renan-r-santos / pixi-kernel Goto Github PK
View Code? Open in Web Editor NEWJupyter kernels using Pixi for reproducible notebooks
License: MIT License
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abkfenrispixi-kernel's Issues
Not working with R kernel without lib paths
Hi Renan! Really awesome that you're getting the multi-kernel support up and running!
I'm having issues getting the R kernel working without specifying the R_LIBS/R_LIBS_USER paths first. I think you should probably be able to use the kernel even without manually having to specify that yourself. Do you think there could be a way around that?
Otherwise, I think it would be worth documenting.
Steps to reproduce:
pixi init
pixi add jupyter pixi-kernel r-irkernel r-base
pixi run jupyter labThen start a notebook with a Pixi-R kernel. I get the following output:
[I 2024-04-12 20:16:28.141 ServerApp] [pixi-kernel] found Pixi 0.19.1
[I 2024-04-12 20:16:28.177 ServerApp] [pixi-kernel] project manifest path: /Users/roaldarbol/Downloads/test-jupy/pixi.toml
[I 2024-04-12 20:16:28.178 ServerApp] [pixi-kernel] launching kernel: ['pixi', 'run', '--manifest-path=/Users/roaldarbol/Downloads/test-jupy/pixi.toml', 'R', '--slave', '-e', "'IRkernel::main()'", '--args', '/Users/roaldarbol/Library/Jupyter/runtime/kernel-8327278f-a84f-4ed3-81b4-13999f630639.json']
[I 2024-04-12 20:16:28.208 ServerApp] Kernel started: 8327278f-a84f-4ed3-81b4-13999f630639
Warning: namespace ‘pbdZMQ’ is not available and has been replaced
by .GlobalEnv when processing object ‘.pbd_env’
Error in library.dynam(lib, package, package.lib) :
shared object ‘digest.dylib’ not found
Calls: loadNamespace -> namespaceImport -> loadNamespace -> library.dynam
Execution halted
[I 2024-04-12 20:16:34.188 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (1/5), new random ports
[I 2024-04-12 20:16:34.228 ServerApp] [pixi-kernel] found Pixi 0.19.1
[I 2024-04-12 20:16:34.259 ServerApp] [pixi-kernel] project manifest path: /Users/roaldarbol/Downloads/test-jupy/pixi.toml
[I 2024-04-12 20:16:34.259 ServerApp] [pixi-kernel] launching kernel: ['pixi', 'run', '--manifest-path=/Users/roaldarbol/Downloads/test-jupy/pixi.toml', 'R', '--slave', '-e', "'IRkernel::main()'", '--args', '/Users/roaldarbol/Library/Jupyter/runtime/kernel-8327278f-a84f-4ed3-81b4-13999f630639.json']
Warning: namespace ‘pbdZMQ’ is not available and has been replaced
by .GlobalEnv when processing object ‘.pbd_env’
Error in library.dynam(lib, package, package.lib) :
shared object ‘digest.dylib’ not found
Calls: loadNamespace -> namespaceImport -> loadNamespace -> library.dynam
Execution halted
[I 2024-04-12 20:16:40.271 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (2/5), new random ports
[I 2024-04-12 20:16:40.300 ServerApp] [pixi-kernel] found Pixi 0.19.1
[I 2024-04-12 20:16:40.333 ServerApp] [pixi-kernel] project manifest path: /Users/roaldarbol/Downloads/test-jupy/pixi.toml
[I 2024-04-12 20:16:40.333 ServerApp] [pixi-kernel] launching kernel: ['pixi', 'run', '--manifest-path=/Users/roaldarbol/Downloads/test-jupy/pixi.toml', 'R', '--slave', '-e', "'IRkernel::main()'", '--args', '/Users/roaldarbol/Library/Jupyter/runtime/kernel-8327278f-a84f-4ed3-81b4-13999f630639.json']
Warning: namespace ‘pbdZMQ’ is not available and has been replaced
by .GlobalEnv when processing object ‘.pbd_env’
Error in library.dynam(lib, package, package.lib) :
shared object ‘digest.dylib’ not found
Calls: loadNamespace -> namespaceImport -> loadNamespace -> library.dynam
Execution halted
[I 2024-04-12 20:16:46.343 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (3/5), new random ports
[I 2024-04-12 20:16:46.388 ServerApp] [pixi-kernel] found Pixi 0.19.1
[I 2024-04-12 20:16:46.422 ServerApp] [pixi-kernel] project manifest path: /Users/roaldarbol/Downloads/test-jupy/pixi.toml
[I 2024-04-12 20:16:46.422 ServerApp] [pixi-kernel] launching kernel: ['pixi', 'run', '--manifest-path=/Users/roaldarbol/Downloads/test-jupy/pixi.toml', 'R', '--slave', '-e', "'IRkernel::main()'", '--args', '/Users/roaldarbol/Library/Jupyter/runtime/kernel-8327278f-a84f-4ed3-81b4-13999f630639.json']
Warning: namespace ‘pbdZMQ’ is not available and has been replaced
by .GlobalEnv when processing object ‘.pbd_env’
Error in library.dynam(lib, package, package.lib) :
shared object ‘digest.dylib’ not found
Calls: loadNamespace -> namespaceImport -> loadNamespace -> library.dynam
Execution halted
[I 2024-04-12 20:16:52.434 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (4/5), new random ports
[I 2024-04-12 20:16:52.476 ServerApp] [pixi-kernel] found Pixi 0.19.1
[I 2024-04-12 20:16:52.508 ServerApp] [pixi-kernel] project manifest path: /Users/roaldarbol/Downloads/test-jupy/pixi.toml
[I 2024-04-12 20:16:52.508 ServerApp] [pixi-kernel] launching kernel: ['pixi', 'run', '--manifest-path=/Users/roaldarbol/Downloads/test-jupy/pixi.toml', 'R', '--slave', '-e', "'IRkernel::main()'", '--args', '/Users/roaldarbol/Library/Jupyter/runtime/kernel-8327278f-a84f-4ed3-81b4-13999f630639.json']
Warning: namespace ‘pbdZMQ’ is not available and has been replaced
by .GlobalEnv when processing object ‘.pbd_env’
Error in library.dynam(lib, package, package.lib) :
shared object ‘digest.dylib’ not found
Calls: loadNamespace -> namespaceImport -> loadNamespace -> library.dynam
Execution halted
[I 2024-04-12 20:16:58.520 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (5/5), new random ports
[I 2024-04-12 20:16:58.561 ServerApp] [pixi-kernel] found Pixi 0.19.1
[I 2024-04-12 20:16:58.592 ServerApp] [pixi-kernel] project manifest path: /Users/roaldarbol/Downloads/test-jupy/pixi.toml
[I 2024-04-12 20:16:58.592 ServerApp] [pixi-kernel] launching kernel: ['pixi', 'run', '--manifest-path=/Users/roaldarbol/Downloads/test-jupy/pixi.toml', 'R', '--slave', '-e', "'IRkernel::main()'", '--args', '/Users/roaldarbol/Library/Jupyter/runtime/kernel-8327278f-a84f-4ed3-81b4-13999f630639.json']
Warning: namespace ‘pbdZMQ’ is not available and has been replaced
by .GlobalEnv when processing object ‘.pbd_env’
Error in library.dynam(lib, package, package.lib) :
shared object ‘digest.dylib’ not found
Calls: loadNamespace -> namespaceImport -> loadNamespace -> library.dynam
Execution halted
[W 2024-04-12 20:17:04.603 ServerApp] AsyncIOLoopKernelRestarter: restart failed
[W 2024-04-12 20:17:04.603 ServerApp] Kernel 8327278f-a84f-4ed3-81b4-13999f630639 died, removing from map.
[W 2024-04-12 20:17:28.229 ServerApp] Timeout waiting for kernel_info reply from 8327278f-a84f-4ed3-81b4-13999f630639Recommend Projects
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