animint rendering blank screen fix

[annartiges]

I tried to run the scatterplot in Rstudio from Chapter 2 to change the legends but animint doesn't render in Rstudio or in a web browser (I tried Firefox and Google), I have the selection menu but no plot.
I tried fixing it with the instruction in the FAQ and the the command animint(scatter, out.dir="test2") and then opening the HTML files in Firefox, neither worked.

Anyone knows where the problem might come from ?

[tdhock]

can you please post the code that you tried?
can you please see if you can get animint2pages() to work? https://rcdata.nau.edu/genomic-ml/animint2-manual/Ch05-sharing.html#pages

[tdhock]

also can you please post your version numbers? windows, R, animint2, web browser?

[annartiges]

Here are the version I used

• animint2 : 2025.1.
• Chrome : 137.0.7151.104
• Firefox : 139.0.1 (64-bit)
• Rstudio : 2025.05.0 Build 496
• R : 4.3.2
• Windows version : Windows 11 24H2

And here is my code :

library(animint2)
library(tidyverse)
library(ggplot2)
data(WorldBank, package="animint2")
WorldBank$Region <- sub(" (all income levels)", "", WorldBank$region, fixed=TRUE)
WorldBank1975 <- subset(WorldBank, year==1975)
scatter <- ggplot()+
  geom_point(
    mapping=aes(x=life.expectancy, y=fertility.rate, color=Region),
    data=WorldBank1975)
scatter
animint(scatter)

I tried using animint2pages() but I have trouble liking it to my github.

[tdhock]

I tried a slightly modified version of your code

library(animint2)
data(WorldBank, package="animint2")
WorldBank$Region <- sub(" (all income levels)", "", WorldBank$region, fixed=TRUE)
WorldBank1975 <- subset(WorldBank, year==1975)
viz <- animint(
  title="my title",
  source="https://github.com/my/source/code",
  scatter=ggplot()+
    geom_point(
      mapping=aes(x=life.expectancy, y=fertility.rate, color=Region),
      data=WorldBank1975))
animint2pages(viz, "issue206-test")

And I got the result below which works for me.

> library(animint2)
> data(WorldBank, package="animint2")
> WorldBank$Region <- sub(" (all income levels)", "", WorldBank$region, fixed=TRUE)
> WorldBank1975 <- subset(WorldBank, year==1975)
> viz <- animint(
+ title="my title",
+ source="https://github.com/my/source/code",
+ scatter=ggplot()+
+ geom_point(
+ mapping=aes(x=life.expectancy, y=fertility.rate, color=Region),
+ data=WorldBank1975))
> animint2pages(viz, "issue206-test")
Le chargement a nécessité le package : gert
Le chargement a nécessité le package : gh
Le chargement a nécessité le package : chromote
Failed with error:  ‘aucun package nommé ‘chromote’ n'est trouvé’
Looking up https credentials for https://github.com/tdhock/issue206-test.git
Transferred 3 of 3 objects...done!
[status] refs/heads/gh-pages: unchanged
[new]     f87248f9ca5904c68aab refs/remotes/origin/gh-pages
Looking up https credentials for https://github.com/tdhock/issue206-test.git
Transferred 14 of 14 objects...done!
[status] refs/heads/gh-pages: unchanged
[updated] f87248f9ca..f1bf579b23 refs/remotes/origin/gh-pages
Visualization will be available at https://tdhock.github.io/issue206-test
Deployment via GitHub Pages may take a few minutes...
$owner_repo
[1] "tdhock/issue206-test"

$local_clone
[1] "/tmp/Rtmp0CWpZR/file77e34732cad5b"

$viz_url
[1] "https://tdhock.github.io/issue206-test"

$gh_pages_url
[1] "https://github.com/tdhock/issue206-test/tree/gh-pages"

[annartiges]

I finally have the plot in Firefox browser !

I tried to use the modified version with viz and had the following error message after installing gert :

A GitHub token is required to create and push to a new repository.
To create a GitHub token, follow these steps:
1. Go to https://github.com/settings/tokens/new?scopes=repo&description=animint2pages
2. Confirm your password if prompted.
3. Ensure that the 'repo' scope is checked.
4. Click 'Generate token' at the bottom of the page.
5. Copy the generated token.
After creating the token, you can set it up in your R environment by running:
Sys.setenv(GITHUB_PAT="yourGithubPAT")
gert::git_config_global_set("user.name", "yourUserName")
gert::git_config_global_set("user.email", "yourEmail")

I created a token and configured user.name and user.email and now it works with just animint(scatter).

[tdhock]

Great to hear that you got it to work! Do you know what you did differently? Is it a different version of Firefox that works for you?
In your original post you wrote that you tried Firefox and Google.
It would be good to know the step-by-step process that some one else could follow in the future to obtain the same solution.

[annartiges]

I used the same Firefox version as the previous times. I forgot to mention in the last comment that I used R in a Ubuntu terminal (version 22.04), this might be what helped as I am more familiar on how to connect to GitHub through Ubuntu.
I used R version 4.1.2.

The steps are the ones I put in my previous comment :

1. Generate a GitHub token
2. Lauch R in an Ubuntu/Linux terminal
3. Download and install the gert package
4. Run : Sys.setenv(GITHUB_PAT="yourGithubtoken")
   gert::git_config_global_set("user.name", "yourUserName")
   gert::git_config_global_set("user.email", "yourEmail")

I tried running the last three commands in RStudio but it doesn't render the graph. I think the connection between RStudio and GitHub does not work properly on my computer.

[tdhock]

Thanks for sharing!
However it is still not clear to me what is the difference between when rendering works for you, and when it does not? (blank screen in firefox window)
Can you please explain what is the difference that makes it work for you?

[tdhock]

is it firefox from apt or snap? (I seem to recall snap firefox was not able to access certain files, but apt firefox was able to)