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pythonPackages.rpy2: 3.2.6 -> 3.3.6, fix test etc. #101327

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merged 1 commit into from Nov 24, 2020
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@omasanori
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@omasanori omasanori commented Oct 22, 2020

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.
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@nixos-discourse nixos-discourse commented Nov 4, 2020

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

- This newer version is compatible with panda 1.0 without any patch.
- rPackages.lazyload is required to run tests.
- The official website is moved to GitHub Pages.

Signed-off-by: Masanori Ogino <167209+omasanori@users.noreply.github.com>
@yurrriq
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@yurrriq yurrriq commented Nov 13, 2020

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

image

@omasanori
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@omasanori omasanori commented Nov 14, 2020

@yurrriq Thank you for testing!

ping? @joelmo

@SuperSandro2000
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@SuperSandro2000 SuperSandro2000 commented Nov 24, 2020

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
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@omasanori omasanori commented Nov 24, 2020

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?

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@jonringer jonringer left a comment

overall LGTM

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

@jonringer jonringer merged commit 0d2f29d into NixOS:master Nov 24, 2020
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@omasanori omasanori deleted the rpy2 branch Nov 24, 2020
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