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R: 3.6.3 --> 4.0.0 & update packages #86081

Merged
merged 3 commits into from May 1, 2020
Merged

R: 3.6.3 --> 4.0.0 & update packages #86081

merged 3 commits into from May 1, 2020

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@jabranham
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jabranham commented Apr 26, 2020

Motivation for this change

Upstream release. Needed to backport a fix for a test which should be removed next time R gets updated. @peti I also updated the packages from CRAN and bioconductor.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.
jabranham added 2 commits Apr 25, 2020
@jabranham jabranham requested a review from peti as a code owner Apr 26, 2020
@ofborg ofborg bot requested a review from timokau Apr 26, 2020
@bcdarwin
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bcdarwin commented Apr 28, 2020

Commit looks OK.

1 package marked as broken and skipped:
spark

6 package failed to build:
python37Packages.rpy2 python38Packages.rpy2 rstudio rstudioWrapper sage sageWithDoc

I think rpy2 is already broken and sage is probably unrelated. Any idea about rstudio?

@jabranham
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jabranham commented Apr 28, 2020

No, I'm not an Rstudio user so I'm not very familiar with it. Did you get an error message?

@bcdarwin
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bcdarwin commented Apr 28, 2020

It seems like the major version bump may have introduced a breaking change to the R CPP API:

[53%] Building CXX object src/cpp/desktop/CMakeFiles/rstudio.dir/DesktopSubMenu.cpp.o
/build/source/src/cpp/r/session/REmbeddedPosix.cpp: In function 'void rstudio::r::session::runEmbeddedR(const rstudio::core::FilePath&, const rstudio::core::FilePath&, bool, bool, SA_TYPE, const rstudio::r::session::Callbacks&, rstudio::r::session::InternalCallbacks*)':
/build/source/src/cpp/r/session/REmbeddedPosix.cpp:107:8: error: 'struct structRstart' has no member named 'R_Slave'
  107 |    Rp->R_Slave = FALSE ;
      |
@jabranham
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jabranham commented Apr 28, 2020

Thanks. I found rstudio/rstudio#6017 which seems geared towards fixing the issue but it was later reverted.

@bcdarwin
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bcdarwin commented Apr 28, 2020

Can we just use fetchpatch to bring in this commit? (I don't see where it was reverted.)

@jabranham
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jabranham commented Apr 28, 2020

Thanks, trying now. It was reverted here: rstudio/rstudio@8259949 and I'm using what seems to be the replacement: rstudio/rstudio@3fb2397

@jabranham
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jabranham commented Apr 29, 2020

Rstudio compiled successfully so pushed here

@ofborg ofborg bot requested review from ehmry, ciil and changlinli Apr 29, 2020
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bcdarwin commented Apr 29, 2020

Would you also update the comment to describe what this patch is for/when it can be removed? Otherwise looks good.

Need the patch to backport a fix so Rstudio compiles against R 4.0.0
@jabranham jabranham force-pushed the jabranham:update-r branch from 18c93e8 to 56be910 Apr 29, 2020
@jabranham
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jabranham commented Apr 29, 2020

Done

@bcdarwin
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bcdarwin commented Apr 29, 2020

@GrahamcOfBorg build rstudio rstudioWrapper

@peti peti self-assigned this Apr 29, 2020
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@peti peti mentioned this pull request Apr 29, 2020
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@jabranham
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jabranham commented May 1, 2020

@ciil
ciil approved these changes May 1, 2020
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ciil left a comment

RStudio build lgtm as well.

@peti peti merged commit 205e4df into NixOS:master May 1, 2020
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18 checks passed
rstudio, rstudioWrapper on aarch64-linux Timed out, unknown build status
Details
Evaluation Performance Report Evaluator Performance Report
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R, R.passthru.tests on aarch64-linux Success
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R, R.passthru.tests on x86_64-linux Success
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grahamcofborg-eval ^.^!
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grahamcofborg-eval-check-maintainers matching changed paths to changed attrs...
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grahamcofborg-eval-check-meta config.nix: checkMeta = true
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grahamcofborg-eval-darwin nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="56be910"; rev="56be910cd3876d7f4d866c6b11320865df60a5d4"; } ./pkgs/t
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grahamcofborg-eval-lib-tests nix-build --arg pkgs import ./. {} ./lib/tests/release.nix
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grahamcofborg-eval-nixos nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="56be910"; rev="56be910cd3876d7f4d866c6b11320865df60a5d4"; } ./nixos/
Details
grahamcofborg-eval-nixos-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="56be910"; rev="56be910cd3876d7f4d866c6b11320865df60a5d4"; } ./nixos/
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grahamcofborg-eval-nixos-options nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="56be910"; rev="56be910cd3876d7f4d866c6b11320865df60a5d4"; } ./nixos/
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grahamcofborg-eval-nixpkgs-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="56be910"; rev="56be910cd3876d7f4d866c6b11320865df60a5d4"; } ./pkgs/t
Details
grahamcofborg-eval-nixpkgs-tarball nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="56be910"; rev="56be910cd3876d7f4d866c6b11320865df60a5d4"; } ./pkgs/t
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grahamcofborg-eval-nixpkgs-unstable-jobset nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="56be910"; rev="56be910cd3876d7f4d866c6b11320865df60a5d4"; } ./pkgs/t
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grahamcofborg-eval-package-list nix-env -qa --json --file .
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grahamcofborg-eval-package-list-no-aliases nix-env -qa --json --file . --arg config { allowAliases = false; }
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rstudio, rstudioWrapper on x86_64-linux Success
Details
@jabranham jabranham deleted the jabranham:update-r branch May 3, 2020
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