-
Notifications
You must be signed in to change notification settings - Fork 4
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
fix cran malformat error #269
Conversation
The issue was that the uniprot data seems to now be gziped. I handle this case now in try_query. Not sure if it is generally handled for any potential case but it at least works for uniprot.
@elena-krismer It is great that you managed to reproduce a similar error message. That helped me to figure out what was actually going on. I assumed the error came from |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Everything looks good currently. I will wait until the tests passed and merge it into the developer. Then I bump the version and write the cran_comments.
I couldn't reproduce the error, but here’s what I discovered:
In some cases,
tryCatch
seems to struggle with capturing errors from C-level functions. Additionally, the error fromcurl::curl_fetch_memory()
isn't being handled properly (see the screenshot below). The error message appears similar, but it's not exactly the same.curl_fetch_memory()
jeroen/curl#257.The error message suggests the url is invalid, so for now, I’ve added an extra validation test to check the URL’s format before proceeding. It seems the issue might stem from some unusual behavior in the interaction between R and C functions, where the original URL possibly "gets lost."