R: 3.6.3 --> 4.0.0 & update packages

[jabranham]

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.

[bcdarwin]

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]

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

[bcdarwin]

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]

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

[bcdarwin]

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

[jabranham]

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

[jabranham]

Rstudio compiled successfully so pushed here

[bcdarwin]

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

[jabranham]

Done

[bcdarwin]

@GrahamcOfBorg build rstudio rstudioWrapper

[peti]

Test builds are running at https://hydra.nixos.org/jobset/nixpkgs/r-updates.

[jabranham]

Hydra build of R packages looks good to me

…

On Wed, Apr 29, 2020, 4:02 AM Peter Simons ***@***.***> wrote: ***@***.**** commented on this pull request. Test builds are running at https://hydra.nixos.org/jobset/nixpkgs/r-updates. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#86081 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC24ZCPOU2JDSNDSNJDKVBDRO7NLBANCNFSM4MRNEIPQ> .

[ciil]

RStudio build lgtm as well.