Error with pipeline execution

[jm71573]

Hello,
When I execute the pipeline, I get the following error:
"Error:
! ❌ Error: UCell is missing. Please check in the input settings chunk and make sure the variable exists/isn't commented out.
Backtrace:
▆

1. └─MARMOT::marmot(...)"

I have all the required packages for MARMOT including UCell installed.

[jm71573]

Hello, I am following up on my above comment regarding the error "UCell is missing".
Thanks,
Matt

[lydiakirsche]

Hi Matt,
thanks for following up and sorry for the late reply! We’ll look into the issue on our side.

In the meantime, could you please try uninstalling UCell and reinstalling it manually via Bioconductor?

BiocManager::install("UCell")

Please let us know whether this resolves the issue.

Best,
Lydia

[jm71573]

Lydia, Thanks for your reply! I just uninstalled and reinstalled UCell and still got the same error message when trying to run MARMOT. Also after I re installed UCell after the process finished it gave me the following message: Warning messages: 1: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\mattj\AppData\Local\R\win-library\4.5\00LOCK\htmltools\libs\x64\htmltools.dll to C:\Users\mattj\AppData\Local\R\win-library\4.5\htmltools\libs\x64\htmltools.dll: Permission denied 2: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\mattj\AppData\Local\R\win-library\4.5\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\mattj\AppData\Local\R\win-library\4.5\rlang\libs\x64\rlang.dll: Permission denied 3: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\mattj\AppData\Local\R\win-library\4.5\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\mattj\AppData\Local\R\win-library\4.5\xfun\libs\x64\xfun.dll: Permission denied 4: In file.copy(savedcopy, lib, recursive = TRUE) : problem copying C:\Users\mattj\AppData\Local\R\win-library\4.5\00LOCK\yaml\libs\x64\yaml.dll to C:\Users\mattj\AppData\Local\R\win-library\4.5\yaml\libs\x64\yaml.dll: Permission denied Thanks, Matt

…

On Thu, Jan 15, 2026 at 2:55 AM Lydia Kirsche ***@***.***> wrote: *lydiakirsche* left a comment (peterleary/MARMOT#2) <#2 (comment)> Hi Matt, thanks for following up and sorry for the late reply! We’ll look into the issue on our side. In the meantime, could you please try uninstalling UCell and reinstalling it manually via Bioconductor? BiocManager::install("UCell") Please let us know whether this resolves the issue. Best, Lydia — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/B3NATXHYNLVXPLRKRBNJ5JD4G5PZ3AVCNFSM6AAAAACOYZY3DOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTONJTHA2TCOBYGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[lydiakirsche]

Hi Matt, thanks for the detailed error message.

We can’t reproduce this issue on our end and also haven't had this issue before. Based on the paths and the .dll files in your output, we assume you’re working on Windows.

The warnings you’re seeing (Permission denied when copying .dll files) may suggest a Windows package-library locking issue, where compiled package binaries are still in use and cannot be overwritten. This can leave dependencies (e.g. rlang, yaml in your case) in a partially installed state, which can then cause downstream errors when running MARMOT or UCell.

I'm not an expert in this but maybe you would like to try for now:

Fully close R/RStudio
Make sure no R.exe or RStudio.exe processes are running (check Task Manager).

Remove leftover lock directories
Manually delete any 00LOCK* folders in:
C:\Users\mattj\AppData\Local\R\win-library\4.5\

Reinstall dependencies from a clean session
Start a fresh R session without loading any packages and run:

install.packages(c("rlang", "yaml", "xfun", "htmltools"), dependencies = TRUE)
install.packages("UCell")

If the problem persists, please let us know and paste the exact MARMOT error message, along with the output of:

sessionInfo()
packageVersion("UCell")

This should help us narrow things down further.
Best,
Lydia