Arch Linux User Repository

@hadallen,

There is no need to downgrade. Update boost to the new version, then rebuild and reinstall rstudio-desktop.

Build logic is slightly changed due to changes in upstream. As they've introduced new project format (quarto), it contradicted with standard Arch package base. In brief, quarto contains pandoc as part of itself, so it's pretty hard to keep together system pandoc and embedded quarto.

So I've "resolved" it such way: if there is "quarto*" package installed, then rstudio-desktop will pick it up and use. Otherwise (not installed), quarto support in rstudio will be disabled.

'quarto' is added as optional dependency.

@AugustinCrochat,

I suspect your issue is not related to RStudio, but rather to R itself, more precisely to its packages dependency hell. I also regularly have odd problems with various R packages (I recall such rmarkdown issue several months ago).

To me the best is not to install any extra R packages system-wide. They're not going to rebuild when R has upgrading. So my recommendation: if you have any installed from AUR, uninstall them.

Also remove ~/R/x86_64-pc-linux-gnu-library/* then try to build them all from scratch.

I update rmarkdown and knitr, but it keeps asking to install again, and I can't knit to PDF.

@hadallen,

There is no need to downgrade. Update boost to the new version, then rebuild and reinstall rstudio-desktop.

latest version of boost-libs (1.79.0-1) stops RStudio from starting. downgrading boost and boost-libs to 1.78.0-3 is a workaround

Hi flying-sheep,

This way of building dependent R packages was here historically, from the very first versions of RStudio. So "it's not me" - it has been done by the previous maintainers.

UPD: Yep, it was introduced somewhere after you have left the package orphaned. I've picked up and adopted working PKGBUILD from other user.

I agree, this needs to be fixed, though.

I'm not sure either these packages are needed during the build only, or for successful run of RStudio. On the other hand, current state of R packages maintenance in Arch is BAD (as well as in other distributions), so if I add them as rstudio-desktop deps, I suspect the chances to build it might get pretty low.

Probably the best is to to build all them (or, may be only few [and add the rest as deps]) in temp directory and remove afterwards. I'll give it a try in a clean environment in a next few days.

UPD: Seems all R packages from dependencies list (at least now), i.e. rmarkdown, renv, testthat, xml2, yaml, are used ONLY for running tests during the build process. So it's safe to install them all into temp dir and remove after build finishes.

Few more notes: rmarkdown may be needed for supporting R markdown projects, so it makes sense to add it to optional dependendencies (may be with next major release of RStudio).

r-testthat seems broken - I couldn't build it. It looks like a circular dependency - it depends on r-dbi, which in turn depends on r-testthat

Oh, you’re installing R packages into the user’s library during install.

Please stop doing that.

You need to either package the r packages as Arch packages and make rstudio-desktop depend on them, or (if they’re a build dependency) install them into a temporary directory during build, use them, and then delete everything.

Thank you for your fast response and rework.

It is a cool feeling to make a suggestion, sleep and update the other system with the proposed changes.

Nice work!

Hi Goetz, Thanks, indeed, I've forgotten to check the case when quarto is not installed.

I suppose there is no reason for assigning a particular pandoc version to a directory - it used only once during configuration (also pandoc versions are changing so fast, therefore if I decide to track them I'll have to update rstudio 2-3 times a week), then pandoc binary always goes to $prefix/rstudio/bin/pandoc/bin/tools/pandoc

P.S. I've just spotted an update (v2022.02.2+485). It looks a bit strange it's dated April 20, however appeared in rstudio repo only now. I assume they run build and test for several days and only then unlock the tag.

Anyway I'll give it a try later today, or tomorrow.

I updated the package and detected following problem: You do not cover properly if Quarto is not installed.

*** PKGBUILD    2022-04-27 19:27:55.014617207 +0200
--- /home/goetz/Downloads/rstudio-desktop/PKGBUILD  2022-04-27 13:34:10.000000000 +0200
***************
*** 38,45 ****
          "cran_multithread.patch"
          "sigstksz_gcc11.patch"
          "10952.patch"
!         "quarto_pandoc_location.patch"
!         "fix_pandoc_version.patch")

  sha256sums=('41e48e21ddc0a9c1ebf06ff16d846b0389720f2ee66d3fcfd5ff0707578b597d'
              'b98e704164f54be596779696a3fcd11be5785c9907a99ec535ff6e9525ad5f9a'
--- 38,44 ----
          "cran_multithread.patch"
          "sigstksz_gcc11.patch"
          "10952.patch"
!         "quarto_pandoc_location.patch")

  sha256sums=('41e48e21ddc0a9c1ebf06ff16d846b0389720f2ee66d3fcfd5ff0707578b597d'
              'b98e704164f54be596779696a3fcd11be5785c9907a99ec535ff6e9525ad5f9a'
***************
*** 49,56 ****
              'c907e6eec5ef324ad498b44fb9926bb5baafc4e0778ca01f6ba9b49dd3a2a980'
              '7b8420db08f848f7baac0f3104c879ac7ce6e27e463f96a6b1c6589cd4b8df82'
              '71c41818d099c07d928aa9689a5fd57bb3dc187b9788a8d5cc528ef6208b7726'
!             'f496c8d012ec7211b7d76240932c1b33fc76c5bb756b354eb00dd5c4344baeab'
!             '867a9112f61b82dd17e4cbe7898756e0981ac1bf63036a1e12a3005e0821c100')

  noextract=("gin-${_ginver}.zip")

--- 48,54 ----
              'c907e6eec5ef324ad498b44fb9926bb5baafc4e0778ca01f6ba9b49dd3a2a980'
              '7b8420db08f848f7baac0f3104c879ac7ce6e27e463f96a6b1c6589cd4b8df82'
              '71c41818d099c07d928aa9689a5fd57bb3dc187b9788a8d5cc528ef6208b7726'
!             'f496c8d012ec7211b7d76240932c1b33fc76c5bb756b354eb00dd5c4344baeab')

  noextract=("gin-${_ginver}.zip")

***************
*** 65,72 ****
      patch -p1 < ${srcdir}/10952.patch
      # Fix for missed path to new pandoc location in upstream
      patch -p1 < ${srcdir}/quarto_pandoc_location.patch
-     # Fix wrong pandoc version
-     patch -p1 < ${srcdir}/fix_pandoc_version.patch

      msg "Extracting dependencies..."
      cd "${srcdir}/${_srcname}/src/gwt"
--- 63,68 ----
***************
*** 109,119 ****
          install -d quarto/bin/tools
          ln -sfT /usr/bin/quarto quarto/bin/quarto
          ln -sfT /usr/bin/pandoc quarto/bin/tools/pandoc
-     else
-         msg "Use pandoc, because Quarto is not used..."
-         cd "${srcdir}/${_srcname}/dependencies"
-         install -d pandoc/2.17.1.1/bin/tools
-         ln -sfT /usr/bin/pandoc pandoc/2.17.1.1/bin/tools/pandoc
      fi

      cd ${srcdir}
--- 105,110 ----

With following patch for setting the correct (actual) Arch-Linux version of pandoc:

From 4ed960ce72f8a4bf5b9d9d04015b96d27d044842 Mon Sep 17 00:00:00 2001
Message-Id: <4ed960ce72f8a4bf5b9d9d04015b96d27d044842.1651079564.git.goetz@web-dev.de>
From: goetz <goetz@web-dev.de>
Date: Wed, 27 Apr 2022 19:12:26 +0200
Subject: [PATCH] fix_pandoc_version

---
 CMakeGlobals.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeGlobals.txt b/CMakeGlobals.txt
index de77b8d1ee..bba07d9d49 100644
--- a/CMakeGlobals.txt
+++ b/CMakeGlobals.txt
@@ -214,7 +214,7 @@ if(NOT DEFINED RSTUDIO_VERIFY_R_VERSION)
 endif()

 # pandoc version
-set(PANDOC_VERSION "2.16.2" CACHE INTERNAL "Pandoc version")
+set(PANDOC_VERSION "2.17.1.1" CACHE INTERNAL "Pandoc version")

 # quarto support
 if(LINUX AND UNAME_M STREQUAL aarch64)
-- 
2.36.0