Are Suggests of Suggests dependencies not installed?

Hi,

Tagging @jeroen and @jimhester as per Travis build report.

I am trying to restore the deployment to gh-pages with pkgdown for the repository https://github.com/iSEE/iSEE
The repository hold a Bioconductor package “iSEE” with vignettes, and it is owned by a GitHub organization of the same name.

As far as I can see, I have set up the keys properly on both Travis and GitHub.

> travis::use_travis_deploy()
ℹ Querying Github deploy keys from repo.
ℹ Getting environment variables for `iSEE/iSEE` on Travis CI.
→ At least one key part is missing (private or public). Deleting old keys and adding new deploy keys
  for Travis CI (`.com`) for repo iSEE to Travis CI and Github
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✓ Added a public deploy key to GitHub for repo `iSEE`.
✓ Added environment variable for `iSEE/iSEE` on Travis CI.
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✓ Added the private SSH key as a deploy key to project `iSEE` on Travis CI as secure environment
  variable `TRAVIS_DEPLOY_KEY`.
✓ Added the public SSH key as a deploy key to project `iSEE` on Github.

In the build (https://travis-ci.com/iSEE/iSEE/builds/147796619) I can see that TRAVIS_DEPLOY_KEY is set (line 770).

$ export TRAVIS_DEPLOY_KEY=[secure]

However, when pkgdown::deploy_site_github() is called at the end of the Travis build, it fails to find the deploy key:

Deploying application
Error: No deploy key found, please setup with `travis::use_travis_deploy()`
Execution halted
Script failed with status 1
failed to deploy

Furthermore, GitHub key settings confirm that the deploy key was “Never used”.

I don’t know if it’s important, but I can also see that the “Preparing deploy” section is empty (line 1126)

Aside from the Travis and GitHub documentation, there is one thread (e.g. https://github.com/isaacs/github/issues/500) that suggests that deploy keys can be more difficult to set up for organizations.

Any help would be greatly appreciated.

Kind regards
Kevin

I just found this thread that describes a workaround: https://github.com/r-lib/pkgdown/issues/1206

In particular, it led to a PR: https://github.com/r-lib/pkgdown/pull/1217/files

Imprint