Hi Andres,
The vignette build still fails on the check, but this time on a later codechunk
and due to a different reason.
Now it seems like there is an issue when using the enrichR package to retrieve
enriched GO terms from the enrichR API. Does the build not allow such requests?
Here is the backtrace:
Quitting from DOtools.Rmd:525-547 [GO analysis2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `scan()`:
! line 9 did not have 2 elements
---
Backtrace:
▆
1. └─DOtools::DO.enrichR(...)
2. └─enrichR::enrichr(genes = df_up[[gene_column]], databases = go_catgs)
3. └─base::lapply(...)
4. └─enrichR (local) FUN(X[[i]], ...)
5. └─utils::read.table(...)
6. └─base::scan(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'DOtools.Rmd' failed with diagnostics:
line 9 did not have 2 elements
--- failed re-building ‘DOtools.Rmd’
Best regards and many thanks
Mariano
> Am 24.10.2025 um 18:03 schrieb Andres Wokaty <[email protected]>:
>
>
> Hi Mariano,
>
> Thanks for your email. There was a permission issue with the cache that
> should now be resolved as I was able to manually build your package. Let's
> see how it does next week.
>
> Andres Wokaty (they/them)
>
> Waldron Lab at CUNY SPH
> Bioconductor Core Team
> From: Bioc-devel <[email protected]> on behalf of Mariano Ruz
> Jurado <[email protected]>
> Sent: Thursday, October 23, 2025 5:03 AM
> To: [email protected] <[email protected]>
> Subject: [Bioc-devel] DOtools vignette build errors due to "Permission Denied"
>
> * This email originates from a sender outside of CUNY. Verify the sender
> before replying or clicking on links and attachments. *
>
> Hello,
> I am the maintainer of the DOtools package and I got an error in the vignette
> build that I cannot reproduce, since it seems to be a permission problem.
> When I look at the build report
> (https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.22/bioc-LATEST/DOtools/nebbiolo2-buildsrc.html__;!!LRXxDv2l!VQFvpsmo0moRYvQVw1X9qBWN5d8P0So9mnh01xkOuWfPUinbSCXrq-26TStQ8BhD8kL3pG7d_TNz5qq-tdtbuKOZB6dsTzOVI38UtnLc$
> )
> I see the following error:
>
> Quitting from DOtools.Rmd:279-286 [annotation]
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> <error/rlang_error>
> Error in `lock()`:
> ! Cannot open lock file: Permission denied
> ---
> Backtrace:
> ▆
> 1. └─DOtools::DO.CellTypist(...)
> 2. └─basilisk::basiliskRun(...)
> 3. └─basilisk::basiliskStart(...)
> 4. └─basilisk::obtainEnvironmentPath(env)
> 5. └─dir.expiry::lockDirectory(envdir, exclusive = !file.exists(envpath))
> 6. └─filelock::lock(plock, exclusive = FALSE)
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> It seems to be a problem related to running python code in a basilisk
> environment.
> Some functions of the DOtools rely heavily on python code and therefore the
> vignette build seems to fail whenever I call such a function.
> Is there a nice way of handling this problem?
>
> Best regards and many thanks,
> Mariano
>
>
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>
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