Issue with web app and with R version for local installation

[CarraraAlessia]

Hello,

I am interested in using BugBase, but I am encountering some issues getting it to run.

1. Web Application Issue:
   When I try to use the BugBase web application at https://bugbase.cs.umn.edu/upload.html, I receive the error: “OTU file was unable to be saved. Please contact us for support.” This happens when I attempt to upload a .biom file—both my own file and the demo file provided by BugBase result in the same error.

2:Local Installation Issue:
I tried installing BugBase locally following the GitHub instructions, but I'm uncertain about the required R version. The Matrix package requires R version 4.4 or higher, yet this R version does not seem to support the biom package, leading to installation issues. As a result, the installation does not complete successfully, and the command run.bugbase.r -h fails to execute fully.

Could you advise on how to resolve these issues with either the web application or the local installation?

Thank you for your help!

Best,
Alessia

[limohulb]

I have a similar problem. How can I solve it?

[HuTianlong1994]

I had the same problem and solve it. As you say: "The Matrix package requires R version 4.4 or higher, yet this R version does not seem to support the biom package, leading to installation issues."

Then, You can install the old "Matrix" and "biom" package by this command in R console: remotes::install_version("Matrix", version = "1.6-1") and remotes::install_version("biom", version = "0.3.12") ,however run.bugbase.r load the package by its package directory, when you open run.bugbase.r, you can find this COMMAND:lib_location <- paste(my_env, "/R_lib", sep='/').

Secondly, copy the packages that were installed default by R to the R_lib where run.bugbase.r load its packages:cp -r /home/YOURCOMPUTERNAME/R/x86_64-pc-linux-gnu-library/4.3/biom ./BugBase-master/R_lib/

Finally, run run.bugbase.r -h successfully.

[CarraraAlessia]

Hi, thank you for your answer! It ran successfully with your suggestion :)

[limohulb]

Thanks. Works perfect.