unknown input format -

[ErickMUO]

Hi DREEP developers,

As previous comments suggested (#3 #4 #1, see comments), I checked the .gpds.rds files in the data folder after installing via devtools::install_github("gambalab/DREEP") and also after manually downloading them from the GitHub page.

The file sizes are still the same (~100 B), and the error persists:

dreep.data <- DREEP::runDREEP(M = data$gficf,
n.markers = 500,
gsea = "simple",
gpds.signatures = c("CTRP2","GDSC"))
12:11:34 Loading GPDS signatures..
Error in readRDS(paste0(find.package("DREEP"), "/data/", i, ".gpds.rds")) :
unknown input format

sessionInfo()
R version 4.5.2 (2025-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS

[gambalab]

Hi, propbabily this is a common problem of LFS datasets on github. Anyway, take the dataset from fig share and place them in the right position. Below the figshare link.

https://figshare.com/articles/dataset/Predicting_drug_response_from_single-cell_expression_profiles_DREEP_/23261234

[gambalab]

Alternatively (it should work either) try to install git-lfs sudo apt-get install git-lfs and clone again the repo

[ErickMUO]

Ohh, I see! You were right — when I checked the content of the file, it was just a tiny pointer file for Git LFS.

After installing Git LFS, cloning the repo, and running git lfs pull, I replaced the data folder in my R library as suggested in the previous comments. Now everything works and I’m able to move forward.

Thanks so much for the quick response!

[Leslieqian1211]

Hi, propbabily this is a common problem of LFS datasets on github. Anyway, take the dataset from fig share and place them in the right position. Below the figshare link.

https://figshare.com/articles/dataset/Predicting_drug_response_from_single-cell_expression_profiles_DREEP_/23261234

thanks a lot