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Does pkgm uninstall remove the symlinks as well?

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#73 9 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
38/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
deno, typescript
Domain
cli, tooling

Research direction

Start by reproducing the sequence with pkgm uninstall libpng.org followed by pkgm install python@3.8, then inspect the installed pkgm/v0.11.1/bin/pkgm paths shown in the stack trace, especially symlink_with_overwrite and the uninstall flow. Done means uninstall removes the package's symlinks and a failed install does not leave stale links or restore the removed package unexpectedly.

Written by the indexing model from the issue text.

Description

I am trying to figure out the dev integration with pkgm. The start of my trouble was when I had a pkgx.yaml file with python@3.8 specified as a dependency, but dev was using python@3.13 from ~/.pkgx/....

Found on dev that the recommended way to use dev for isolated environments is to use pkgm. So, I installed python@3.8 via:

pkgm install python@3.8

I noticed I was getting this error:

❯ pkgm install python@3.8
× nothing provides: q!
│ we haven’t pkgd this yet. can you?
╰─➤ https://docs.pkgx.sh/pantry

I got past that error only if I removed the pkgx.yaml file – once I did that and tried to re-run, I got this error:

error: Uncaught (in promise) AlreadyExists: File exists (os error 17): symlink '/Users/sanch/.local/pkgs/libpng.org/v1.6.40/lib/libpng.la' -> '/Users/sanch/.local/lib/libpng.la'
  Deno.symlinkSync(src, dst);
       ^
    at Object.symlinkSync (ext:deno_fs/30_fs.js:504:3)
    at symlink_with_overwrite (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:501:8)
    at processEntry (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:419:7)
    at eventLoopTick (ext:core/01_core.js:178:7)
    at async processEntry (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:412:9)
    at async symlink (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:397:7)
    at async install (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:159:7)
    at async file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:65:20

ok, so there's already a libpng.la in ~/.local. So, i tried uninstalling (and sudo uninstalling, to remove it from /usr/bin/local, in case it was there too). pasting a big log chunk here - but the idea is that I have libpng.org, i uninstall it and it goes away, i install python@3.8 and it throws an error, and then libpng.org has magically reappeared.

~/L/Mo/com~apple~CloudDocs/Documents/berkeley/fall 2025 ·············· 12:32:36
❯ pkgm list
/usr/local/pkgs/tcl-lang.org/v8.6.13
/usr/local/pkgs/sqlite.org/v3.44.2
/usr/local/pkgs/bytereef.org/mpdecimal/v2.5.1
/usr/local/pkgs/sourceware.org/libffi/v3.4.4
/usr/local/pkgs/sourceware.org/bzip2/v1.0.8
/usr/local/pkgs/openssl.org/v1.1.1w
/usr/local/pkgs/tukaani.org/xz/v5.4.5
/usr/local/pkgs/freetype.org/v2.13.2
/usr/local/pkgs/pkgx.sh/v2.7.0
/usr/local/pkgs/pkgx.sh/v1.5.0
/usr/local/pkgs/zlib.net/v1.3.0
/usr/local/pkgs/gnu.org/readline/v8.2.0
/usr/local/pkgs/invisible-island.net/ncurses/v6.4.0
/usr/local/pkgs/libexpat.github.io/v2.5.0
/usr/local/pkgs/pip.pypa.io/v23.3.2
/usr/local/pkgs/curl.se/ca-certs/v2023.12.12
/usr/local/pkgs/x.org/x11/v1.8.11
/usr/local/pkgs/x.org/protocol/v2023.2.0
/usr/local/pkgs/x.org/xau/v1.0.11
/usr/local/pkgs/x.org/xdmcp/v1.1.4
/usr/local/pkgs/x.org/exts/v1.3.5
~/.local/pkgs/libpng.org/v1.6.40
~/.local/pkgs/tcl-lang.org/v8.6.13
~/.local/pkgs/sqlite.org/v3.44.2
~/.local/pkgs/bytereef.org/mpdecimal/v2.5.1
~/.local/pkgs/sourceware.org/libffi/v3.4.4
~/.local/pkgs/sourceware.org/bzip2/v1.0.8
~/.local/pkgs/freedesktop.org/pkg-config/v0.29.2
~/.local/pkgs/github.com/spencerkimball/stargazers/v0.0.0
~/.local/pkgs/openssl.org/v1.1.1w
~/.local/pkgs/tukaani.org/xz/v5.4.5
~/.local/pkgs/freetype.org/v2.13.2
~/.local/pkgs/pkgx.sh/v2.7.0
~/.local/pkgs/pkgx.sh/v1.5.0
~/.local/pkgs/pkgx.sh/dev/v1.5.0
~/.local/pkgs/zlib.net/v1.3.0
~/.local/pkgs/gnu.org/readline/v8.2.0
~/.local/pkgs/invisible-island.net/ncurses/v6.4.0
~/.local/pkgs/libexpat.github.io/v2.5.0
~/.local/pkgs/pip.pypa.io/v23.3.2
~/.local/pkgs/curl.se/ca-certs/v2023.12.12
~/.local/pkgs/x.org/x11/v1.8.11
~/.local/pkgs/x.org/protocol/v2023.2.0
~/.local/pkgs/x.org/util-macros/v1.20.0
~/.local/pkgs/x.org/xau/v1.0.11
~/.local/pkgs/x.org/xdmcp/v1.1.4
~/.local/pkgs/x.org/exts/v1.3.5
~/.local/pkgs/x.org/xcb/v1.16.0

~/L/Mo/com~apple~CloudDocs/Documents/berkeley/fall 2025 ·············· 12:33:46
❯ pkgm uninstall libpng.org
uninstalling ~/.local/pkgs/libpng.org

~/L/Mo/com~apple~CloudDocs/Documents/berkeley/fall 2025 ·············· 12:34:00
❯ pkgm install python@3.8
error: Uncaught (in promise) AlreadyExists: File exists (os error 17): symlink '/Users/sanch/.local/pkgs/libpng.org/v1.6.40/lib/libpng.la' -> '/Users/sanch/.local/lib/libpng.la'
  Deno.symlinkSync(src, dst);
       ^
    at Object.symlinkSync (ext:deno_fs/30_fs.js:504:3)
    at symlink_with_overwrite (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:501:8)
    at processEntry (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:419:7)
    at eventLoopTick (ext:core/01_core.js:178:7)
    at async processEntry (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:412:9)
    at async symlink (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:397:7)
    at async install (file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:159:7)
    at async file:///Users/sanch/.pkgx/pkgx.sh/pkgm/v0.11.1/bin/pkgm:65:20

~/L/Mo/com~apple~CloudDocs/Documents/berkeley/fall 2025 ··········· 8s 12:34:13
❯ pkgm list
/usr/local/pkgs/tcl-lang.org/v8.6.13
/usr/local/pkgs/sqlite.org/v3.44.2
/usr/local/pkgs/bytereef.org/mpdecimal/v2.5.1
/usr/local/pkgs/sourceware.org/libffi/v3.4.4
/usr/local/pkgs/sourceware.org/bzip2/v1.0.8
/usr/local/pkgs/openssl.org/v1.1.1w
/usr/local/pkgs/tukaani.org/xz/v5.4.5
/usr/local/pkgs/freetype.org/v2.13.2
/usr/local/pkgs/pkgx.sh/v2.7.0
/usr/local/pkgs/pkgx.sh/v1.5.0
/usr/local/pkgs/zlib.net/v1.3.0
/usr/local/pkgs/gnu.org/readline/v8.2.0
/usr/local/pkgs/invisible-island.net/ncurses/v6.4.0
/usr/local/pkgs/libexpat.github.io/v2.5.0
/usr/local/pkgs/pip.pypa.io/v23.3.2
/usr/local/pkgs/curl.se/ca-certs/v2023.12.12
/usr/local/pkgs/x.org/x11/v1.8.11
/usr/local/pkgs/x.org/protocol/v2023.2.0
/usr/local/pkgs/x.org/xau/v1.0.11
/usr/local/pkgs/x.org/xdmcp/v1.1.4
/usr/local/pkgs/x.org/exts/v1.3.5
~/.local/pkgs/libpng.org/v1.6.40
~/.local/pkgs/tcl-lang.org/v8.6.13
~/.local/pkgs/sqlite.org/v3.44.2
~/.local/pkgs/bytereef.org/mpdecimal/v2.5.1
~/.local/pkgs/sourceware.org/libffi/v3.4.4
~/.local/pkgs/sourceware.org/bzip2/v1.0.8
~/.local/pkgs/freedesktop.org/pkg-config/v0.29.2
~/.local/pkgs/github.com/spencerkimball/stargazers/v0.0.0
~/.local/pkgs/openssl.org/v1.1.1w
~/.local/pkgs/tukaani.org/xz/v5.4.5
~/.local/pkgs/freetype.org/v2.13.2
~/.local/pkgs/pkgx.sh/v2.7.0
~/.local/pkgs/pkgx.sh/v1.5.0
~/.local/pkgs/pkgx.sh/dev/v1.5.0
~/.local/pkgs/zlib.net/v1.3.0
~/.local/pkgs/gnu.org/readline/v8.2.0
~/.local/pkgs/invisible-island.net/ncurses/v6.4.0
~/.local/pkgs/libexpat.github.io/v2.5.0
~/.local/pkgs/pip.pypa.io/v23.3.2
~/.local/pkgs/curl.se/ca-certs/v2023.12.12
~/.local/pkgs/x.org/x11/v1.8.11
~/.local/pkgs/x.org/protocol/v2023.2.0
~/.local/pkgs/x.org/util-macros/v1.20.0
~/.local/pkgs/x.org/xau/v1.0.11
~/.local/pkgs/x.org/xdmcp/v1.1.4
~/.local/pkgs/x.org/exts/v1.3.5
~/.local/pkgs/x.org/xcb/v1.16.0
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