237},
     mrclass	= {62J05 (62F40 62G05 62J20)},
     mrnumber	= {4048583},
     doi		= {10.1214/18-STS694}
   }
   
   @article{white1980heteroskedasticconsistentcovest,
     author	= {White, Halbert},
     title		= {A heteroskedasticity-consistent covariance matrix
   		  estimator and a direct test for heteroskedasticity},
     journal	= {Econometrica},
     fjournal	= {Econometrica. Journal of the Econometric Society},
     volume	= {48},
     year		= {1980},
     number	= {4},
     pages		= {817--838},
     issn		= {0012-9682},
     mrclass	= {62J05 (62G10)},
     mrnumber	= {575027},
     mrreviewer	= {Norbert Christopeit},
     doi		= {10.2307/1912934}
   }
   
   @article{white1980usinglsapproxunknownregfuncs,
     author	= {White, Halbert},
     title		= {Using least squares to approximate unknown regression
   		  functions},
     journal	= {Internat. Econom. Rev.},
     fjournal	= {International Economic Review},
     volume	= {21},
     year		= {1980},
     number	= {1},
     pages		= {149--170},
     issn		= {0020-6598},
     mrclass	= {62J02 (62P20)},
     mrnumber	= {572464},
     mrreviewer	= {V. K. Srivastava},
     doi		= {10.2307/2526245}
   }
   

3. Added importFrom(Rdpack,reprompt) to the NAMESPACE file

4. Wrote an roxygen2 file with the following roxygen2 comment

   CLICK ME

   #' Compute the White sandwich estimator of standard errors for
   #' ordinary least squares (OLS) regression. This is based on the series of
   #' papers \insertCite{white1980usinglsapproxunknownregfuncs}{Rdpack} and
   #' \insertCite{white1980heteroskedasticconsistentcovest}{Rdpack}. For more details
   #' \insertCite{@see also @buja2019modelsasapproximationspart1 and @buja2019modelsasapproximationspart2;textual}{Rdpack}
   #'
   #' @param lm_object (lm) : lm object
   #'
   #' @return (matrix) : White sandwich estimator of variance for OLS regression
   #' @export
   #'
   #' @importFrom Rdpack reprompt
   #' @references
   #'     \insertAllCited{}
   #' @examples
   #' \dontrun{
   #' n <- 1e5
   #' X <- stats::rnorm(n, 0, 1)
   #' y <- 2 + X * 1 + stats::rnorm(n, 0, 10)
   #' lm_fit <- stats::lm(y ~ X)
   #' sandwich_qr_var <- comp_sandwich_qr_var(lm_fit)
   #' }

5. Final rendered the package documentation using devtools::document() which doesn't throw any error, but Rdpack::viewRd("./man/comp_sandwich_qr_var.Rd", type = "html") throws the warnings above. The BibTeX references are also not being rendered in the html file.

Could I please get assistance with resolving the issue? I'm not sure what I'm doing wrong here.

I cannot install Rdpack, and am getting the following output

install.packages("Rdpack")
Installing package into ‘/home/d.bernstein/R/x86_64-redhat-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/Rdpack_0.11-1.tar.gz'
Content type 'unknown' length 693897 bytes (677 KB)
==================================================
downloaded 677 KB

• installing source package ‘Rdpack’ ...
  ** package ‘Rdpack’ successfully unpacked and MD5 sums checked
  ** R
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  converting help for package ‘Rdpack’
  finding HTML links ... done
  RStudio_reprompt html
  Rd_combo html
  Rdapply html
  Rdo2Rdf html
  Rdo_append_argument html
  Rdo_collect_metadata html
  Rdo_empty_sections html
  Rdo_fetch html
  Rdo_flatinsert html
  Rdo_get_argument_names html
  Rdo_get_insert_pos html
  Rdo_get_item_labels html
  Rdo_insert html
  Rdo_insert_element html
  Rdo_is_newline html
  Rdo_locate html
  Rdo_locate_leaves html
  Rdo_macro html
  Rdo_modify html
  Rdo_modify_simple html
  Rdo_piecetag html
  Rdo_remove_srcref html
  Rdo_reparse html
  Rdo_sections html
  Rdo_set_section html
  Rdo_show html
  Rdo_tag html
  Rdo_tags html
  Rdo_which html
  Rdpack-package html

Error: argument is of length zero

• removing ‘/home/d.bernstein/R/x86_64-redhat-linux-gnu-library/3.3/Rdpack’
  Warning in install.packages :
  installation of package ‘Rdpack’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmp6RfIXR/downloaded_packages’

Recently (beginning of June 2022) warnings like Escaped LaTeX specials: \& started to appear in Rd files containing such escaped characters in the documentation files. It is sufficient to remove the offending backslashes if they are directly in the Rd or roxygen2 documentation.

These escapes are however correct syntax in bib files. Removing the backslashes from the bib file works but it is annoying and renders such bib entries incorrect for use in LaTeX.

Rdpack v2.3.1.9000 uploaded here today contains a fix which removes superfluous \ (backslashes), if present.

Please test and report comments any problems. It is entirely possible that there are undesired side effects, such as removing backslashes when they are really needed. In such cases, if possible, please include an example with a complete bibentry along with explanation of what went wrong.

Many thanks for this hugely useful package. This is a question I fear may be annoying, given the amount of work you and others put into this tool and those it relies on, so apologies in advance. I have recently cleaned by bibliography databases and, in the process, converted them to biblatex/biber format. As a concsequence, Rdpack (or, as I suspect, bibtex) does not recognise some entry types. Recoding the databases is not big deal, but I am wondering all the same if adding support for biber would require substantial recodign/redesign? I suspect the answer is yes, but wanted to ask.

Best regards

Markus Jantti

Thanks for this fantastic package. I have started integrating it in one of my packages but I find the syntax for the various citation commands a bit too complicated. Would it be possible to create commands using the same syntax as natbib? http://texdoc.net/texmf-dist/doc/latex/natbib/natnotes.pdf

These are quite mnemonic and widely used commands (in LaTeX), at least the \citep \citet variants.

\insertCite{Smith2019;textual}{Quartet}. renders a breaking whitespace between the citation and the ensuing full stop. (This can be particularly ugly where the full stop wraps onto the following line.)

Potentially related, if less obviously an error, is the addition of a space after DOIs in rendered citations (but not after URLs, or other endings of a citation):

Not sure whether this is an Rdpack issue, or something further downstream?

This may sound too ambitious -- but it will be great there is support for Citation Style Language (CSL) (https://citationstyles.org/), which is possible in package vignettes through a unified REFERENCES.bib.

A side effect of Rd is that citations will be duplicated which will make the package considerably closer to the 5MB ceiling for CRAN; hope R could be smarter with citations.

By all means thanks for the excellent work.

This is to announce that version 2.0 of Rdpack will almost certainly use package rbibutils to import BibTeX files.

The change should be transparent to packages. At the time of writing this, all reverse dependencies of Rdpack on CRAN and Bioconductor pass the checks as before. The exception is that now warnings are issued if there are duplicated keys in REFERENCES.bib, which seems the right thing to do. This affected three packages.

Hi, I'm not sure whether this question is properly directed at Rdpack. In my inst file, I have a following entry
@article{example, title = {A new method to simulate the {Bingham} and related distributions in directional data analysis with applications}, journal = {arXiv:1310.8110 [math, stat]}, author = {Kent, John T. and Ganeiber, Asaad M. and Mardia, Kanti V.}, month = oct, year = {2013}, note = {arXiv: 1310.8110}, }
and Rdpack generates the following entry in my Rd file
Kent JT, Ganeiber AM, Mardia KV (2013). “A new method to simulate the Bingham and related distributions in directional data analysis with applications.” arXiv:1310.8110 [math, stat]. 1310.8110, http://arxiv.org/abs/1310.8110..

When submitting a package to CRAN, however, this is accepted as a note with a message that arxiv entry needs to be accompanied with https, not http. So I was wondering if this can be handled at Rdpack level to give a manual url.

I added some citation macros. As insertRef, they all work in both Rd and roxygen2 documentation.The help page of insert_ref gives some information and examples. Some features are under development.

Feedback and comments will be highly valuable.

Here is the entry from the NEWS file:

• new Rd macros for citations, see below.

• new Rd macro \insertCite inserts citation(s) for one or more keys and
  records the keys for \insertAllCited (see below).

• new Rd macro \insertCiteOnly is similar to \insertCite but does not record
  the keys.

• \insertNoCite records the keys but does not produce a citation.

• \insertAllCited prints a bibliography including all references recorded by
  \insertAllCited and \insertNoCite.

Hi Dr. Boshnakov,

After the recent update, newer builds with {devtools::build()} and {R CMD INSTALL} show the message that never appeared before

genre {PhD} {Thesis} is currently unknown to bibConvert; using Misc instead

I see no reason why such a parsing issue message occurs considering the REFERENCES.bib file has no item under item type of 'Thesis' at all. As in your troubleshooting note, it still compiles and all the messages are appearing. However, due to that message that repeatedly appears, it's quite slowing down the entire build time. Thanks for your time in advance and as always I appreciate your efforts in building and developing this wonderful package.

@incollection{LopPaqStu09emaa,
  editor = { Thomas Bartz-Beielstein  and  Marco Chiarandini  and  Lu{\'i}s Paquete  and  Mike Preuss },
  year = 2010,
  address = {Berlin, Germany},
  publisher = {Springer},
  booktitle = {Experimental Methods for the Analysis of
                  Optimization Algorithms},
  author = { Manuel L{\'o}pez-Ib{\'a}{\~n}ez  and  Lu{\'i}s Paquete  and  Thomas St{\"u}tzle },
  title = {Exploratory Analysis of Stochastic Local Search
                  Algorithms in Biobjective Optimization},
  pages = {209--222},
  doi = {10.1007/978-3-642-02538-9_9},
 }

The above gets rendered as:

Manuel López-Ibáñez, Lu'is Paquete and Thomas Stützle (2010). “Exploratory Analysis of Stochastic Local Search Algorithms in Biobjective Optimization.” In Thomas Bartz-Beielstein, Marco Chiarandini, Lu'is Paquete and Mike Preuss (eds.), Experimental Methods for the Analysis of Optimization Algorithms, pp. 209–222. Springer, Berlin, Germany. doi: 10.1007/978-3-642-02538-9_9.

Thank you for the nice package. I am trying to follow the same steps on GitHub. However, the references I generated on the R help page are different. Do you know why?

The reference part shows \Sexpr[results=rd,stage=build]{Rdpack::insert_ref(key=" xxx",package="xxx")} not the reference format I expected.

Feature request

A provision to insert citation using a syntax similar to latex and rmarkdown.

For example the following code in the roxygen2 documentation

Blah blah [see @doe99, pp. 33-35; also @smith04, ch. 1].

Blah blah [@doe99, pp. 33-35, 38-39 and *passim*].

Blah blah [@smith04; @doe99].

will add the relevant rdpack syntax (\insertRef{dow99}{package}, \insertRef{smith04}{package}) to the @references tag to be processed as a bibliography list by rdpack and roxygen2.

In help files Rdpack will automatically configure author to an abbreviated style, for example:
Boshnakov GN (2018) Rdpack: Update and Manipulate Rd Documentation Objects.
A useful feature would be the ability to change this style as is possible in LaTeX. Using again the example above, a common citation style would include the author's first name:
Georgi N. Boshnakov (2018) Rdpack: Update and Manipulate Rd Documentation Objects.

In R6 documentation, both the class and methods are documented using all usual roxygen tags but only the description and details tags can be different for the class and the methods. As such, citations in method description field are listed in the class reference section only and actually not discovered at class level since cited at method level.

First off, thanks for this very useful package!

As stated in the title, I'm having a problem with the encoding of special characters on windows. I read the corresponding part of the readme, but did not manage to solve this issue without modifying the Rdpack package itself (or maybe by switching everything to native encoding, but I'd like to avoid that).

My setup is

• windows 10
• R v4.1.0
• Manual install of Rdpack from the master branch of this repo (though I had the same problems with the CRAN version)
• Local package-project where all files are encoded as UTF-8 (DESCRIPTION, R-files, Rd-files, bibliography) and I have specified this in the DESCRIPTION file.

If I try to cite bibliography entries containing special characters (German umlauts most of the time), they do not show up correctly in the output. A minimal example producing this issue for me would be for example:

\insertRef{DiaLop2020ejor}{Rdpack}

Below is a more detailed example .Rd illustrating this behavior, and the corresponding HTML produced when installing the package. It seems to me that the output of \Sexpr is always expected to have native encoding (i.e. latin1 on my machine) and e.g. \InsertRef produces strings that are UTF-8 encoded. Wrapping the corresponding R functions in enc2native seems to fix the issue.

Content of an .Rd file:

\name{someTest}
\alias{someTest}
\title{Encoding Test}

\section{Trying to write the umlaut oe:}{
    \describe{
        \item{Normal Rd:}{ö}
        \item{\code{\\Sexpr}:}{\Sexpr[results=rd,stage=build]{("ö")}}
        \item{Encoding in \code{\\Sexpr:}}{\Sexpr[results=rd,stage=build]{Encoding("ö")}}
        \item{\code{\\Sexpr} with \code{enc2utf8}}{\Sexpr[results=rd,stage=build]{enc2utf8("ö")}}
        \item{\code{\\Sexpr} with \code{enc2native}}{\Sexpr[results=rd,stage=build]{enc2native("ö")}}
    }
}

\section{Trying to cite something:}{
    \describe{
        \item{\code{\\insertRef}:}{\insertRef{DiaLop2020ejor}{Rdpack}}
        \item{\code{\\Sexpr}:}{\Sexpr[results=rd,stage=build]{Rdpack::insert_all_ref(t(c('DiaLop2020ejor', 'Rdpack')))}}
        \item{Encoding in \code{\\Sexpr}:}{\Sexpr[results=rd,stage=build]{Encoding(Rdpack::insert_all_ref(t(c('DiaLop2020ejor', 'Rdpack'))))}}
        \item{\code{\\Sexpr} with \code{enc2native}:}{\Sexpr[results=rd,stage=build]{enc2native(Rdpack::insert_all_ref(t(c('DiaLop2020ejor', 'Rdpack'))))}}
    }
}

Screenshot of the rendered help page:

HTML generated by R CMD INSTALL --html .

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: Encoding Test</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link rel="stylesheet" type="text/css" href="R.css" />
</head><body>

<table width="100%" summary="page for someTest {SomePackage}"><tr><td>someTest {SomePackage}</td><td style="text-align: right;">R Documentation</td></tr></table>

<h2>Encoding Test</h2>

<h3>Trying to write the umlaut oe:</h3>


<dl>
<dt>Normal Rd:</dt><dd><p>ö</p>
</dd>
<dt><code>\Sexpr</code>:</dt><dd><p>ö</p>
</dd>
<dt>Encoding in <code>\Sexpr:</code></dt><dd><p>latin1</p>
</dd>
<dt><code>\Sexpr</code> with <code>enc2utf8</code></dt><dd><p>ö</p>
</dd>
<dt><code>\Sexpr</code> with <code>enc2native</code></dt><dd><p>ö</p>
</dd>
</dl>



<h3>Trying to cite something:</h3>


<dl>
<dt><code>\insertRef</code>:</dt><dd><p>Juan
Esteban Diaz, Manuel López-Ibáñez (2021).
&ldquo;Incorporating Decision-Maker's Preferences into the Automatic Configuration of Bi-Objective Optimisation Algorithms.&rdquo;
<em>European Journal of Operational Research</em>, <b>289</b>(3), 1209&ndash;1222.
doi: <a href="https://doi.org/10.1016/j.ejor.2020.07.059">10.1016/j.ejor.2020.07.059</a>.</p>
</dd>
<dt><code>\Sexpr</code>:</dt><dd><p>Juan
Esteban Diaz, Manuel López-Ibáñez (2021).
&ldquo;Incorporating Decision-Maker's Preferences into the Automatic Configuration of Bi-Objective Optimisation Algorithms.&rdquo;
<em>European Journal of Operational Research</em>, <b>289</b>(3), 1209&ndash;1222.
doi: <a href="https://doi.org/10.1016/j.ejor.2020.07.059">10.1016/j.ejor.2020.07.059</a>.</p>
</dd>
<dt>Encoding in <code>\Sexpr</code>:</dt><dd><p>UTF-8</p>
</dd>
<dt><code>\Sexpr</code> with <code>enc2native</code>:</dt><dd><p>Juan
Esteban Diaz, Manuel López-Ibáñez (2021).
&ldquo;Incorporating Decision-Maker's Preferences into the Automatic Configuration of Bi-Objective Optimisation Algorithms.&rdquo;
<em>European Journal of Operational Research</em>, <b>289</b>(3), 1209&ndash;1222.
doi: <a href="https://doi.org/10.1016/j.ejor.2020.07.059">10.1016/j.ejor.2020.07.059</a>.</p>
</dd>
</dl>


<hr /><div style="text-align: center;">[Package <em>SomePackage</em> version 5.5.110 <a href="00Index.html">Index</a>]</div>
</body></html>

When I attempt to include markdown-formatted italic text in a textual citation, my documentation object appears as "Internal Server Error"

Non-italic

\insertCite{@sensu @Author2000}{MyPackage}

Successfully appears in place as "sensu Author (2000)"

Italic

\insertCite{@_sensu_ @Author2000}{MyPackage}

In the generated Rd file, this produces \insertCite{@\emph{sensu} @Steel2006}{TreeTools}, which I expect to render as "sensu Author (2000)".

Instead, the documentation page does not render; I just see a blank page reading "Internal Server Error".

If no file is open in the editor, an error is shown

Instead it should be more clear that a file is expected to be open. I didn't know what this addin is, I tried clicking it, and got this random error.

I have an R package called GUSMap that I have been developing and I have starting using Rdpack for managing my references. However, I'm finding that the first time I cite a reference, all the authors are displayed (this happens in this file). Can Rdpack be forced to convert intext citations to et al when there are more than 3 authors?

Thanks.

When building the package, I get the following warnings:

• installing the package to process help pages
  Warning in parseLatex(x) : x:1: unexpected '}'
  Loading required namespace: eaf
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:2: unexpected '}'
  Warning in parseLatex(x) : x:2: unexpected '}'
  Warning in parse_Rd(tmpcon, fragment = TRUE, macros = macros) :
  :2: unknown macro '\nGrunert'
  Warning in parse_Rd(tmpcon, fragment = TRUE, macros = macros) :
  :2: unknown macro '\nGrunert'
  Warning in parse_Rd(tmpcon, fragment = TRUE, macros = macros) :
  :2: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'
  Warning in parseLatex(x) : x:1: unexpected '}'

The REFERENCES.bib
file appears to be correct according to bibtex itself.

Currently, the URLs generated by Rdpack for doi field are not https. This gives a message in CRAN:

URL: http://doi.org/10.1007/3-540-44719-9_15 (moved to https://doi.org/10.1007/3-540-44719-9_15)
From: man/eaf-package.Rd
Status: 200
Message: OK

Although this message is harmless, it would be nice to directly generate https links.

It looks like this issue has been partly solved before:
https://stat.ethz.ch/pipermail/r-devel/2023-November/083007.html
But I'm getting checkRd errors on Ubuntu-latest (devel) only, when using GH actions: https://github.com/mikeroswell/MeanRarity/actions/runs/7200026411/job/19613024879
Thanks!

FYI, the "A puzzling message in devtools development mode" has actually been fixed in spelling.

I am trying to use Rdpack for a pkgdown site where i have a lot of references. I can't seem to translate your instructions. I'm sure it's me but i was wondering if you could add a Rmd vignette example linking to some references in your REFERENCES.bib?

Line breaks between multiple references are missing in html documentation, when \insertAllCited{} is used. However, the line breaks appear in pdf documentation.

For example in germinationmetrics
html

Rdpack::viewRd("./man/CUGerm.Rd", type = "html")
Rdpack::viewRd("./man/FirstGermTime.Rd", type = "html")

pdf
https://github.com/aravind-j/germinationmetrics/blob/master/germinationmetrics.pdf (Page 3-5)

I'm rendering documentation in a CRAN package, using the \insertAllCited{} to generate a bibliography.

When running devtools::check_win_devel(), CRAN's pre-submission checks return a note:

Found the following URLs which should use \doi (with the DOI name only):
File 'SomeFile.Rd':
https://doi.org/10.2307/some-doi

It looks like Rdpack is generating a \url field where a \doi would do. Is this something that can be modified in the package?

Hi, I had some occasions where 'series' title appears in the compiled output when items of '@inproceedings', '@book' type articles are compiled. I wish I knew how to report an issue in a concrete manner, but I'm more than happy to cooperate in order to remove the name of a field showing up. One of such examples would be an item

@inproceedings{he_neighborhood_2005,
	address = {Washington, DC, USA},
	series = {{ICCV} '05},
	title = {Neighborhood {Preserving} {Embedding}},
	isbn = {0-7695-2334-X-02},
	url = {http://dx.doi.org/10.1109/ICCV.2005.167},
	doi = {10.1109/ICCV.2005.167},
	booktitle = {Proceedings of the {Tenth} {IEEE} {International} {Conference} on {Computer} {Vision} - {Volume} 2},
	publisher = {IEEE Computer Society},
	author = {He, Xiaofei and Cai, Deng and Yan, Shuicheng and Zhang, Hong-Jiang},
	year = {2005},
	pages = {1208--1213}
}

and the corresponding output would look like this
,

where the text 'series' appears before ICCV.

Hi @GeoBosh

It looks like the insertCite hook is using a partial argument.

I couldn't find it in the code but when testing a package with \insertCite{...}, I get the following warning:

Warning in Rdpack::insert_citeOnly(key = "wu2012camera", package = "zenith",  :
  partial argument match of 'key' to 'keys'

Best,
Marcel

As shown here: https://mlopez-ibanez.github.io/eaf/reference/whv_rect.html

Citing this entry:

@article{DiaLop2020ejor,
  author =       { Juan Esteban Diaz and Manuel L{\'o}pez-Ib{\'a}{\~n}ez },
  title =        {Incorporating Decision-Maker's Preferences into the Automatic
                  Configuration of Bi-Objective Optimisation Algorithms},
  journal =      {European Journal of Operational Research},
  year =         2021,
  volume =       289,
  number =       3,
  pages =        {1209--1222},
  doi =          {10.1016/j.ejor.2020.07.059},
}

with \insertCite{DiaLop2022ejor;textual}{eaf}renders as Diaz and López-Ibá{ñ}ez (2021) but the bibliography entry does not show those superfluous braces.

I have tried various ways to encode the name and none works.