6 ms·

Thoughts on “Dependency hell is NP-complete”

95 points by cwp 10y ago

jpollock 10y ago
I didn't understand why it would be NP-complete, dependencies represent an acyclic graph. However, this is the killer: "Two different versions of a package cannot be installed simultaneously." Get rid of that, and your problems disappear. Which is why my linux server has: 1 gcc-4.8-base:amd64 2 gcc-4.9-base:amd64 3 gcc-5-base:amd64 4 gcc-6-base:amd64
- amelius 10y ago
  > "Two different versions of a package cannot be installed simultaneously." It seems that the problem then might not even have a solution in all cases. So perhaps we should rethink the problem.
  - Dylan16807 10y ago
    It's easy to turn an acyclic graph into a bunch of directories, or to turn a cyclic graph into a bunch of directories and symlinks. If you allow side-by-side versions then the only remaining failure case is a dependency that doesn't exist. Nothing to rethink there.
- lazyjones 10y ago
  > dependencies represent an acyclic graph AFAICT that's not always true. Several scripting languages allow circular dependencies (Node.js, Perl) and so do some popular package managers (with specific workarounds, but the point is that such dependency constellations exist): https://www.debian.org/doc/debian-policy/ch-relationships.html https://www.debian.org/doc/debian-policy/ch-relationships.ht... Perhaps the problem needs to be examined differently depending on allowed/existing-in-the-wild circular dependencies.
  - dozzie 10y ago
    >> dependencies represent an acyclic graph > AFAICT that's not always true. And you are right. apt-get has "upgrade" and "dist-upgrade" commands for a long, long time for a reason (the latter allows to upgrade packages in the presence of dependency cycles and some other cases that would be nasty if left in the middle of upgrade; obviously, no changes that need dist-upgrade land in Debian stable).
thinkpad20 10y ago
Nix has a different approach to the problem, with its own set of benefits and drawbacks: packages do not specify version ranges of their dependencies at all; instead they reference them via variables (most commonly -- more generally they can be any arbitrary expression). For example if I'm writing a python package which depends on flask, I might list `flask` as a dependency of my package, or perhaps `flask11` or something. # pseudocode my_package = buildPythonPackage { name = "my_package"; source = ./path/to/source; dependencies = [flask]; }; Whatever that variable resolves to is the thing which will be built (and is itself defined in a similar way), so "version resolution" is replaced with a pure computation, the evaluation of an expression. This approach offers a great deal of advantages, including very fast (roughly linear) calculation of what to build, full determinism in what gets built, and the ability to specify any arbitrary nix expression as a dependency, say some C library or a command-line tool, rather than being limited just to specifying packages written for your particular language. However, of course, it does come with some drawbacks. Among them is the requirement that you often can't simply use nix out-of-the-box to build your code; depending on how developed the nix ecosystem is for a particular language, you might have to figure out for language X how packages are built, tested, installed, and linked together, and write the appropriate abstractions in nix. It also means that you won't automatically pick up later versions of a dependency when you (re)build it, which means you might miss out on updates. However, this latter drawback is arguably a benefit, because by the same token you won't accidentally pull in regressions due to an update in a dependency.
- skrebbel 10y ago
  I don't understand this. You're saying that the way the dependencies are written down (with code, not declarations) changes the NP-completeness characteristics of dependency resolution. I strongly doubt that, just like a search in an unindexed database table is O(N) no matter whether you write it as an SQL query or a for loop. What assumptions about dependencies does Nix make / weaken that makes resolution linear-time? Any of those 4 Russ Cox lists? Or did Nix come up with some genius insight that shows that there's more than 4 core assumptions in the NP Completeness proof and the 5th one is the one that can be safely dropped?
Too 10y ago
> I am personally very interested in the idea of allowing packages to mark their dependencies as either "shared" or "internal". We could then disallow shared dependencies from duplicating, but allow internal dependencies to duplicate freely. CMake has this feature. You can mark dependencies as either public, private or interface. With public meaning that sub dependencies can be reached through public interfaces and private that they just stay inside the program and can be replaced while still maintaining full backwards compatibility with your public interface.
- deleted 10y ago
  [deleted]
tolmasky 10y ago
At some point we will do a more in depth write-up about this, but I think we have a very unique take on this at RunKit as we've effectively installed every version of every package. It's actually more interesting than that, we've installed every reasonable combinatorial dependency result of every version of every package on npm. Long story short, I think there was tremendous insight in npm 2's original model of having every dependency duplicated. Beyond allowing neat things like diffing two versions of the same package (https://runkit.com/tolmasky/api-diff-example-4 https://runkit.com/tolmasky/api-diff-example-4 ), I think it most accurately portrays the meaning of a package/version. The fundamental problem with trying to "unify" all the dependencies a program will need, is that it almost guarantees that code will be running in an untested state. Package A was written when Dependency 1 was at version 1.0.0. By assigning it the semver range 1.x.x (instead of the strict 1.0.0 dependency), that means that at some later point it will run against code its never seen or was tested against before. Sure, semver ranges are supposed to protect against this having a "meaningful" effect, but this simply kicks the can down the responsibility chain, changing the error to "human error" as if it makes a difference. For example, let's say at the time of publishing Dependency 1 had a bug that Package A accounted for. According to semver, a fix for this bug would qualify as a 1.0.1, but now Package A's workaround may actually break. The fact of the matter is: 1. rarely is code fully tested, 2. humans can't be trusted to properly assign semver, 3. semver doesn't even account for every possible "meaningful" change (I've seen performance changes that had devastating effects despite the "result" being the same). Different code is different code. Now, you may be saying, what does this have to do with npm, it sounds like what you want is strict versioning -- the problem is that compounding this already tenuous situation with versions that change depending on the combination of dependencies you have in order to maximize deduping makes this problem even worse. Let me give you a security example: 1. Package A relies on Dependency 1, ranged at 1.x.x. 2. Dependency 1 is found to have a security problem, so a 1.0.1 fix is issued. 3. Package A correctly no longer suffers from this problem. Later, Package B is added, which someone has maliciously, 10 sup-denendencies deep, added a strict dependency to Dependency 1 1.0.0. The deduping algorithm now says: 1. 1.x.x and 1.0.0 are the requirements, I will use 1.0.0. Now Package A is using an insecure version of Dependency 1. Previously, if every package was given its own dependencies, the issue would be scoped to Package B, instead it now infects everyone that relies on this Dependency. Sure, you can fix this by saying "dedupe after giving every package its highest possible dependency", but now you still suffer from monkey-patching affecting other code. You end up with very difficult to understand results. Sometimes, all the code uses the same package, other times not, seemingly randomly. The problem is that a performance issue is being turned into a functional issue. Package should be black boxes, not things you change the guts of regularly. There exists a tool for sharing dependencies: "peerDependencies". This says "I expect this to be around" vs. "I am including this". The basic idea here is that you would never say "let's arbitrarily replace functions I've written in my program with approximately the same function in order to be able to be able to share them and reduce program size". This is nuts! Package versions should be considered hashes that only coincidentally have human names. NPM 2 is the closest I've seen anything come to this, and it creates the least surprises. Most the remedies I've seen revolve around solving performance or efficiency problems this has. But I think it should first be important to make it right, THEN make it fast. You can definitely imagine a system that uses content-hashes to get the space efficiency without the cost of the conceptual separation. In fact, IED does this quite well: https://github.com/alexanderGugel/ied https://github.com/alexanderGugel/ied
hellbanner 10y ago
Relevant: The Science of Security, arguing against Turing Complete programs when less powerful will suffice https://www.youtube.com/watch?v=v8F8BqSa-XY https://www.youtube.com/watch?v=v8F8BqSa-XY
zzzcpan 10y ago
If you keep dependencies resolved at all times and operate on packages with hardcoded versions of dependencies, as Nix does, you can avoid that NP-problem. Sadly, I remember people involved in Go packaging discussions being dismissive of Nix's ideas.
- sagichmal 10y ago
  You remember incorrectly. Nix, unfortunately, just isn't suitable for non-final dependency resolution, i.e. libraries. And that's an important part of the mandate for language packaging discussions.
  - zzzcpan 10y ago
    Nix itself isn't suitable for many things, but the ideas those guys came up with are great and work well.
deleted 10y ago
[deleted]

95 points by cwp 10y ago

I didn't understand why it would be NP-complete, dependencies represent an acyclic graph. However, this is the killer: "Two different versions of a package cannot be installed simultaneously." Get rid of that, and your problems disappear. Which is why my linux server has: 1 gcc-4.8-base:amd64 2 gcc-4.9-base:amd64 3 gcc-5-base:amd64 4 gcc-6-base:amd64

amelius 10y ago
> "Two different versions of a package cannot be installed simultaneously." It seems that the problem then might not even have a solution in all cases. So perhaps we should rethink the problem.
- Dylan16807 10y ago
  It's easy to turn an acyclic graph into a bunch of directories, or to turn a cyclic graph into a bunch of directories and symlinks. If you allow side-by-side versions then the only remaining failure case is a dependency that doesn't exist. Nothing to rethink there.
lazyjones 10y ago
> dependencies represent an acyclic graph AFAICT that's not always true. Several scripting languages allow circular dependencies (Node.js, Perl) and so do some popular package managers (with specific workarounds, but the point is that such dependency constellations exist): https://www.debian.org/doc/debian-policy/ch-relationships.html https://www.debian.org/doc/debian-policy/ch-relationships.ht... Perhaps the problem needs to be examined differently depending on allowed/existing-in-the-wild circular dependencies.
- dozzie 10y ago
  >> dependencies represent an acyclic graph > AFAICT that's not always true. And you are right. apt-get has "upgrade" and "dist-upgrade" commands for a long, long time for a reason (the latter allows to upgrade packages in the presence of dependency cycles and some other cases that would be nasty if left in the middle of upgrade; obviously, no changes that need dist-upgrade land in Debian stable).

thinkpad20 10y ago

Nix has a different approach to the problem, with its own set of benefits and drawbacks: packages do not specify version ranges of their dependencies at all; instead they reference them via variables (most commonly -- more generally they can be any arbitrary expression). For example if I'm writing a python package which depends on flask, I might list `flask` as a dependency of my package, or perhaps `flask11` or something. # pseudocode my_package = buildPythonPackage { name = "my_package"; source = ./path/to/source; dependencies = [flask]; }; Whatever that variable resolves to is the thing which will be built (and is itself defined in a similar way), so "version resolution" is replaced with a pure computation, the evaluation of an expression. This approach offers a great deal of advantages, including very fast (roughly linear) calculation of what to build, full determinism in what gets built, and the ability to specify any arbitrary nix expression as a dependency, say some C library or a command-line tool, rather than being limited just to specifying packages written for your particular language. However, of course, it does come with some drawbacks. Among them is the requirement that you often can't simply use nix out-of-the-box to build your code; depending on how developed the nix ecosystem is for a particular language, you might have to figure out for language X how packages are built, tested, installed, and linked together, and write the appropriate abstractions in nix. It also means that you won't automatically pick up later versions of a dependency when you (re)build it, which means you might miss out on updates. However, this latter drawback is arguably a benefit, because by the same token you won't accidentally pull in regressions due to an update in a dependency.

skrebbel 10y ago
I don't understand this. You're saying that the way the dependencies are written down (with code, not declarations) changes the NP-completeness characteristics of dependency resolution. I strongly doubt that, just like a search in an unindexed database table is O(N) no matter whether you write it as an SQL query or a for loop. What assumptions about dependencies does Nix make / weaken that makes resolution linear-time? Any of those 4 Russ Cox lists? Or did Nix come up with some genius insight that shows that there's more than 4 core assumptions in the NP Completeness proof and the 5th one is the one that can be safely dropped?

Too 10y ago

> I am personally very interested in the idea of allowing packages to mark their dependencies as either "shared" or "internal". We could then disallow shared dependencies from duplicating, but allow internal dependencies to duplicate freely. CMake has this feature. You can mark dependencies as either public, private or interface. With public meaning that sub dependencies can be reached through public interfaces and private that they just stay inside the program and can be replaced while still maintaining full backwards compatibility with your public interface.

deleted 10y ago
[deleted]

tolmasky 10y ago

At some point we will do a more in depth write-up about this, but I think we have a very unique take on this at RunKit as we've effectively installed every version of every package. It's actually more interesting than that, we've installed every reasonable combinatorial dependency result of every version of every package on npm. Long story short, I think there was tremendous insight in npm 2's original model of having every dependency duplicated. Beyond allowing neat things like diffing two versions of the same package (https://runkit.com/tolmasky/api-diff-example-4 https://runkit.com/tolmasky/api-diff-example-4 ), I think it most accurately portrays the meaning of a package/version. The fundamental problem with trying to "unify" all the dependencies a program will need, is that it almost guarantees that code will be running in an untested state. Package A was written when Dependency 1 was at version 1.0.0. By assigning it the semver range 1.x.x (instead of the strict 1.0.0 dependency), that means that at some later point it will run against code its never seen or was tested against before. Sure, semver ranges are supposed to protect against this having a "meaningful" effect, but this simply kicks the can down the responsibility chain, changing the error to "human error" as if it makes a difference. For example, let's say at the time of publishing Dependency 1 had a bug that Package A accounted for. According to semver, a fix for this bug would qualify as a 1.0.1, but now Package A's workaround may actually break. The fact of the matter is: 1. rarely is code fully tested, 2. humans can't be trusted to properly assign semver, 3. semver doesn't even account for every possible "meaningful" change (I've seen performance changes that had devastating effects despite the "result" being the same). Different code is different code. Now, you may be saying, what does this have to do with npm, it sounds like what you want is strict versioning -- the problem is that compounding this already tenuous situation with versions that change depending on the combination of dependencies you have in order to maximize deduping makes this problem even worse. Let me give you a security example: 1. Package A relies on Dependency 1, ranged at 1.x.x. 2. Dependency 1 is found to have a security problem, so a 1.0.1 fix is issued. 3. Package A correctly no longer suffers from this problem. Later, Package B is added, which someone has maliciously, 10 sup-denendencies deep, added a strict dependency to Dependency 1 1.0.0. The deduping algorithm now says: 1. 1.x.x and 1.0.0 are the requirements, I will use 1.0.0. Now Package A is using an insecure version of Dependency 1. Previously, if every package was given its own dependencies, the issue would be scoped to Package B, instead it now infects everyone that relies on this Dependency. Sure, you can fix this by saying "dedupe after giving every package its highest possible dependency", but now you still suffer from monkey-patching affecting other code. You end up with very difficult to understand results. Sometimes, all the code uses the same package, other times not, seemingly randomly. The problem is that a performance issue is being turned into a functional issue. Package should be black boxes, not things you change the guts of regularly. There exists a tool for sharing dependencies: "peerDependencies". This says "I expect this to be around" vs. "I am including this". The basic idea here is that you would never say "let's arbitrarily replace functions I've written in my program with approximately the same function in order to be able to be able to share them and reduce program size". This is nuts! Package versions should be considered hashes that only coincidentally have human names. NPM 2 is the closest I've seen anything come to this, and it creates the least surprises. Most the remedies I've seen revolve around solving performance or efficiency problems this has. But I think it should first be important to make it right, THEN make it fast. You can definitely imagine a system that uses content-hashes to get the space efficiency without the cost of the conceptual separation. In fact, IED does this quite well: https://github.com/alexanderGugel/ied https://github.com/alexanderGugel/ied

hellbanner 10y ago

Relevant: The Science of Security, arguing against Turing Complete programs when less powerful will suffice https://www.youtube.com/watch?v=v8F8BqSa-XY https://www.youtube.com/watch?v=v8F8BqSa-XY

zzzcpan 10y ago

If you keep dependencies resolved at all times and operate on packages with hardcoded versions of dependencies, as Nix does, you can avoid that NP-problem. Sadly, I remember people involved in Go packaging discussions being dismissive of Nix's ideas.

sagichmal 10y ago
You remember incorrectly. Nix, unfortunately, just isn't suitable for non-final dependency resolution, i.e. libraries. And that's an important part of the mandate for language packaging discussions.
- zzzcpan 10y ago
  Nix itself isn't suitable for many things, but the ideas those guys came up with are great and work well.

deleted 10y ago

[deleted]