--without-sysreqs is not working?

[eitsupi]

#15 70.89 [INFO] Adding /usr/local/bin/R-4.3.1 -> /opt/R/4.3.1/bin/R
#15 70.89 [INFO] Adding R-release alias to R 4.3.1
#15 70.89 [INFO] Setting default CRAN mirror
#15 70.89 [INFO] Setting up P3M
#15 70.89 [INFO] Setting up automatic system requirements installation.

I noticed the above log even though I added the --without-sysreqs flag in the following location.
https://github.com/rocker-org/devcontainer-features/blob/69598501ac7fc591878b9e29ca8e730768c4fa10/src/r-rig/install.sh#L331

It seems --without-sysreqs does nothing?

rig/src/linux.rs

Lines 609 to 633 in 74bb252

	fn set_sysreqs(vers: Option<Vec<String>>) -> Result<(), Box<dyn Error>> {
	info!("Setting up automatic system requirements installation.");
	let vers = match vers {
	Some(x) => x,
	None => sc_get_list()?,
	};
	let rcode = r#"
	Sys.setenv(PKG_SYSREQS = "true")
	Sys.setenv(PKG_SYSREQS2 = "true")
	"#;
	for ver in vers {
	let ver = check_installed(&ver)?;
	let path = Path::new(R_ROOT).join(ver.as_str());
	let profile = path.join("lib/R/library/base/R/Rprofile".to_string());
	if !profile.exists() {
	continue;
	}
	append_to_file(&profile, vec![rcode.to_string()])?;
	}
	Ok(())
	}

[gaborcsardi]

Yeah, it would actually need to set

PKG_SYSREQS="false"

because the default is true now in pak.

[eitsupi]

Yeah, it would actually need to set

PKG_SYSREQS="false"

because the default is true now in pak.

Thanks for the quick reply, I didn't know the default values of pak had changed.

I question the need to opt out of it.
Because I often see behavior like apt installing pandoc when the latest pandoc is already installed from GitHub.
(Probably not a problem in the US, but Ubuntu's default mirror is very slow where I live, so I don't want to install anything with apt if at all possible.)

[gaborcsardi]

If you install pandoc from the deb package in their GH releases page, then pak should not update it.

[eitsupi]

If you install pandoc from the deb package in their GH releases page, then pak should not update it.

Yes, ideally. But perhaps not at this time.

> system("pandoc --version")
pandoc 3.1.1
Features: +server +lua
Scripting engine: Lua 5.4
User data directory: /home/vscode/.local/share/pandoc
Copyright (C) 2006-2023 John MacFarlane. Web:  https://pandoc.org
This is free software; see the source for copying conditions. There is no
warranty, not even for merchantability or fitness for a particular purpose.
> pak::pak("rmarkdown")
✔ Loading metadata database ... done
                                                                           
→ Will install 29 packages.
→ Will download 29 packages with unknown size.
+ base64enc     0.1-3  [dl]
+ bslib         0.5.1  [dl]
+ cachem        1.0.8  [dl]
+ cli           3.6.1  [dl]
+ digest        0.6.33 [dl]
+ ellipsis      0.3.2  [dl]
+ evaluate      0.21   [dl]
+ fastmap       1.1.1  [dl]
+ fontawesome   0.5.2  [dl]
+ fs            1.6.3  [dl] + ✔ make
+ glue          1.6.2  [dl]
+ highr         0.10   [dl]
+ htmltools     0.5.6  [dl]
+ jquerylib     0.1.4  [dl]
+ knitr         1.44   [dl] + ✖ pandoc
+ lifecycle     1.0.3  [dl]
+ magrittr      2.0.3  [dl]
+ memoise       2.0.1  [dl]
+ mime          0.12   [dl]
+ R6            2.5.1  [dl]
+ rappdirs      0.3.3  [dl]
+ rmarkdown     2.24   [dl] + ✖ pandoc
+ sass          0.4.7  [dl] + ✔ make
+ stringi       1.7.12 [dl] + ✔ libicu-dev
+ stringr       1.5.0  [dl]
+ tinytex       0.46   [dl]
+ vctrs         0.6.3  [dl]
+ xfun          0.40   [dl]
+ yaml          2.3.7  [dl]
→ Will install 1 system package:

[gaborcsardi]

This is what I see:

root@47d274b2de55:~# curl -LO https://github.com/jgm/pandoc/releases/download/3.1.8/pandoc-3.1.8-1-arm64.deb
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 31.8M  100 31.8M    0     0  19.9M      0  0:00:01  0:00:01 --:--:-- 35.8M

root@47d274b2de55:~# apt install ./pandoc-3.1.8-1-arm64.deb
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Note, selecting 'pandoc' instead of './pandoc-3.1.8-1-arm64.deb'
Suggested packages:
  texlive-latex-recommended texlive-xetex texlive-fonts-recommended
The following NEW packages will be installed:
  pandoc
0 upgraded, 1 newly installed, 0 to remove and 6 not upgraded.
Need to get 0 B/33.4 MB of archives.
After this operation, 162 MB of additional disk space will be used.
Get:1 /root/pandoc-3.1.8-1-arm64.deb pandoc arm64 3.1.8-1 [33.4 MB]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package pandoc.
(Reading database ... 33237 files and directories currently installed.)
Preparing to unpack /root/pandoc-3.1.8-1-arm64.deb ...
Unpacking pandoc (3.1.8-1) ...
Setting up pandoc (3.1.8-1) ...

and then pak does not touch pandoc:

root@47d274b2de55:~# R -q -e 'pak::pkg_install("knitr?reinstall")'
> pak::pkg_install("knitr?reinstall")
✔ Loading metadata database ... done

→ Will install 1 package.
→ The package (895.05 kB) is cached.
+ knitr   1.44 [bld] + ✔ pandoc
✔ All system requirements are already installed.

ℹ No downloads are needed, 1 pkg (895.05 kB) is cached
ℹ Building knitr 1.44
✔ Built knitr 1.44 (318ms)
✔ Installed knitr 1.44  (43ms)
✔ 1 pkg + 4 deps: kept 4, added 1 [2.2s]

[eitsupi]

Thanks for letting me know that pak works well with the deb package.
I had created a simlink to the pandoc bundled with RStudio to make the pandoc command executable.
This is a special case and may not be of much concern, but I recall that cargo and rustc installed via rustup were also ignored.

[gaborcsardi]

Yes, system requirements use the packages of the distro. If you tend to install software other ways, then it is indeed best to opt out.