[Bug]: phase1b R CMD and pkgdown check errors due to Bad credentials

[audreyyeoCH]

What happened?

Hi @cicdguy , could you kindly share what the Bad credentials error could be related to please for package phase1b ? PR here

R version 4.4.2

Which version(s) of R were you using?

Other

Relevant log output

Quitting from introduction.Rmd:156-161 [load]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Failed to install 'phase1b' from GitHub:
  HTTP error 401.
  Bad credentials

  Rate limit remaining: 59/60
  Rate limit reset at: 2025-06-12 14:08:55 UTC

  
---
Backtrace:
    ▆
 1. └─devtools::install_github("https://github.com/Genentech/phase1b")
 2.   ├─pkgbuild::with_build_tools(...)
 3.   └─remotes:::install_remotes(...)
 4.     └─base::tryCatch(...)
 5.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Code of Conduct

• I agree to follow this project's Code of Conduct.

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[cicdguy]

It looks like remotes or the vignette (via rmarkwdown) is trying to install phase1b as part of the pipeline. The remotes (invoked within devtools) R package has been deprecated and heavily relies on a working GitHub PAT to authenticate with GitHub to install packages.

As you can see in the backtrace, the invocation looks like this:

devtools::install_github("https://github.com/Genentech/phase1b")

Let me see what I can do here.

[cicdguy]

Can we try commenting this line out: https://github.com/Genentech/phase1b/blob/0007a3d4a3427565ecd610362c1a195f2006010c/README.rmd#L26

[audreyyeoCH]

Can we try commenting this line out: https://github.com/Genentech/phase1b/blob/0007a3d4a3427565ecd610362c1a195f2006010c/README.rmd#L26

thank you @cicdguy ! I am still getting the same error when i comment this out on the readme.rmd file... citing

Quitting from introduction.Rmd:156-161 [load]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Failed to install 'phase1b' from GitHub:
  HTTP error 401.
  Bad credentials

  Rate limit remaining: 55/60
  Rate limit reset at: 2025-06-13 08:49:56 UTC

might you know why this is so ?
is the github PAT working as normal ? thanks a lot again !

[audreyyeoCH]

Hi @cicdguy, could you kindly share your feedback on the message above ?

[cicdguy]

Going to try this to see if it works: Genentech/phase1b#139

[audreyyeoCH]

Hi @cicdguy thanks for the new PR, the R CMD checks give the same error as above, what else could be its source ? Could you kindly cast an eye on this again please ?

So far I have done this

Can we try commenting this line out: https:

//github.com/Genentech/phase1b/blob/0007a3d4a3427565ecd610362c1a195f2006010c/README.rmd#L26

and merged this PR Genentech/phase1b#139

Thanks in advance for your help !

[cicdguy]

Looks like a failing snapshot test: https://github.com/Genentech/phase1b/actions/runs/15709199814/job/44262464683#step:44:6809

[audreyyeoCH]

Looks like a failing snapshot test: https://github.com/Genentech/phase1b/actions/runs/15709199814/job/44262464683#step:44:6809

indeed! Thank you @cicdguy . It seems it passed in a more recent PR, but I will have a second look. In the current check result....this error still shows up, can you kindly have a look why it comes up again please ?:
which looks like

! Failed to render 'vignettes/introduction.Rmd'.
✖ Quitting from introduction.Rmd:156-161 [load]
✖ Warning messages:
✖ 1: The label(s) fig:betadiff not found
✖ 2: The label(s) fig:ex1-prior not found
✖ 3: The label(s) fig:ex1-prior not found
✖ 4: The label(s) fig:ex1:betadiff1 not found
✖ 5: The label(s) fig:ex1:betadiff1 not found
Caused by error:
! Failed to install 'phase1b' from GitHub:
HTTP error 401.
Bad credentials

Rate limit remaining: 59/60
Rate limit reset at: 2025-06-24 14:25:52 UTC

Backtrace:
▆

1. └─devtools::install_github("https://github.com/Genentech/phase1b")
2. ├─pkgbuild::with_build_tools(...)
3. └─remotes:::install_remotes(...)

4. └─base::tryCatch(...)
   

5.   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   

6.     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   

7.       └─value[[3L]](cond)
   

Execution halted
Error: Process completed with exit code 1.

[cicdguy]

In the current check result...

Which one? Is it an open PR? If so, make sure to rebase from the default branch to bring the updated pipeline definition into your current branch.

[audreyyeoCH]

In the current check result...

Which one? Is it an open PR? If so, make sure to rebase from the default branch to bring the updated pipeline definition into your current branch.

indeed, yes the current one here. Thanks again, and sorry to bother again

[cicdguy]

Pushed Genentech/phase1b@a4ed15f
Let's see if that does the trick.

Long term, I recommend replacing devtools with pak for better reliability and performance.

[audreyyeoCH]

Pushed Genentech/phase1b@a4ed15f Let's see if that does the trick.

Long term, I recommend replacing devtools with pak for better reliability and performance.

thanks again @cicdguy for taking the time and for your patience with my questions. Yes let's see how this goes. Re: pak, should we just change it now / next PR ?

[cicdguy]

No urgency for pak - I was suggesting this more from a vignette perspective.

[audreyyeoCH]

it worked, thank you @cicdguy ! 🥳