Does pkgm uninstall remove the symlinks as well?

[sanchitram1]

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

[sanchitram1]

my question is what's happening in the uninstall process? am I missing an additional thing that I gotta remove?

[jhheider]

looking at

pkgm/pkgm.ts

Lines 540 to 620 in e3934de

	async function uninstall(arg: string) {
	let found: { project: string } | undefined =
	(await hooks.usePantry().find(arg))?.[0];
	if (!found) {
	found = await plumbing.which(arg);
	}
	if (!found) {
	console.error(`no such pkg: ${arg}`);
	return false;
	}
	const set = new Set<string>();
	const files: Path[] = [];
	let dirs: Path[] = [];
	const pkg_dirs: Path[] = [];
	const root = install_prefix();
	const dir = root.join("pkgs", found.project);
	if (!dir.isDirectory()) {
	console.error(`not installed: ${dir}`);
	if (
	root.string == "/usr/local" &&
	Path.home().join(".local/pkgs", found.project).isDirectory()
	) {
	console.error(
	`%c! rerun without \`sudo\` to uninstall ~/.local/pkgs/${found.project}`,
	"color:yellow",
	);
	} else if (new Path("/usr/local/pkgs").join(found.project).isDirectory()) {
	console.error(
	`%c! rerun as \`sudo\` to uninstall /usr/local/pkgs/${found.project}`,
	"color:yellow",
	);
	}
	return false;
	}
	console.error("%cuninstalling", "color:red", dir);
	pkg_dirs.push(dir);
	for await (const [pkgdir, { isDirectory }] of dir.ls()) {
	if (!isDirectory) continue;
	for await (const { path, isDirectory } of walk(pkgdir.string)) {
	const leaf = new Path(path).relative({ to: pkgdir });
	const resolved_path = root.join(leaf);
	if (set.has(resolved_path.string)) continue;
	if (!resolved_path.exists()) continue;
	if (isDirectory) {
	dirs.push(resolved_path);
	} else {
	files.push(resolved_path);
	}
	}
	}
	// we need to delete this in a heirachical fashion or they don’t delete
	dirs = dirs.sort().reverse();
	if (files.length == 0) {
	console.error("unexpectedly not installed");
	Deno.exit(1);
	}
	for (const path of files) {
	if (!path.isDirectory()) {
	Deno.removeSync(path.string);
	}
	}
	for (const path of dirs) {
	if (path.isDirectory()) {
	try {
	Deno.removeSync(path.string);
	} catch {
	// some dirs will not be removable
	}
	}
	}
	for (const path of pkg_dirs) {
	Deno.removeSync(path.string, { recursive: true });
	}
	return true;
	}

it looks possible the symlinks aren't being cleaned up... maybe? Hence, when it tries to symlink in the new copy, it's erroring. Try this:

pkgx uninstall libpng.org
ls -l /Users/sanch/.local/pkgs/libpng.org/v1.6.40/lib/libpng.la
ls -l /Users/sanch/.local/lib/libpng.la

we would hope both of those would be gone on uninstall. you mentioned sudo, so it's just possible you've got a root-owned inode that you can't fix as user.

[sanchitram1]

looks like the symlink does exist!

~/Library/Mobile Documents/com~apple~CloudDocs/Documents/berkeley/fall 2025 ························· 12:48:01
❯ sudo pkgm uninstall libpng.org
uninstalling /usr/local/pkgs/libpng.org

~/Library/Mobile Documents/com~apple~CloudDocs/Documents/berkeley/fall 2025 ························· 12:48:05
❯ ls -l /Users/sanch/.local/pkgs/libpng.org/v1.6.40/lib/libpng.la
ls: /Users/sanch/.local/pkgs/libpng.org/v1.6.40/lib/libpng.la: No such file or directory

~/Library/Mobile Documents/com~apple~CloudDocs/Documents/berkeley/fall 2025 ························· 12:48:16
❯ ls -l /Users/sanch/.local/lib/libpng.la                        
lrwxr-xr-x  1 sanch  staff  57 Oct 31 12:19 /Users/sanch/.local/lib/libpng.la -> /Users/sanch/.local/pkgs/libpng.org/v1.6.40/lib/libpng.la

[jhheider]

sounds like a pkgm uninstall bug. does removing the symlink get you working?

[sanchitram1]

it's the symlinks – I ran into the next symlink problem:

error: Uncaught (in promise) AlreadyExists: File exists (os error 17): symlink '/usr/local/pkgs/pip.pypa.io/v23.3.2/bin/pip3' -> '/usr/local/bin/pip3'
  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

i'll go ahead and remove all the symlinks and see if it works out

[sanchitram1]

~/Library/Mobile Documents/com~apple~CloudDocs/Documents/berkeley/fall 2025 ························· 12:54:05
❯ sudo pkgm uninstall pip.pypa.io   
uninstalling /usr/local/pkgs/pip.pypa.io
unexpectedly not installed

hmm…? that's a fun turn of phrase . looks like pip is refusing to uninstall for some reason. should I try to manually delete and see what happens then?

[jhheider]

yep. sounds like uninstall needs work, and perhaps install needs to give the option to be a bit more aggressive about clobbering things.

[mxcl]

You need to upgrade pkgx, you probs haven’t done that in a while. I thought we included a version check in pkgm but I guess not.

-q! is a new(ish) pkgx flag

[sanchitram1]

looks like i've got the latest of all:

❯ pkgm --version
pkgm 0.11.1

~ ·········································································································· 14:20:43
❯ pkgx --version
pkgx 2.7.0

~ ·········································································································· 14:21:12
❯ dev --version
dev 1.5.0