nanoporetech / dorado

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Error with cmake #857

Closed ipatop closed 5 days ago

ipatop commented 1 month ago

Issue Report

Hi, I am trying to install and get started with dorado (thanks for this amazing tool :) and I am encountering this error when ruining cmake.

/n/groups/churchman/inp346/scripts/cmake-3.29.3/bin/cmake -S . -B cmake-build -- Build type: -- Submodule update fatal: reference is not a tree: 88544847c51397004a31cf2817c334624c6350cf Unable to checkout '88544847c51397004a31cf2817c334624c6350cf' in submodule path 'dorado/3rdparty/indicators' CMake Error at cmake/UpdateSubmodules.cmake:18 (message): git submodule update --init --recursive failed with 1, please checkout submodules Call Stack (most recent call first): cmake/UpdateSubmodules.cmake:25 (git_submodule_update) CMakeLists.txt:74 (include)

And the I get this error when running the submodule update

git submodule update --init --recursive fatal: reference is not a tree: 88544847c51397004a31cf2817c334624c6350cf Unable to checkout '88544847c51397004a31cf2817c334624c6350cf' in submodule path 'dorado/3rdparty/indicators'

Thanks in advance,

malton-ont commented 1 month ago

Hi @ipatop,

This looks to be an error from the git submodule command that is invoked as part of our configuration step. That particular submodule is pointed at a commit in a PR that we submitted which has yet to be merged. This should just work. Can you confirm a few details for me?

malton-ont commented 5 days ago

We've recently run into this issue ourselves. Updating git resolved it, so I recommend you do likewise.