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: �g 1. �|�wDOtools::DO.CellTypist(...) 2. �|�wbasilisk::basiliskRun(...) 3. �|�wbasilisk::basiliskStart(...) 4. �|�wbasilisk::obtainEnvironmentPath(env) 5. �|�wdir.expiry::lockDirectory(envdir, exclusive = !file.exists(envpath)) 6. �|�wfilelock::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 [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!LRXxDv2l!VQFvpsmo0moRYvQVw1X9qBWN5d8P0So9mnh01xkOuWfPUinbSCXrq-26TStQ8BhD8kL3pG7d_TNz5qq-tdtbuKOZB6dsTzOVI7F2zAbG$ [[alternative HTML version deleted]]
_______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
