b-rodrigues
commented
1 day ago Many thanks for testing, this is very valuable input!
I think there should be a renv2nix vignette, which give concrete examples. The function help is extensive, but misses examples and often vignettes are easier as a start.
Yes absolutely, I just didn’t want to write one yet until the api would be stabilized. We are still in an dev/exploratory phase.
Is the workflow: You open R in the renv environment and call
renv2nix(project_path = ".")or should you be outside of the renv enviroment or is this irrelevant?
No, ideally, you should copy the renv.lock file into a new folder, and call renv2nix() there. This is to avoid the issues you had with the .Rprofile file. Both {renv} and {rix} rely on project-level .Rprofile files to correctly set up projects, so if you use the same folder for both, you will have issues.
When i tried it on a toy project it worked fine, although i got the warning message:
### .Rprofile file already exists. You may want to call rix_init(rprofile_action = 'append') manually to ensure correct functioning of your Nix environment. ###Since
renvprojects always have a.Rprofilei found this confusing, shouldn't renv2nix then not just do that? What is the problem if this is not done?
{renv} creates an .Rprofile file to bootstrap {renv} itself, and {rix} uses it to ensure that Nix projects are nicely hermetic, and that no interactions with user-level R library of packages happen. As said before, ideally you should create a separate folder. This will be nicely documented in the vignette and also in renv2nix() documentation.
When I tried
revn2nixon my real project, I got the following warning message (I use Visual Studio Code):## .Rprofile file already exists. You may want to call rix_init(rprofile_action = 'append') manually to ensure correct functioning of your Nix environment. ### cannot open the connectionwarning messages from top-level task callback 'vsc.workspace' Warning message: In file(con, "w") : cannot open file '/tmp/RtmppLc1a1/vscode-R/workspace.json': No such file or directoryWhat does this vsc. workspace connection problem mean?
No idea, as I don’t use VScode. But maybe try in a separate folder, call renv2nix() there, then nix-build, nix-shell and then start VScode from that shell. See if this happens again.
However, the main problem was that
nix-buildfailed with: So datathin is not found, but required by CSFAtlasTools (personal package). But there is actually datathin with correct github repo url and rev
So what happens here is that {datathin} is dependency of {CSFAtlasTools} but it’s on Github. However, the way {rix} is setup, {datathin} will be listed as coming from CRAN:
propagatedBuildInputs = builtins.attrValues {
inherit (pkgs.rPackages) <- this package set is mirroring CRAN
datathin;
};
})But renv2nix() then detects that {datathin} comes from github and correctly includes the right code to install it from Github. But still, from the point of view of {CSFAtlasTools}, {datathin} is being included as a dependency that should come from CRAN. This issue is described here: https://docs.ropensci.org/rix/articles/z-advanced-topic-handling-packages-with-remote-dependencies.html
You should rewrite the expression a little (as described in the vignette) to make it work. For now, {rix} doesn’t handle remote dependencies automatically, and I don’t know if it ever will. It is not an easy issue to solve.
(why is the commit ID called "RemoteSha" in renv.lock called "rev" here?).
That’s just internal jargon.
So is the problem just the order?
No, it’s that the way {rix} doesn’t handle packages with remote dependencies automatically. Some manualy rewriting is needed.
mihem
@b-rodrigues Thanks for renv2nix. As i said I think this is super useful so I was excited to test this new feature.
This is more a collection of problems/ideas than a formal bug report.
I think there should be a renv2nix vignette, which give concrete examples. The function help is extensive, but misses examples and often vignettes are easier as a start.
Is the workflow: You open R in the renv environment and call
renv2nix(project_path = ".")or should you be outside of the renv enviroment or is this irrelevant?When i tried it on a toy project it worked fine, although i got the warning message:
Since
renvprojects always have a.Rprofilei found this confusing, shouldn't renv2nix then not just do that? What is the problem if this is not done?When I tried
revn2nixon my real project, I got the following warning message (I use Visual Studio Code):What does this vsc. workspace connection problem mean?
However, the main problem was that
nix-buildfailed with:The corresponding lines in default.nix:
So datathin is not found, but required by CSFAtlasTools (personal package). But there is actually datathin with correct github repo url and rev (why is the commit ID called "RemoteSha" in renv.lock called "rev" here?). So is the problem just the order?
Thanks!