Closed kalavattam closed 8 months ago
cihga39871
commented
12 months ago Hi Kris,
Thank you for your support of Atria and for reporting this issue. I previously made some changes to the build script, probably it is why the building fails on a fresh system.
I have added Pkg.update() in build_atria.jl. It should work now. If you still find errors, please don't hesitate to let me know.
cd Atria # the github repo
git pull
julia build_atria.jlThank you, Eric
kalavattam
commented
12 months ago Thank you, Eric. The change was working for a time, but some errors occurred later in the build process. In particular, I encountered a segmentation fault during the build process of Atria with Julia. The issue occurs after successful installation and precompilation of dependencies:
Expected Behavior: The build process should complete without errors, allowing Atria to be fully operational. Actual Behavior: The build process is interrupted by a segmentation fault, preventing the completion of the Atria build. Julia version: 1.8.5 Operating System: macOS Ventura 13.3.1 Environment information:
Any insights or suggestions to resolve this issue would be greatly appreciated.
Thanks, Kris
cihga39871
commented
12 months ago Thank you, Kris. I used to have this kind of seg fault on CentOS, but I am unsure of the exact cause. My experience is to use Julia v1.9.3, and the build will pass.
But before that, could you please try the following code to see whether the code passes unit tests in Julia v1.8.5?
# bash
cd Atria # git repo
julia --project
# julia
using Pkg
Pkg.test()If there are errors during the test, please let me know. If it passes unit test, there is something wrong in Julia's PackageCompiler and we can use Julia v1.9.
If you are switching to Julia v1.9, please delete Manifest.toml before building it.
# bash
cd Atria
rm Mani*toml
# julia
using Pkg
Pkg.update()
Pkg.instantiate()
Pkg.test()If the unit test passes without error, you can proceed to run julia build_atria.jl
I really appreciate your support,
Eric
kalavattam
commented
12 months ago Hi Eric,
Thank you for your suggestions. I've run the unit tests in Julia v1.8.5, and they passed successfully, which suggests that the issue might be related to Julia's PackageCompiler. Following your advice, I proceeded with the installation using Julia 1.9.4. (However, I now see that your previous messages suggests using Julia 1.9.3.)
The installation process appeared to be successful, although I did encounter some warnings related to BioSequences during both the unit testing and installation phases. Here are the details:
Given these warnings, do you think it's advisable to proceed with Julia 1.9.4, or would you recommend trying an installation with Julia 1.9.3 instead? I'm looking for the most stable and error-free environment for our purposes.
Any further guidance or recommendations you can provide would be greatly appreciated.
Best, Kris
cihga39871
commented
12 months ago Hi, Kris.
The method overwrite of BioSequences is intended in Atria. The binary building runs the unit test as incremental compilation, so if you successfully built with Julia v1.9.4, you are good to go. Julia 1.9.4 was just released and it won't break code of 1.9.3.
To make a most bug-free environment, I suggest you stick to 1.9.4.
I checked the docs of PackageCompiler, the method overwrite I did in Atria is not recommended in the updated discussions. The binary building in Julia 1.8.5 might be related to it.
In the future, I will maintain a modified BioSequences Package in my own github and make it the dependency. This would fix the potential issue.
Thank you so much for your time and support.
cihga39871
commented
12 months ago TODO:
Hello,
First, I'd like to say thank you for developing and maintaining this great program. I'm currently attempting to install Atria on macOS Ventura 13.3.1. This is my first time trying to install it on a non-Linux system. I've followed the same steps that have previously worked well on Linux, but I'm encountering an error during the build process. Could you please assist me in troubleshooting this error? I apologize if I've overlooked an obvious solution or missed something in the documentation. Thank you for your time and assistance.
Here's the process I followed:
Here's the pertinent output in the terminal:
I would greatly appreciate any guidance or suggestions you might have.
Thanks, Kris