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VCCRI / Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data
GNU General Public License v3.0
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installation erro #24

Closed AidenSb closed 3 years ago

AidenSb commented 3 years ago

Hi everyone, I'm trying to install Sierra and getting this Error.

"Error: Failed to install 'Sierra' from GitHub: System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines): E> Quitting from lines 27-41 (Sierra_vignette.rmd) E> Error: processing vignette 'Sierra_vignette.rmd' failed with diagnostics: E> argument is of length zero E> --- failed re-building ‘Sierra_vignette.rmd’ E> E> SUMMARY: processing the following file failed: E> ‘Sierra_vignette.rmd’ E> E> Error: Vignette re-building failed. E> Execution halted"

Seems you need to update the vignette file or do you guys have any idea?

Cheers Aiden

rj-patrick commented 3 years ago

Hi Aiden,

This may be related to your BiocStyle version (an issue that has cropped up before). Try updating to the latest version and reinstalling Sierra.

Cheers, Ralph

AidenSb commented 3 years ago

Hi Ralph, Updating BioStyle didn't help. I still get the same error.

rj-patrick commented 3 years ago

Hi Aiden,

Could you please tell me what version of R you are using, as well as the versions of the knitr and BiocStyle packages you have installed? e.g. with sessionInfo()

AidenSb commented 3 years ago

Hi, these are the version of R and packages. R 3.6.2 knitr 1.30 BiocStyle 2.14.4

rj-patrick commented 3 years ago

Thanks Aiden. I can replicate the error compiling the vignette with that combination of BiocStyle and knitr versions. Not sure why this is occurring at the moment, but a fix to get the vignette compiled without error should be downgrading the knitr version. On my system knitr version 1.28 works - devtools::install_version("knitr", version = "1.28", repos = "http://cran.us.r-project.org")

Let me know if that fixes the issue for you.

AidenSb commented 3 years ago

Thanks Ralph, downgrading knitr to 1.28 solved the problem.

rj-patrick commented 3 years ago

Okay great, I will close this issue now.