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[Bug]: ImportError: libstdc++.so.6: cannot open shared object file: No such file or directory #2394

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ineiti opened this issue Oct 30, 2024 · 3 comments
Open

[Bug]: ImportError: libstdc++.so.6: cannot open shared object file: No such file or directory #2394

ineiti opened this issue Oct 30, 2024 · 3 comments
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@gcurtis
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bug Something isn't working triage Issue needs triage

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@ineiti
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ineiti commented Oct 30, 2024 •
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What happened?

I'm trying to run jupyter-lab in a devbox environment, but I get the above error.
On my mac M2 14.6.1 it works without problems.

I found #1276, but the last comment says Resolved in latest devbox., which doesn't seem to be the case :(

Steps to reproduce

  1. git clone https://github.com/c4dt/eid-workshop/ -b devbox_bug
  2. cd eid-workshop
  3. devbox shell --pure
  4. jupyter-lab

Command

shell

devbox.json

{
  "$schema": "https://raw.githubusercontent.com/jetify-com/devbox/0.12.0/.schema/devbox.schema.json",
  "packages": [
    "python311Packages.pip@latest",
    "nodejs@latest",
    "python311@latest",
    "less@latest"
  ],
  "shell": {
    "init_hook": [
      ". $VENV_DIR/bin/activate",
      "echo Ensuring npm and python packages are installed",
      "npm ci --silent",
      "pip install -r requirements.txt -q",
      "npx tslab install"
    ],
    "scripts": {
      "jupyter": [
        "jupyter-lab -y"
      ],
      "clean": [
        "jupyter nbconvert --clear-output --inplace *.ipynb"
      ]
    }
  },
  "env": {
    "PATH": "$PATH:$PWD/node_modules/.bin"
  }
}

Devbox version

0.13.6

Nix version

2.24.7

What system does this bug occur on?

Linux (x86-64)

Debug logs

ineiti@fricklebox:~/tmp/eid-workshop$ DEVBOX_DEBUG=1 devbox run -- jupyter-lab
time=2024-10-30T17:04:17.657+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:125 msg="searching for config file (including parent directories)" path=.
time=2024-10-30T17:04:17.657+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:146 msg="trying config file" path=devbox.json
time=2024-10-30T17:04:17.657+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:133 msg="config file found" path=/home/ineiti/tmp/eid-workshop/devbox.json dur=315.696µs
time=2024-10-30T17:04:17.657+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:17.657+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:17.657+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:17.657+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
time=2024-10-30T17:04:17.658+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:125 msg="searching for config file (including parent directories)" path=.
time=2024-10-30T17:04:17.658+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:146 msg="trying config file" path=devbox.json
time=2024-10-30T17:04:17.658+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:133 msg="config file found" path=/home/ineiti/tmp/eid-workshop/devbox.json dur=159.258µs
time=2024-10-30T17:04:17.658+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:17.658+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:17.658+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:17.658+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
time=2024-10-30T17:04:17.682+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/nix.go:342 msg="nix --version --debug output" out="nix (Nix) 2.24.7\nSystem type: x86_64-linux\nAdditional system types: i686-linux, x86_64-v1-linux, x86_64-v2-linux\nFeatures: gc, signed-caches\nSystem configuration file: /etc/nix/nix.conf\nUser configuration files: /home/ineiti/.config/nix/nix.conf:/etc/xdg/nix/nix.conf\nStore directory: /nix/store\nState directory: /nix/var/nix\nData directory: /nix/store/s429drnj3jp5dbxib74r3q0rypknvw48-nix-2.24.7/share\n"
time=2024-10-30T17:04:17.682+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:60 msg="nix command starting" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' eval --impure --raw --expr builtins.currentSystem" cmd.path=/home/ineiti/.nix-profile/bin/nix
time=2024-10-30T17:04:17.707+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:67 msg="nix command exited" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' eval --impure --raw --expr builtins.currentSystem" cmd.path=/home/ineiti/.nix-profile/bin/nix cmd.pid=2495442 cmd.code=0 cmd.dur=25.139021ms
time=2024-10-30T17:04:17.707+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/boxcli/run.go:104 msg="run script" script=jupyter-lab args=[]
time=2024-10-30T17:04:17.707+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:125 msg="searching for config file (including parent directories)" path=.
time=2024-10-30T17:04:17.707+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:146 msg="trying config file" path=devbox.json
time=2024-10-30T17:04:17.707+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:133 msg="config file found" path=/home/ineiti/tmp/eid-workshop/devbox.json dur=170.087µs
time=2024-10-30T17:04:17.708+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:17.708+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:17.708+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:17.708+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
time=2024-10-30T17:04:17.708+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:17.708+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:17.708+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:17.708+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
time=2024-10-30T17:04:17.709+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:17.709+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:17.709+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:17.709+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
Info: Ensuring packages are installed.
time=2024-10-30T17:04:17.710+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/plugin/plugin.go:85 msg="creating files for package" pkg=nodejs@latest
time=2024-10-30T17:04:17.710+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/plugin/plugin.go:85 msg="creating files for package" pkg=python311@latest
time=2024-10-30T17:04:17.710+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/plugin/plugin.go:128 msg="Creating file %q from contentPath: %q" /home/ineiti/tmp/eid-workshop/.devbox/virtenv/python311/bin/venvShellHook.sh=python/venvShellHook.sh
time=2024-10-30T17:04:17.711+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:17.711+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:17.711+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:17.711+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
time=2024-10-30T17:04:17.711+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:60 msg="nix command starting" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' store info --store daemon --json" cmd.path=/home/ineiti/.nix-profile/bin/nix
time=2024-10-30T17:04:17.738+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:67 msg="nix command exited" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' store info --store daemon --json" cmd.path=/home/ineiti/.nix-profile/bin/nix cmd.stderr="cannot connect to socket at '/nix/var/nix/daemon-socket/socket': No such file or directory" cmd.pid=2495445 cmd.code=1 cmd.dur=27.411679ms
time=2024-10-30T17:04:17.739+01:00 level=ERROR source=go.jetpack.io/devbox/internal/devbox/providers/nixcache/setup.go:81 msg="nixcache: skipping setup: error connecting to nix daemon, assuming single-user install" err="command nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' store info --store daemon --json: nix: command error: nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' store info --store daemon --json: cannot connect to socket at '/nix/var/nix/daemon-socket/socket': No such file or directory: exit code 1: error: cannot connect to socket at '/nix/var/nix/daemon-socket/socket': No such file or directory\n"
time=2024-10-30T17:04:17.862+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:60 msg="nix command starting" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' path-info --offline --json /nix/store/dgn6hj686lzl8148fzy3h51h07jaf2i6-less-661 /nix/store/psgpg8dsnp37np7ab0ki7ig2d83638s4-less-661-man /nix/store/b4hrc7i8hzfzhvmq5qffyb748zkc4lkr-python3.11-pip-24.0 /nix/store/hvjfxrx4h92qm9y1jvw44ndy8fk61wlc-python3.11-pip-24.0-man /nix/store/xsrv93rg8vi05k9ig6v9mcvcyn01n6n2-nodejs-22.8.0 /nix/store/0bygl9k94j0xkxq7cmxnpqdqf8va5k7j-python3-3.11.10" cmd.path=/home/ineiti/.nix-profile/bin/nix
time=2024-10-30T17:04:17.891+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:67 msg="nix command exited" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' path-info --offline --json /nix/store/dgn6hj686lzl8148fzy3h51h07jaf2i6-less-661 /nix/store/psgpg8dsnp37np7ab0ki7ig2d83638s4-less-661-man /nix/store/b4hrc7i8hzfzhvmq5qffyb748zkc4lkr-python3.11-pip-24.0 /nix/store/hvjfxrx4h92qm9y1jvw44ndy8fk61wlc-python3.11-pip-24.0-man /nix/store/xsrv93rg8vi05k9ig6v9mcvcyn01n6n2-nodejs-22.8.0 /nix/store/0bygl9k94j0xkxq7cmxnpqdqf8va5k7j-python3-3.11.10" cmd.path=/home/ineiti/.nix-profile/bin/nix cmd.pid=2495448 cmd.code=0 cmd.dur=29.388973ms
time=2024-10-30T17:04:17.891+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:17.891+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:17.891+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:17.891+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
time=2024-10-30T17:04:17.891+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/plugin/plugin.go:85 msg="creating files for package" pkg=nodejs@latest
time=2024-10-30T17:04:17.891+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/plugin/plugin.go:85 msg="creating files for package" pkg=python311
time=2024-10-30T17:04:17.891+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/plugin/plugin.go:128 msg="Creating file %q from contentPath: %q" /home/ineiti/tmp/eid-workshop/.devbox/virtenv/python311/bin/venvShellHook.sh=python/venvShellHook.sh
time=2024-10-30T17:04:17.892+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:17.892+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:17.892+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:17.892+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
⣾ Computing the Devbox environment...
time=2024-10-30T17:04:17.892+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/nix.go:85 msg="running print-dev-env cmd" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' print-dev-env --json path:/home/ineiti/tmp/eid-workshop/.devbox/gen/flake"
time=2024-10-30T17:04:17.893+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:60 msg="nix command starting" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' print-dev-env --json path:/home/ineiti/tmp/eid-workshop/.devbox/gen/fl⢿ Computing the Devbox environment...
time=2024-10-30T17:04:18.201+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:67 msg="nix command exited" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' print-dev-env --json path:/home/ineiti/tmp/eid-workshop/.devbox/gen/flak✓ Computed the Devbox environment.
time=2024-10-30T17:04:18.202+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:60 msg="nix command starting" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' profile list --profile /home/ineiti/tmp/eid-workshop/.devbox/nix/profile/default --json" cmd.path=/home/ineiti/.nix-profile/bin/nix
time=2024-10-30T17:04:18.227+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/command.go:67 msg="nix command exited" cmd.args="nix --extra-experimental-features ca-derivations --option experimental-features 'nix-command flakes fetch-closure' profile list --profile /home/ineiti/tmp/eid-workshop/.devbox/nix/profile/default --json" cmd.path=/home/ineiti/.nix-profile/bin/nix cmd.pid=2495459 cmd.code=0 cmd.dur=25.323265ms
time=2024-10-30T17:04:18.227+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:18.227+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:18.227+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:18.227+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
time=2024-10-30T17:04:18.228+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:18.228+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:18.228+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:18.228+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
time=2024-10-30T17:04:18.228+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:706 msg="current environment PATH" path=/home/ineiti/.nix-profile/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:721 msg="nix environment PATH" path=/nix/store/znqwpxy9jlxcgi2ms2hga0ch87bbbr9g-patchelf-0.15.0/bin:/nix/store/zlzz2z48s7ry0hkl55xiqp5a73b4mzrg-gcc-wrapper-12.3.0/bin:/nix/store/0b9bsznqs6pdg42dxcwvrlmarjn2p6a1-gcc-12.3.0/bin:/nix/store/nvh3jgs8pqghnsfzbv28004xkigiw8gc-glibc-2.38-23-bin/bin:/nix/store/vwkvhj69z4qqgmpa2lwm97kabf12p26r-coreutils-9.3/bin:/nix/store/h8d2j0prdf7pnpgyrgkxrrbfwnmxbq6y-binutils-wrapper-2.40/bin:/nix/store/p58l5qmzifl20qmjs3xfpl01f0mqlza2-binutils-2.40/bin:/nix/store/b4hrc7i8hzfzhvmq5qffyb748zkc4lkr-python3.11-pip-24.0/bin:/nix/store/zy22nlap6gznpjhqry4w0hgw5mf62q3f-python3-3.11.9/bin:/nix/store/xsrv93rg8vi05k9ig6v9mcvcyn01n6n2-nodejs-22.8.0/bin:/nix/store/0bygl9k94j0xkxq7cmxnpqdqf8va5k7j-python3-3.11.10/bin:/nix/store/dgn6hj686lzl8148fzy3h51h07jaf2i6-less-661/bin:/nix/store/vwkvhj69z4qqgmpa2lwm97kabf12p26r-coreutils-9.3/bin:/nix/store/qyzfglbrqb5ck0dgljplin2bvc4995w7-findutils-4.9.0/bin:/nix/store/x6y2i213maj6ibcn0qzgg7graif5qcvi-diffutils-3.10/bin:/nix/store/g5p3ky90xa05ggg5szyb0pbbl2vp7n03-gnused-4.9/bin:/nix/store/p2r51wfg9m3ga7pp7avslpfhfa7w5y83-gnugrep-3.11/bin:/nix/store/cmn958i8qym0qvmvydl23fh3bm3fbhl7-gawk-5.2.2/bin:/nix/store/f5qy259g9b4qh0hwz22z5j5bq3m53cpv-gnutar-1.35/bin:/nix/store/kmr52zpw7wazxywqvzgpdx0vnn9prd3v-gzip-1.13/bin:/nix/store/w1mar48lwkavwy64mvj567lwaqnm2l11-bzip2-1.0.8-bin/bin:/nix/store/9dh2csn531by6b1vr9jv85v4k17xwkid-gnumake-4.4.1/bin:/nix/store/lf0wpjrj8yx4gsmw2s3xfl58ixmqk8qa-bash-5.2-p15/bin:/nix/store/pinwlz7294p37d2sbkdpjildzxii42vv-patch-2.7.6/bin:/nix/store/skrzk0g88jf9rg28labqsyxv7gg357q1-xz-5.4.4-bin/bin:/nix/store/h5pshzq92r2xcv6w1p10cmkar4nyv0xp-file-5.45/bin
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:755 msg="PATH after plugins and config" path=/home/ineiti/tmp/eid-workshop/.devbox/nix/profile/default/bin:/nix/store/znqwpxy9jlxcgi2ms2hga0ch87bbbr9g-patchelf-0.15.0/bin:/nix/store/zlzz2z48s7ry0hkl55xiqp5a73b4mzrg-gcc-wrapper-12.3.0/bin:/nix/store/0b9bsznqs6pdg42dxcwvrlmarjn2p6a1-gcc-12.3.0/bin:/nix/store/nvh3jgs8pqghnsfzbv28004xkigiw8gc-glibc-2.38-23-bin/bin:/nix/store/vwkvhj69z4qqgmpa2lwm97kabf12p26r-coreutils-9.3/bin:/nix/store/h8d2j0prdf7pnpgyrgkxrrbfwnmxbq6y-binutils-wrapper-2.40/bin:/nix/store/p58l5qmzifl20qmjs3xfpl01f0mqlza2-binutils-2.40/bin:/nix/store/b4hrc7i8hzfzhvmq5qffyb748zkc4lkr-python3.11-pip-24.0/bin:/nix/store/zy22nlap6gznpjhqry4w0hgw5mf62q3f-python3-3.11.9/bin:/nix/store/xsrv93rg8vi05k9ig6v9mcvcyn01n6n2-nodejs-22.8.0/bin:/nix/store/0bygl9k94j0xkxq7cmxnpqdqf8va5k7j-python3-3.11.10/bin:/nix/store/dgn6hj686lzl8148fzy3h51h07jaf2i6-less-661/bin:/nix/store/qyzfglbrqb5ck0dgljplin2bvc4995w7-findutils-4.9.0/bin:/nix/store/x6y2i213maj6ibcn0qzgg7graif5qcvi-diffutils-3.10/bin:/nix/store/g5p3ky90xa05ggg5szyb0pbbl2vp7n03-gnused-4.9/bin:/nix/store/p2r51wfg9m3ga7pp7avslpfhfa7w5y83-gnugrep-3.11/bin:/nix/store/cmn958i8qym0qvmvydl23fh3bm3fbhl7-gawk-5.2.2/bin:/nix/store/f5qy259g9b4qh0hwz22z5j5bq3m53cpv-gnutar-1.35/bin:/nix/store/kmr52zpw7wazxywqvzgpdx0vnn9prd3v-gzip-1.13/bin:/nix/store/w1mar48lwkavwy64mvj567lwaqnm2l11-bzip2-1.0.8-bin/bin:/nix/store/9dh2csn531by6b1vr9jv85v4k17xwkid-gnumake-4.4.1/bin:/nix/store/lf0wpjrj8yx4gsmw2s3xfl58ixmqk8qa-bash-5.2-p15/bin:/nix/store/pinwlz7294p37d2sbkdpjildzxii42vv-patch-2.7.6/bin:/nix/store/skrzk0g88jf9rg28labqsyxv7gg357q1-xz-5.4.4-bin/bin:/nix/store/h5pshzq92r2xcv6w1p10cmkar4nyv0xp-file-5.45/bin:/home/ineiti/tmp/eid-workshop/node_modules/.bin
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:773 msg="filtering out buildInput from PATH" path=/nix/store/b4hrc7i8hzfzhvmq5qffyb748zkc4lkr-python3.11-pip-24.0/bin input=/nix/store/b4hrc7i8hzfzhvmq5qffyb748zkc4lkr-python3.11-pip-24.0
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:773 msg="filtering out buildInput from PATH" path=/nix/store/xsrv93rg8vi05k9ig6v9mcvcyn01n6n2-nodejs-22.8.0/bin input=/nix/store/xsrv93rg8vi05k9ig6v9mcvcyn01n6n2-nodejs-22.8.0
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:773 msg="filtering out buildInput from PATH" path=/nix/store/0bygl9k94j0xkxq7cmxnpqdqf8va5k7j-python3-3.11.10/bin input=/nix/store/0bygl9k94j0xkxq7cmxnpqdqf8va5k7j-python3-3.11.10
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:773 msg="filtering out buildInput from PATH" path=/nix/store/dgn6hj686lzl8148fzy3h51h07jaf2i6-less-661/bin input=/nix/store/dgn6hj686lzl8148fzy3h51h07jaf2i6-less-661
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:779 msg="PATH after filtering buildInputs" inputs="[/nix/store/b4hrc7i8hzfzhvmq5qffyb748zkc4lkr-python3.11-pip-24.0 /nix/store/hvjfxrx4h92qm9y1jvw44ndy8fk61wlc-python3.11-pip-24.0-man /nix/store/xsrv93rg8vi05k9ig6v9mcvcyn01n6n2-nodejs-22.8.0 /nix/store/0bygl9k94j0xkxq7cmxnpqdqf8va5k7j-python3-3.11.10 /nix/store/dgn6hj686lzl8148fzy3h51h07jaf2i6-less-661 /nix/store/psgpg8dsnp37np7ab0ki7ig2d83638s4-less-661-man]" path=/home/ineiti/tmp/eid-workshop/.devbox/nix/profile/default/bin:/nix/store/znqwpxy9jlxcgi2ms2hga0ch87bbbr9g-patchelf-0.15.0/bin:/nix/store/zlzz2z48s7ry0hkl55xiqp5a73b4mzrg-gcc-wrapper-12.3.0/bin:/nix/store/0b9bsznqs6pdg42dxcwvrlmarjn2p6a1-gcc-12.3.0/bin:/nix/store/nvh3jgs8pqghnsfzbv28004xkigiw8gc-glibc-2.38-23-bin/bin:/nix/store/vwkvhj69z4qqgmpa2lwm97kabf12p26r-coreutils-9.3/bin:/nix/store/h8d2j0prdf7pnpgyrgkxrrbfwnmxbq6y-binutils-wrapper-2.40/bin:/nix/store/p58l5qmzifl20qmjs3xfpl01f0mqlza2-binutils-2.40/bin:/nix/store/zy22nlap6gznpjhqry4w0hgw5mf62q3f-python3-3.11.9/bin:/nix/store/qyzfglbrqb5ck0dgljplin2bvc4995w7-findutils-4.9.0/bin:/nix/store/x6y2i213maj6ibcn0qzgg7graif5qcvi-diffutils-3.10/bin:/nix/store/g5p3ky90xa05ggg5szyb0pbbl2vp7n03-gnused-4.9/bin:/nix/store/p2r51wfg9m3ga7pp7avslpfhfa7w5y83-gnugrep-3.11/bin:/nix/store/cmn958i8qym0qvmvydl23fh3bm3fbhl7-gawk-5.2.2/bin:/nix/store/f5qy259g9b4qh0hwz22z5j5bq3m53cpv-gnutar-1.35/bin:/nix/store/kmr52zpw7wazxywqvzgpdx0vnn9prd3v-gzip-1.13/bin:/nix/store/w1mar48lwkavwy64mvj567lwaqnm2l11-bzip2-1.0.8-bin/bin:/nix/store/9dh2csn531by6b1vr9jv85v4k17xwkid-gnumake-4.4.1/bin:/nix/store/lf0wpjrj8yx4gsmw2s3xfl58ixmqk8qa-bash-5.2-p15/bin:/nix/store/pinwlz7294p37d2sbkdpjildzxii42vv-patch-2.7.6/bin:/nix/store/skrzk0g88jf9rg28labqsyxv7gg357q1-xz-5.4.4-bin/bin:/nix/store/h5pshzq92r2xcv6w1p10cmkar4nyv0xp-file-5.45/bin:/home/ineiti/tmp/eid-workshop/node_modules/.bin
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:798 msg="new path stack is" path_stack=DEVBOX_NIX_ENV_PATH_5a821f8fbdd7a814c124c12888f06093f210fbe0ab8659a472f605f12d4d1fa9:DEVBOX_INIT_PATH
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devbox/devbox.go:800 msg="computed environment PATH" path=/home/ineiti/tmp/eid-workshop/.devbox/nix/profile/default/bin:/nix/store/znqwpxy9jlxcgi2ms2hga0ch87bbbr9g-patchelf-0.15.0/bin:/nix/store/zlzz2z48s7ry0hkl55xiqp5a73b4mzrg-gcc-wrapper-12.3.0/bin:/nix/store/0b9bsznqs6pdg42dxcwvrlmarjn2p6a1-gcc-12.3.0/bin:/nix/store/nvh3jgs8pqghnsfzbv28004xkigiw8gc-glibc-2.38-23-bin/bin:/nix/store/vwkvhj69z4qqgmpa2lwm97kabf12p26r-coreutils-9.3/bin:/nix/store/h8d2j0prdf7pnpgyrgkxrrbfwnmxbq6y-binutils-wrapper-2.40/bin:/nix/store/p58l5qmzifl20qmjs3xfpl01f0mqlza2-binutils-2.40/bin:/nix/store/zy22nlap6gznpjhqry4w0hgw5mf62q3f-python3-3.11.9/bin:/nix/store/qyzfglbrqb5ck0dgljplin2bvc4995w7-findutils-4.9.0/bin:/nix/store/x6y2i213maj6ibcn0qzgg7graif5qcvi-diffutils-3.10/bin:/nix/store/g5p3ky90xa05ggg5szyb0pbbl2vp7n03-gnused-4.9/bin:/nix/store/p2r51wfg9m3ga7pp7avslpfhfa7w5y83-gnugrep-3.11/bin:/nix/store/cmn958i8qym0qvmvydl23fh3bm3fbhl7-gawk-5.2.2/bin:/nix/store/f5qy259g9b4qh0hwz22z5j5bq3m53cpv-gnutar-1.35/bin:/nix/store/kmr52zpw7wazxywqvzgpdx0vnn9prd3v-gzip-1.13/bin:/nix/store/w1mar48lwkavwy64mvj567lwaqnm2l11-bzip2-1.0.8-bin/bin:/nix/store/9dh2csn531by6b1vr9jv85v4k17xwkid-gnumake-4.4.1/bin:/nix/store/lf0wpjrj8yx4gsmw2s3xfl58ixmqk8qa-bash-5.2-p15/bin:/nix/store/pinwlz7294p37d2sbkdpjildzxii42vv-patch-2.7.6/bin:/nix/store/skrzk0g88jf9rg28labqsyxv7gg357q1-xz-5.4.4-bin/bin:/nix/store/h5pshzq92r2xcv6w1p10cmkar4nyv0xp-file-5.45/bin:/home/ineiti/tmp/eid-workshop/node_modules/.bin:/home/ineiti/tmp/eid-workshop/.devbox/virtenv/runx/bin:/home/ineiti/.nix-profile/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
time=2024-10-30T17:04:18.229+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/nix/run.go:36 msg="executing script" cmd="[/usr/bin/sh -c "/home/ineiti/tmp/eid-workshop/.devbox/gen/scripts/.cmd.sh"]"
Ensuring npm and python packages are installed
Traceback (most recent call last):
File "/home/ineiti/tmp/eid-workshop/.venv/bin/jupyter-lab", line 5, in
from jupyterlab.labapp import main
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/jupyterlab/init.py", line 8, in
from .handlers.announcements import (
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/jupyterlab/handlers/announcements.py", line 15, in
from jupyterlab_server.translation_utils import translator
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/jupyterlab_server/init.py", line 6, in
from .app import LabServerApp
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/jupyterlab_server/app.py", line 10, in
from jupyter_server.extension.application import ExtensionApp, ExtensionAppJinjaMixin
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/jupyter_server/extension/application.py", line 17, in
from jupyter_server.serverapp import ServerApp
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/jupyter_server/serverapp.py", line 33, in
import jupyter_client
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/jupyter_client/init.py", line 3, in
from .asynchronous import AsyncKernelClient
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/jupyter_client/asynchronous/init.py", line 1, in
from .client import AsyncKernelClient # noqa
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/jupyter_client/asynchronous/client.py", line 8, in
import zmq.asyncio
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/zmq/init.py", line 52, in
from zmq import backend
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/zmq/backend/init.py", line 30, in
raise original_error from None
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/zmq/backend/init.py", line 25, in
_ns = select_backend(first)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/zmq/backend/select.py", line 31, in select_backend
mod = import_module(name)
^^^^^^^^^^^^^^^^^^^
File "/home/ineiti/tmp/eid-workshop/.devbox/nix/profile/default/lib/python3.11/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ineiti/tmp/eid-workshop/.venv/lib/python3.11/site-packages/zmq/backend/cython/init.py", line 6, in
from . import _zmq
ImportError: libstdc++.so.6: cannot open shared object file: No such file or directory
Error: error running script "jupyter-lab" in Devbox: exit status 1

time=2024-10-30T17:04:23.073+01:00 level=ERROR source=go.jetpack.io/devbox/internal/boxcli/midcobra/debug.go:70 msg="command error" execid=417ea56cf92e426ebc4de86637de4b15 stack="error running script "jupyter-lab" in Devbox: exit status 1\ngo.jetpack.io/devbox/internal/boxcli.runScriptCmd\n\tgo.jetpack.io/devbox/internal/boxcli/run.go:127\ngo.jetpack.io/devbox/internal/boxcli.runCmd.func1\n\tgo.jetpack.io/devbox/internal/boxcli/run.go:50\ngithub.com/spf13/cobra.(*Command).execute\n\tgithub.com/spf13/[email protected]/command.go:983\ngithub.com/spf13/cobra.(*Command).ExecuteC\n\tgithub.com/spf13/[email protected]/command.go:1115\ngithub.com/spf13/cobra.(*Command).Execute\n\tgithub.com/spf13/[email protected]/command.go:1039\ngo.jetpack.io/devbox/internal/boxcli/midcobra.(*midcobraExecutable).Execute\n\tgo.jetpack.io/devbox/internal/boxcli/midcobra/midcobra.go:61\ngo.jetpack.io/devbox/internal/boxcli.Execute\n\tgo.jetpack.io/devbox/internal/boxcli/root.go:116\ngo.jetpack.io/devbox/internal/boxcli.Main\n\tgo.jetpack.io/devbox/internal/boxcli/root.go:139\nmain.main\n\t./main.go:11\nruntime.main\n\truntime/proc.go:272\nruntime.goexit\n\truntime/asm_amd64.s:1700"
time=2024-10-30T17:04:23.073+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:125 msg="searching for config file (including parent directories)" path=.
time=2024-10-30T17:04:23.073+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:146 msg="trying config file" path=devbox.json
time=2024-10-30T17:04:23.074+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devconfig/config.go:133 msg="config file found" path=/home/ineiti/tmp/eid-workshop/devbox.json dur=375.149µs
time=2024-10-30T17:04:23.074+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311Packages.pip mode=auto
time=2024-10-30T17:04:23.074+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=nodejs mode=auto
time=2024-10-30T17:04:23.074+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=python311 mode=auto
time=2024-10-30T17:04:23.074+01:00 level=DEBUG source=go.jetpack.io/devbox/internal/devpkg/package.go:200 msg="package doesn't need patching" pkg=less mode=auto
ineiti@fricklebox:~/tmp/eid-workshop$
@ineiti ineiti added bug Something isn't working triage Issue needs triage labels Oct 30, 2024
@ineiti
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ineiti commented Oct 30, 2024

Interestingly, if I use the jupyter package instead of installing it manually, then it works on both mac and linux!?!

You can

git clone https://github.com/c4dt/eid-workshop/ -b devbox_bug_2

which works.

@gcurtis gcurtis self-assigned this Oct 30, 2024
@gcurtis
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gcurtis commented Oct 30, 2024

@ineiti could you try replacing python311@latest with [email protected]?

Devbox should be auto-patching Python on Linux to fix this, but the logs say it isn't. I think there might be a bug where the version in the package name is tripping it up.

@ineiti
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ineiti commented Oct 31, 2024

@gcurtis Great - that did it, thanks a lot!

I used [email protected], and it worked.

Shall I keep the issue open? As there seems something fishy going on with the python311@latest package, which other people might stumble upon.

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