correctly prebuild vignettes and name each code chunks (#102)

ropensci · Dec 12, 2023 · 3709fa6 · 3709fa6
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diff --git a/vignettes/.gitignore b/vignettes/.gitignore
@@ -1,2 +1 @@
 *.html
-*.R
diff --git a/vignettes/create_cran_vignettes.R b/vignettes/create_cran_vignettes.R
@@ -0,0 +1,15 @@
+# Use this to create the vignette to prevent CRAN checks from failing when
+# gitignore API is not available.
+
+# https://ropensci.org/blog/2019/12/08/precompute-vignettes/
+
+library(fs)
+
+infiles <- dir_ls("vignettes", glob = "*.orig")
+outfiles <- fs::path_ext_remove(infiles)
+
+purrr::walk2(infiles, outfiles, knitr::knit)
+
+fs::dir_delete("vignettes/figure")
+fs::dir_copy("figure", "vignettes/figure", overwrite = TRUE)
+fs::dir_delete("figure")
diff --git a/vignettes/unnamed-chunk-10-1.png → vignettes/figure/finding-data.Rmd-10-1.png b/vignettes/unnamed-chunk-10-1.png → vignettes/figure/finding-data.Rmd-10-1.png
diff --git a/vignettes/unnamed-chunk-12-1.png → vignettes/figure/finding-data.Rmd-12-1.png b/vignettes/unnamed-chunk-12-1.png → vignettes/figure/finding-data.Rmd-12-1.png
diff --git a/vignettes/unnamed-chunk-12-2.png → vignettes/figure/finding-data.Rmd-12-2.png b/vignettes/unnamed-chunk-12-2.png → vignettes/figure/finding-data.Rmd-12-2.png
diff --git a/vignettes/unnamed-chunk-12-3.png → vignettes/figure/finding-data.Rmd-12-3.png b/vignettes/unnamed-chunk-12-3.png → vignettes/figure/finding-data.Rmd-12-3.png
diff --git a/vignettes/unnamed-chunk-12-4.png → vignettes/figure/finding-data.Rmd-12-4.png b/vignettes/unnamed-chunk-12-4.png → vignettes/figure/finding-data.Rmd-12-4.png
diff --git a/vignettes/unnamed-chunk-12-5.png → vignettes/figure/finding-data.Rmd-12-5.png b/vignettes/unnamed-chunk-12-5.png → vignettes/figure/finding-data.Rmd-12-5.png
diff --git a/vignettes/unnamed-chunk-12-6.png → vignettes/figure/finding-data.Rmd-12-6.png b/vignettes/unnamed-chunk-12-6.png → vignettes/figure/finding-data.Rmd-12-6.png
diff --git a/vignettes/unnamed-chunk-12-7.png → vignettes/figure/finding-data.Rmd-12-7.png b/vignettes/unnamed-chunk-12-7.png → vignettes/figure/finding-data.Rmd-12-7.png
diff --git a/vignettes/unnamed-chunk-12-8.png → vignettes/figure/finding-data.Rmd-12-8.png b/vignettes/unnamed-chunk-12-8.png → vignettes/figure/finding-data.Rmd-12-8.png
diff --git a/vignettes/figure/finding-data.Rmd-3-1.png b/vignettes/figure/finding-data.Rmd-3-1.png
diff --git a/vignettes/figure/finding-data.Rmd-5-1.png b/vignettes/figure/finding-data.Rmd-5-1.png
diff --git a/vignettes/unnamed-chunk-7-1.png → vignettes/figure/finding-data.Rmd-7-1.png b/vignettes/unnamed-chunk-7-1.png → vignettes/figure/finding-data.Rmd-7-1.png
diff --git a/vignettes/unnamed-chunk-7-2.png → vignettes/figure/finding-data.Rmd-7-2.png b/vignettes/unnamed-chunk-7-2.png → vignettes/figure/finding-data.Rmd-7-2.png
diff --git a/vignettes/unnamed-chunk-7-3.png → vignettes/figure/finding-data.Rmd-7-3.png b/vignettes/unnamed-chunk-7-3.png → vignettes/figure/finding-data.Rmd-7-3.png
diff --git a/vignettes/unnamed-chunk-7-4.png → vignettes/figure/finding-data.Rmd-7-4.png b/vignettes/unnamed-chunk-7-4.png → vignettes/figure/finding-data.Rmd-7-4.png
diff --git a/vignettes/unnamed-chunk-7-5.png → vignettes/figure/finding-data.Rmd-7-5.png b/vignettes/unnamed-chunk-7-5.png → vignettes/figure/finding-data.Rmd-7-5.png
diff --git a/vignettes/unnamed-chunk-7-6.png → vignettes/figure/finding-data.Rmd-7-6.png b/vignettes/unnamed-chunk-7-6.png → vignettes/figure/finding-data.Rmd-7-6.png
diff --git a/vignettes/figure/language-support.Rmd-3-1.png b/vignettes/figure/language-support.Rmd-3-1.png
diff --git a/vignettes/unnamed-chunk-3-10.png → ...ttes/figure/language-support.Rmd-3-10.png b/vignettes/unnamed-chunk-3-10.png → ...ttes/figure/language-support.Rmd-3-10.png
diff --git a/vignettes/figure/language-support.Rmd-3-2.png b/vignettes/figure/language-support.Rmd-3-2.png
diff --git a/vignettes/figure/language-support.Rmd-3-3.png b/vignettes/figure/language-support.Rmd-3-3.png
diff --git a/vignettes/figure/language-support.Rmd-3-4.png b/vignettes/figure/language-support.Rmd-3-4.png
diff --git a/vignettes/figure/language-support.Rmd-3-5.png b/vignettes/figure/language-support.Rmd-3-5.png
diff --git a/vignettes/figure/language-support.Rmd-3-6.png b/vignettes/figure/language-support.Rmd-3-6.png
diff --git a/vignettes/figure/language-support.Rmd-3-7.png b/vignettes/figure/language-support.Rmd-3-7.png
diff --git a/vignettes/unnamed-chunk-3-8.png → ...ettes/figure/language-support.Rmd-3-8.png b/vignettes/unnamed-chunk-3-8.png → ...ettes/figure/language-support.Rmd-3-8.png
diff --git a/vignettes/unnamed-chunk-3-9.png → ...ettes/figure/language-support.Rmd-3-9.png b/vignettes/unnamed-chunk-3-9.png → ...ettes/figure/language-support.Rmd-3-9.png
diff --git a/vignettes/figure/rnaturalearth.Rmd-3-1.png b/vignettes/figure/rnaturalearth.Rmd-3-1.png
diff --git a/vignettes/figure/rnaturalearth.Rmd-3-2.png b/vignettes/figure/rnaturalearth.Rmd-3-2.png
diff --git a/vignettes/figure/rnaturalearth.Rmd-3-3.png b/vignettes/figure/rnaturalearth.Rmd-3-3.png
diff --git a/vignettes/figure/rnaturalearth.Rmd-3-4.png b/vignettes/figure/rnaturalearth.Rmd-3-4.png
diff --git a/vignettes/figure/rnaturalearth.Rmd-3-5.png b/vignettes/figure/rnaturalearth.Rmd-3-5.png
diff --git a/vignettes/figure/rnaturalearth.Rmd-5-1.png b/vignettes/figure/rnaturalearth.Rmd-5-1.png
diff --git a/vignettes/unnamed-chunk-3-1.png → ...ttes/figure/what-is-a-country.Rmd-3-1.png b/vignettes/unnamed-chunk-3-1.png → ...ttes/figure/what-is-a-country.Rmd-3-1.png
diff --git a/vignettes/unnamed-chunk-3-2.png → ...ttes/figure/what-is-a-country.Rmd-3-2.png b/vignettes/unnamed-chunk-3-2.png → ...ttes/figure/what-is-a-country.Rmd-3-2.png
diff --git a/vignettes/unnamed-chunk-3-3.png → ...ttes/figure/what-is-a-country.Rmd-3-3.png b/vignettes/unnamed-chunk-3-3.png → ...ttes/figure/what-is-a-country.Rmd-3-3.png
diff --git a/vignettes/figure/what-is-a-country.Rmd-3-4.png b/vignettes/figure/what-is-a-country.Rmd-3-4.png
diff --git a/vignettes/unnamed-chunk-3-5.png → ...ttes/figure/what-is-a-country.Rmd-3-5.png b/vignettes/unnamed-chunk-3-5.png → ...ttes/figure/what-is-a-country.Rmd-3-5.png
diff --git a/vignettes/unnamed-chunk-3-6.png → ...ttes/figure/what-is-a-country.Rmd-3-6.png b/vignettes/unnamed-chunk-3-6.png → ...ttes/figure/what-is-a-country.Rmd-3-6.png
diff --git a/vignettes/figure/what-is-a-country.Rmd-3-7.png b/vignettes/figure/what-is-a-country.Rmd-3-7.png
diff --git a/vignettes/unnamed-chunk-4-1.png → ...ttes/figure/what-is-a-country.Rmd-4-1.png b/vignettes/unnamed-chunk-4-1.png → ...ttes/figure/what-is-a-country.Rmd-4-1.png
diff --git a/vignettes/unnamed-chunk-4-2.png → ...ttes/figure/what-is-a-country.Rmd-4-2.png b/vignettes/unnamed-chunk-4-2.png → ...ttes/figure/what-is-a-country.Rmd-4-2.png
diff --git a/vignettes/unnamed-chunk-4-3.png → ...ttes/figure/what-is-a-country.Rmd-4-3.png b/vignettes/unnamed-chunk-4-3.png → ...ttes/figure/what-is-a-country.Rmd-4-3.png
diff --git a/vignettes/unnamed-chunk-5-1.png → ...ttes/figure/what-is-a-country.Rmd-5-1.png b/vignettes/unnamed-chunk-5-1.png → ...ttes/figure/what-is-a-country.Rmd-5-1.png
diff --git a/vignettes/unnamed-chunk-5-2.png → ...ttes/figure/what-is-a-country.Rmd-5-2.png b/vignettes/unnamed-chunk-5-2.png → ...ttes/figure/what-is-a-country.Rmd-5-2.png
diff --git a/vignettes/unnamed-chunk-5-3.png → ...ttes/figure/what-is-a-country.Rmd-5-3.png b/vignettes/unnamed-chunk-5-3.png → ...ttes/figure/what-is-a-country.Rmd-5-3.png
diff --git a/vignettes/unnamed-chunk-5-4.png → ...ttes/figure/what-is-a-country.Rmd-5-4.png b/vignettes/unnamed-chunk-5-4.png → ...ttes/figure/what-is-a-country.Rmd-5-4.png
diff --git a/vignettes/finding-data.Rmd b/vignettes/finding-data.Rmd
@@ -92,7 +92,7 @@ plot(
 #> Geodetic CRS:  WGS 84
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-1.png)
+![](figure/finding-data.Rmd-3-1.png)
 
 ### Cultural vector data
 
@@ -178,7 +178,7 @@ plot(
 #> Geodetic CRS:  WGS 84
 ```
 
-![plot of chunk unnamed-chunk-5](figure/unnamed-chunk-5-1.png)
+![](figure/finding-data.Rmd-5-1.png)
 
 ## Searching for countries and continents
 
@@ -196,18 +196,18 @@ head(df)
 #> Bounding box:  xmin: -109.4537 ymin: -55.9185 xmax: 140.9776 ymax: 7.35578
 #> Geodetic CRS:  WGS 84
 #> # A tibble: 6 × 169
-#>   featurecla   scalerank LABELRANK SOVEREIGNT SOV_A3 ADM0_DIF
-#>   <chr>            <int>     <int> <chr>      <chr>     <int>
-#> 1 Admin-0 sov…         5         2 Indonesia  IDN           0
-#> 2 Admin-0 sov…         5         3 Malaysia   MYS           0
-#> 3 Admin-0 sov…         0         2 Chile      CHL           0
-#> 4 Admin-0 sov…         0         3 Bolivia    BOL           0
-#> 5 Admin-0 sov…         0         2 Peru       PER           0
-#> 6 Admin-0 sov…         0         2 Argentina  ARG           0
+#>   featurecla  scalerank LABELRANK SOVEREIGNT SOV_A3 ADM0_DIF
+#>   <chr>           <int>     <int> <chr>      <chr>     <int>
+#> 1 Admin-0 so…         5         2 Indonesia  IDN           0
+#> 2 Admin-0 so…         5         3 Malaysia   MYS           0
+#> 3 Admin-0 so…         0         2 Chile      CHL           0
+#> 4 Admin-0 so…         0         3 Bolivia    BOL           0
+#> 5 Admin-0 so…         0         2 Peru       PER           0
+#> 6 Admin-0 so…         0         2 Argentina  ARG           0
 #> # ℹ 163 more variables: LEVEL <int>, TYPE <chr>, TLC <chr>,
 #> #   ADMIN <chr>, ADM0_A3 <chr>, GEOU_DIF <int>,
-#> #   GEOUNIT <chr>, GU_A3 <chr>, SU_DIF <int>, SUBUNIT <chr>,
-#> #   SU_A3 <chr>, BRK_DIFF <int>, NAME <chr>,
+#> #   GEOUNIT <chr>, GU_A3 <chr>, SU_DIF <int>,
+#> #   SUBUNIT <chr>, SU_A3 <chr>, BRK_DIFF <int>, NAME <chr>,
 #> #   NAME_LONG <chr>, BRK_A3 <chr>, BRK_NAME <chr>,
 #> #   BRK_GROUP <chr>, ABBREV <chr>, POSTAL <chr>,
 #> #   FORMAL_EN <chr>, FORMAL_FR <chr>, NAME_CIAWF <chr>, …
@@ -224,10 +224,7 @@ lapply(df$ADMIN[1:6], \(x) {
 })
 ```
 
-<div class="figure">
-<img src="figure/unnamed-chunk-7-1.png" alt="plot of chunk unnamed-chunk-7" width="50%" /><img src="figure/unnamed-chunk-7-2.png" alt="plot of chunk unnamed-chunk-7" width="50%" /><img src="figure/unnamed-chunk-7-3.png" alt="plot of chunk unnamed-chunk-7" width="50%" /><img src="figure/unnamed-chunk-7-4.png" alt="plot of chunk unnamed-chunk-7" width="50%" /><img src="figure/unnamed-chunk-7-5.png" alt="plot of chunk unnamed-chunk-7" width="50%" /><img src="figure/unnamed-chunk-7-6.png" alt="plot of chunk unnamed-chunk-7" width="50%" />
-<p class="caption">plot of chunk unnamed-chunk-7</p>
-</div>
+<img src="figure/finding-data.Rmd-7-1.png" width="50%" /><img src="figure/finding-data.Rmd-7-2.png" width="50%" /><img src="figure/finding-data.Rmd-7-3.png" width="50%" /><img src="figure/finding-data.Rmd-7-4.png" width="50%" /><img src="figure/finding-data.Rmd-7-5.png" width="50%" /><img src="figure/finding-data.Rmd-7-6.png" width="50%" />
 
 Suppose that we want to search the polygons for the US, how should we spell it?
 
@@ -254,7 +251,7 @@ We can now get the data.
 plot(ne_countries(country = "United States of America")["geometry"])
 ```
 
-![plot of chunk unnamed-chunk-10](figure/unnamed-chunk-10-1.png)
+![](figure/finding-data.Rmd-10-1.png)
 ### Continents
 
 Finally, let's create plots for each continent using the `ne_countries` function with the continent parameter.
@@ -281,7 +278,4 @@ lapply(unique(df$CONTINENT), \(x) {
 })
 ```
 
-<div class="figure">
-<img src="figure/unnamed-chunk-12-1.png" alt="plot of chunk unnamed-chunk-12" width="50%" /><img src="figure/unnamed-chunk-12-2.png" alt="plot of chunk unnamed-chunk-12" width="50%" /><img src="figure/unnamed-chunk-12-3.png" alt="plot of chunk unnamed-chunk-12" width="50%" /><img src="figure/unnamed-chunk-12-4.png" alt="plot of chunk unnamed-chunk-12" width="50%" /><img src="figure/unnamed-chunk-12-5.png" alt="plot of chunk unnamed-chunk-12" width="50%" /><img src="figure/unnamed-chunk-12-6.png" alt="plot of chunk unnamed-chunk-12" width="50%" /><img src="figure/unnamed-chunk-12-7.png" alt="plot of chunk unnamed-chunk-12" width="50%" /><img src="figure/unnamed-chunk-12-8.png" alt="plot of chunk unnamed-chunk-12" width="50%" />
-<p class="caption">plot of chunk unnamed-chunk-12</p>
-</div>
+<img src="figure/finding-data.Rmd-12-1.png" width="50%" /><img src="figure/finding-data.Rmd-12-2.png" width="50%" /><img src="figure/finding-data.Rmd-12-3.png" width="50%" /><img src="figure/finding-data.Rmd-12-4.png" width="50%" /><img src="figure/finding-data.Rmd-12-5.png" width="50%" /><img src="figure/finding-data.Rmd-12-6.png" width="50%" /><img src="figure/finding-data.Rmd-12-7.png" width="50%" /><img src="figure/finding-data.Rmd-12-8.png" width="50%" />
diff --git a/vignettes/finding-data.Rmd.orig b/vignettes/finding-data.Rmd.orig
@@ -7,7 +7,7 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r, include = FALSE}
+```{r finding-data.Rmd-1, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
@@ -25,7 +25,7 @@ There are a lot of data that can be downloaded from [Natural Earth](https://www.
 
 ### Physical vector data
 
-```{r, eval=TRUE}
+```{r finding-data.Rmd-2, eval=TRUE, fig.cap=''}
 data(df_layers_physical)
 
 knitr::kable(
@@ -36,7 +36,7 @@ knitr::kable(
 
 Based on the previous table, we know that we can download the `ocean` vector at small scale (110). Note that scales are defined as one of `110`, `50`, `10` or `small`, `medium`, `large`.
 
-```{r}
+```{r finding-data.Rmd-3, fig.cap=''}
 plot(
   ne_download(type = "ocean", category = "physical", scale = "small")["geometry"],
   col = "lightblue"
@@ -45,7 +45,7 @@ plot(
 
 ### Cultural vector data
 
-```{r, eval=TRUE}
+```{r finding-data.Rmd-4, eval=TRUE, fig.cap=''}
 data(df_layers_cultural)
 
 knitr::kable(
@@ -54,7 +54,7 @@ knitr::kable(
 )
 ```
 
-```{r}
+```{r finding-data.Rmd-5, fig.cap=''}
 plot(
   ne_download(
     type = "airports",
@@ -71,7 +71,7 @@ plot(
 In this article, we explore how we can search for data available to download within `rnaturalearth`. Let's begin by loading country data using the `read_sf()` function from the `sf` package. In the following code snippet, we read the Natural Earth dataset, which contains information about the sovereignty of countries.
 
 
-```{r}
+```{r finding-data.Rmd-6, fig.cap=''}
 df <- read_sf("/vsizip/vsicurl/https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/cultural/ne_10m_admin_0_sovereignty.zip")
 
 head(df)
@@ -81,7 +81,7 @@ head(df)
 
 One way to search for countries is to search within the `ADMIN` vector. Let's start by plotting some of the first countries.
 
-```{r, echo=-1, fig.show="hold", out.width="50%", results='hide'}
+```{r finding-data.Rmd-7, echo=-1, fig.show="hold", out.width="50%", results='hide', fig.cap=''}
 par(mfrow = c(2, 3))
 lapply(df$ADMIN[1:6], \(x) {
   plot(ne_countries(country = x)["geometry"], main = x)
@@ -90,7 +90,7 @@ lapply(df$ADMIN[1:6], \(x) {
 
 Suppose that we want to search the polygons for the US, how should we spell it?
 
-```{r, eval=FALSE}
+```{r finding-data.Rmd-8, eval=FALSE, fig.cap=''}
 ne_countries(country = "USA")
 ne_countries(country = "United States")
 ne_countries(country = "United States Of America")
@@ -99,23 +99,23 @@ ne_countries(country = "United States of America")
 
 One possibility consists to search within the `ADMIN` vector using a regular expression to find all occurrences of the word *states*.
 
-```{r}
+```{r finding-data.Rmd-9, fig.cap=''}
 df$ADMIN[grepl("states", df$ADMIN, ignore.case = TRUE)]
 ```
 We can now get the data.
 
-```{r}
+```{r finding-data.Rmd-10, fig.cap=''}
 plot(ne_countries(country = "United States of America")["geometry"])
 ```
 ### Continents
 
 Finally, let's create plots for each continent using the `ne_countries` function with the continent parameter.
 
-```{r}
+```{r finding-data.Rmd-11, fig.cap=''}
 unique(df$CONTINENT)
 ```
 
-```{r, echo=-1, fig.show="hold", out.width="50%", results='hide'}
+```{r finding-data.Rmd-12, echo=-1, fig.show="hold", out.width="50%", results='hide', fig.cap=''}
 par(mfrow = c(2, 4))
 lapply(unique(df$CONTINENT), \(x) {
   plot(

diff --git a/vignettes/language-support.Rmd b/vignettes/language-support.Rmd
@@ -42,7 +42,7 @@ terra::plot(ne_countries(continent = "africa"))
 #> max.plot = 168 to plot all
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-1.png)
+![](figure/language-support.Rmd-3-1.png)
 
 ```r
 
@@ -64,7 +64,7 @@ ggplot(sfaf) +
   geom_sf(data = sfafc)
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-2.png)
+![](figure/language-support.Rmd-3-2.png)
 
 ```r
 
@@ -77,7 +77,7 @@ ggplot(sfaf) +
   geom_text_repel(aes(x = X, y = Y, label = name), size = 3)
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-3.png)
+![](figure/language-support.Rmd-3-3.png)
 
 ```r
 
@@ -88,7 +88,7 @@ ggplot(sfaf) +
   geom_text_repel(aes(x = X, y = Y, label = name_es), size = 3)
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-4.png)
+![](figure/language-support.Rmd-3-4.png)
 
 ```r
 
@@ -102,7 +102,7 @@ ggplot(sfaf) +
   )
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-5.png)
+![](figure/language-support.Rmd-3-5.png)
 
 ```r
 
@@ -132,7 +132,7 @@ ggplot(sfaf) +
   )
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-6.png)
+![](figure/language-support.Rmd-3-6.png)
 
 ```r
 
@@ -162,7 +162,7 @@ ggplot(sfaf) +
   )
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-7.png)
+![](figure/language-support.Rmd-3-7.png)
 
 ```r
 
@@ -174,7 +174,7 @@ tm_shape(sfaf) +
   tm_text("name", size = 0.75)
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-8.png)
+![](figure/language-support.Rmd-3-8.png)
 
 ```r
 
@@ -184,7 +184,7 @@ tm_shape(sfaf) +
   tm_text("name_es", size = 0.75)
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-9.png)
+![](figure/language-support.Rmd-3-9.png)
 
 ```r
 
@@ -194,4 +194,4 @@ tm_shape(sfaf) +
   tm_text("name_de", size = 0.75)
 ```
 
-![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-10.png)
+![](figure/language-support.Rmd-3-10.png)