Support for {renv} projects

wurli commented 6 months ago

NB, this issue has previously been discussed at jalvesaq/Nvim-R/issues/445.

Problem description

When a project uses {renv}, {nvimcom} is not available, meaning a good deal of R.nvim breaks. The reason for this is that in {renv} projects the .libPaths() are reset, meaning R can no longer find {nvimcom}, which will have been installed by R.nvim into the libpath where most other package installations also live.

Current workaround

The workaround people seem to have been using is to:

Create a new libpath directory somewhere, e.g. called nvimcomlib
Create a symlink within this libpath that points to the existing nvimcom installation
Set the RENV_CONFIG_EXTERNAL_LIBRARIES environmental variable to point to this new libpath, which tells {renv} it can also look for package installations here

There are a few issues with this workaround:

You need to go through these steps each time you update R
Symlinks may be hard to create, e.g. on Windows without admin privileges
It requires some esoteric knowledge, both about {renv} and R.nvim

Suggested approach for seamless {renv} support

When R.nvim is installed, instead of dropping {nvimcom} into the user's default libpath directory, keep this package in its own dedicated directory somewhere else
Then, let R know that it can also look for package installations in this alternative location, e.g. by setting the R_LIBS environmental variable before R starts up
At the same time, set the RENV_CONFIG_EXTERNAL_LIBRARIES environmental variable to the same value, thereby making {nvimcom} available in {renv} projects

I'm not that familiar with with what happens when R.nvim is installed, so I don't know how realistic/well informed this approach is. However, {renv} is pretty widely used - a quick GitHub search reveals 9.1k repos with a renv.lock file - so in my humble opinion, it's worth seriously considering adding official support.

PMassicotte commented 6 months ago

That is interesting, I just opened like 5-6 old projects using renv and I had no issues. When I open such project, I see that nvimcom is being installed.

wurli commented 6 months ago

Interesting indeed! Have you previously done any additional setup to get renv working with R.nvim?

PMassicotte commented 6 months ago

Nothing I can think of. I just had a look inside one of the renv.lock file and nvimcom is not even listed. Humm I am not sure what is goin on!

wurli commented 6 months ago

That's very strange - if renv installs nvimcom, it must have already cached it or be configured to know where to look for it, since nvimcom isn't on CRAN. Either way, I'm 99% sure it won't Just Work™ from a fresh system. Would be great if others could test and confirm 🙏

wklimowicz commented 6 months ago

I've had this problem before and just tested it now. I bypass renv by setting export R_PROFILE_USER="~/.Rprofile" in my .zshrc, which bypasses the project .Rprofile and essentially deactivates renv.

The reason for this is that with R_PROFILE_USER unset, renv loads, and tries to install R packages but loading my ~/.Rprofile first. I have a messy .Rprofile which has library calls to remotes and rlang which breaks the renv process. I'm sure I could fix this by tidying my .Rprofile.

If I open a renv project without R_PROFILE_USER and no ~/.RProfile everything works fine for me, nvimcom compiles and R.nvim loads with no issues.

hongyuanjia commented 6 months ago

I can confirm that R.nvim works fine with {renv} with no issue. The only step needed is to completely exit Neovim after renv::init() and open Neovim again. {nvimcom} will be installed in renv folder but will not appear in renv.lock.

PMassicotte commented 2 months ago

Can we close this? I am using renv all the time and I am facing no issues. @wurli are you experiencing any current problems with renv?

Nand1sh commented 2 months ago

@PMassicotte I believe I am facing the same issue. rnvimserver dumps core upon first interaction with a renv enabled project. I could not replicate this in my journal for scripts or projects that do not use renv. Also, as @wurli suggested, this problem occurs only after a fresh boot. If I were to first open a regular project and then move on to one with renv enabled then everything works great.

PMassicotte commented 2 months ago

What is the value of

setwd = "nvim",

Nand1sh commented 2 months ago

:echo getcwd() in Neovim's command mode and getwd() in R console both point to my renv project's directory namely "/home/nand1sh/Study/LWE_RESEARCH".

PMassicotte commented 2 months ago

Do you use built-in terminal or something else?

Nand1sh commented 2 months ago

Yes, I use the built in terminal for R in R.nvim.

PMassicotte commented 2 months ago

That is interesting. I can not reproduce the problem at the moment. When I open a renv project for the first time, I see that nvimcom is being installed (takes 2–3 seconds). Then I am ready to go. Do you have any logs to share?

Nand1sh commented 2 months ago

Hey, this helps! If I wait for a few seconds and then start R, I get no issues. Only if I start R immediately after opening a .R file in a renv enabled project do I get this-

Jul 31 16:30:43 archlinux systemd-coredump[1096]: Process 1059 (rnvimserver) of user 1000 terminated abnormally with signal 11/SEGV, processing...
Jul 31 16:30:43 archlinux systemd[1]: Created slice Slice /system/systemd-coredump.
Jul 31 16:30:43 archlinux systemd[1]: Started Process Core Dump (PID 1096/UID 0).
Jul 31 16:30:43 archlinux systemd-coredump[1097]: [🡕] Process 1059 (rnvimserver) of user 1000 dumped core.

                                                  Stack trace of thread 1059:
                                                  #0  0x00007a498ab79fad pthread_cancel (libc.so.6 + 0x90fad)
                                                  #1  0x00005a7681e249bb n/a (/home/nand1sh/Study/LWE_RESEARCH/renv/library/linux-arch-rolling/R-4>
                                                  #2  0x0000000000000000 n/a (n/a + 0x0)
                                                  ELF object binary architecture: AMD x86-64
Jul 31 16:30:43 archlinux systemd[1]: systemd-coredump@0-1096-0.service: Deactivated successfully.

However, unlike you I do not get a prompt saying that nvimcom is being installed. Is it because I have the --quiet argument enabled for R.nvim?

jalvesaq commented 2 months ago

The R_args config option is used only to launch R in the terminal emulator for interactive use. The message that nvimcom is being installed is always displayed with vim.api.nvim_echo() (see scripts/before_rns.R, line 115, and lua/r/server.lua, line 73).

PMassicotte commented 2 months ago

Hey, this helps! If I wait for a few seconds and then start R, I get no issues. Only if I start R immediately after opening a .R file in a renv enabled project do I get this-

Jul 31 16:30:43 archlinux systemd-coredump[1096]: Process 1059 (rnvimserver) of user 1000 terminated abnormally with signal 11/SEGV, processing...
Jul 31 16:30:43 archlinux systemd[1]: Created slice Slice /system/systemd-coredump.
Jul 31 16:30:43 archlinux systemd[1]: Started Process Core Dump (PID 1096/UID 0).
Jul 31 16:30:43 archlinux systemd-coredump[1097]: [🡕] Process 1059 (rnvimserver) of user 1000 dumped core.

                                                  Stack trace of thread 1059:
                                                  #0  0x00007a498ab79fad pthread_cancel (libc.so.6 + 0x90fad)
                                                  #1  0x00005a7681e249bb n/a (/home/nand1sh/Study/LWE_RESEARCH/renv/library/linux-arch-rolling/R-4>
                                                  #2  0x0000000000000000 n/a (n/a + 0x0)
                                                  ELF object binary architecture: AMD x86-64
Jul 31 16:30:43 archlinux systemd[1]: systemd-coredump@0-1096-0.service: Deactivated successfully.

However, unlike you I do not get a prompt saying that nvimcom is being installed. Is it because I have the --quiet argument enabled for R.nvim?

I am using auto-open in my config, so it is likely waiting for the initialization to be done before loading R. My guess is that you just have to wait 2-3 seconds before opening the terminal in an renv project.

Nand1sh commented 2 months ago

I see. Thanks for the clarification @jalvesaq and @PMassicotte!

R-nvim / R.nvim