pythonPackages.rpy2: 3.2.6 -> 3.3.6, fix test etc.

[omasanori]

Motivation for this change

This change updates rpy2 to the latest version and rebases a local patch to that version.

Fixes #81345.
Fixes #100259.

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.

[nixos-discourse]

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/prs-ready-for-review/3032/359

[yurrriq]

This builds for me on NixOS 20.09, and appears to work as expected, based on https://rpy2.github.io/doc/v3.3.x/html/introduction.html#graphics-and-plots

[omasanori]

@yurrriq Thank you for testing!

ping? @joelmo

[SuperSandro2000]

Fails to build for me on linux-x86_64:

unpacking sources
unpacking source archive /nix/store/kckxwy4ngbarm8dnls31h6khbhyj1yc0-lazyeval_0.2.2.tar.gz
source root is lazyeval
setting SOURCE_DATE_EPOCH to timestamp 1552672207 of file lazyeval/MD5
patching sources
configuring
building
running tests
installing
Error: package or namespace load failed for 'utils':
 .onLoad failed in loadNamespace() for 'utils', details:
  call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
  error: cannot popen '/nix/store/nsqal2vl76faah1hs5i8h8glzhlidbp7-which-2.21/bin/which 'uname' 2>/dev/null', probable reason 'Cannot allocate memory'
Error: package or namespace load failed for 'stats':
 .onLoad failed in loadNamespace() for 'utils', details:
  call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
  error: cannot popen '/nix/store/nsqal2vl76faah1hs5i8h8glzhlidbp7-which-2.21/bin/which 'uname' 2>/dev/null', probable reason 'Cannot allocate memory'
During startup - Warning messages:
1: package 'utils' in options("defaultPackages") was not found
2: package 'stats' in options("defaultPackages") was not found
* installing *source* package 'lazyeval' ...
** package 'lazyeval' successfully unpacked and MD5 sums checked
** using staged installation
Error : .onLoad failed in loadNamespace() for 'utils', details:
  call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
  error: cannot popen '/nix/store/nsqal2vl76faah1hs5i8h8glzhlidbp7-which-2.21/bin/which 'uname' 2>/dev/null', probable reason 'Cannot allocate memory'
ERROR: installing package DESCRIPTION failed for package 'lazyeval'
* removing '/nix/store/d18q27vnxzxjki13wynzpf9a249ccpyb-r-lazyeval-0.2.2/library/lazyeval'
Warning in q("no", status = status, runLast = FALSE) :
  system call failed: No such file or directory
builder for '/nix/store/p5r2j6hngwj3bpkjc91x5dsn0cxd7vgc-r-lazyeval-0.2.2.drv' failed with exit code 1
cannot build derivation '/nix/store/lf1q5mhi298g0c9khi72fkfsalm7vmrw-python3.7-rpy2-3.3.6.drv': 1 dependencies couldn't be built
error: build of '/nix/store/lf1q5mhi298g0c9khi72fkfsalm7vmrw-python3.7-rpy2-3.3.6.drv' failed

I am working on darwin support which fails due to missing dependencies in R.

Does not build on darwin because of #103624

[omasanori]

Thank you for testing, @SuperSandro2000!
It seems that rPackages.lazyeval failed for some reasons. Would you make a new issue for the package, after nix-building it?

[jonringer]

overall LGTM

https://github.com/NixOS/nixpkgs/pull/101327
2 packages built:
python37Packages.rpy2 python38Packages.rpy2