renv::install("duckdb") hangs indefinitely

[philiporlando]

I may have found a bug with Positron's R console, but I wanted to ask here before opening an issue.

I've started a fresh Positron project using R 4.1.1. After successfully installing {renv}, I'm able to call renv::install() on most R packages without any issues.

renv::install("dplyr")
# # Downloading packages -------------------------------------------------------
# - Downloading cli from CRAN ...                 OK [554.8 Kb in 0.28s]
# - Downloading withr from CRAN ...               OK [101 Kb]
# Successfully downloaded 2 packages in 0.79 seconds.

However, renv::install("duckdb") appears to be hanging indefinitely:

renv::install("duckdb")
# # Downloading packages -------------------------------------------------------
# - Downloading duckdb from CRAN ...              OK [file is up to date]
# Successfully downloaded 1 package in 0.55 seconds.
# 
# The following package(s) will be installed:
# - DBI    [1.2.3]
# - duckdb [1.0.0-2]
# These packages will be installed into "~/Projects/dockerized-duckplyr-demo/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

# Do you want to proceed? [Y/n]: 
y

# # Installing packages --------------------------------------------------------
# - Installing DBI ...                            OK [linked from cache]
# - Installing duckdb ...                         

So far I've been waiting ~15 minutes for this to install and nothing has changed.

[jthomasmock]

Hmm. I'm not able to reproduce locally with a brand-new project. Could you drop sessioninfo and Positron info from Positron > About Positron?

> renv::init()
The following package(s) will be updated in the lockfile:

# RSPM -----------------------------------------------------------------------
- renv   [* -> 1.0.7]

The version of R recorded in the lockfile will be updated:
- R      [* -> 4.4.0]

- Lockfile written to "~/test-duckdb/renv.lock".
- renv activated -- please restart the R session.

## ---- RESTARTED SESSION

R 4.4.0 exited (preparing for restart)

R 4.4.0 restarted.
- Project '~/test-duckdb' loaded. [renv 1.0.7]
> renv::install("duckdb")
# Downloading packages -------------------------------------------------------
- Downloading duckdb from CRAN ...              OK [9.3 Mb in 1.5s]
- Downloading DBI from CRAN ...                 OK [905.4 Kb in 1.6s]
Successfully downloaded 2 packages in 5.8 seconds.

The following package(s) will be installed:
- DBI    [1.2.3]
- duckdb [1.0.0-2]
These packages will be installed into "~/test-duckdb/renv/library/macos/R-4.4/aarch64-apple-darwin20".

Do you want to proceed? [Y/n]: 
Y

# Installing packages --------------------------------------------------------
- Installing DBI ...                            OK [installed binary and cached in 13s]
- Installing duckdb ...                         OK [installed binary and cached in 0.7s]
Successfully installed 2 packages in 14 seconds.

[philiporlando]

Positron Version: 2024.07.0 build 125
Code - OSS Version: 1.91.0
Commit: cae4905332a0f41a6233e196b48a6679b832000a
Date: 2024-07-31T22:15:48.921Z
Electron: 29.4.0
Chromium: 122.0.6261.156
Node.js: 20.9.0
V8: 12.2.281.27-electron.0
OS: Linux x64 5.15.0-117-generic

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.4.1 tools_4.4.1  

[DavisVaughan]

Is it perhaps trying to build duckdb from source? That package takes a long long time to build from source, so it could just be in the middle of compiling it. If I remember correctly, upwards of 15-20 min is not unreasonable.

Do you see the same in RStudio? Or does it quickly pull in a binary for you there?

[kevinushey]

In any case, manually setting the repositories via e.g.

options(repos = c(P3M = "https://packagemanager.posit.co/cran/latest"))

should also suffice?

[philiporlando]

Manually setting the repos is working for me.

> options(repos = c(P3M = "https://packagemanager.posit.co/cran/latest"))
> renv::install("duckdb", rebuild = TRUE)
# Downloading packages -------------------------------------------------------
- Downloading duckdb from P3M ...               OK [file is up to date]
Successfully downloaded 1 package in 8.7 seconds.

The following package(s) will be installed:
- duckdb [1.0.0-2]
These packages will be installed into "~/Projects/test-positron-duckdb/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu".

Do you want to proceed? [Y/n]: 
y

# Installing packages --------------------------------------------------------
- Installing duckdb ...                         OK [installed binary and cached in 14s]
Successfully installed 1 package in 17 seconds.
Warning message:
In file(file, "rt") :
  cannot open file '/usr/lib/R/doc/CRAN_mirrors.csv': No such file or directory

[juliasilge]

I opened this issue to improve this experience: rstudio/renv#1963

I do want to note that if I run renv::diagnostics() in Positron, I see this:

$ repos                               : Named chr "https://cran.rstudio.com/"
  ..- attr(*, "names")= chr "CRAN"

[DavisVaughan]

Oh, we do that in ark.
https://github.com/posit-dev/ark/blob/9387883055176bb0493b9893cd392f53a1bda0ed/crates/ark/src/modules/positron/options.R#L30-L45

@kevinushey is that borking something?

[juliasilge]

I opened this, for improvements needed on the Positron end: #4255