Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Merged
merged 1 commit into from Nov 24, 2020
Merged

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

merged 1 commit into from Nov 24, 2020

Conversation

omasanori
Copy link
Contributor

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.

@ofborg ofborg bot requested a review from joelmo October 22, 2020 07:04
@omasanori omasanori mentioned this pull request Oct 23, 2020
Closed
10 tasks
@nixos-discourse
Copy link

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

@omasanori
pythonPackages.rpy2: 3.2.6 -> 3.3.6, fix test etc.
4a2a6b4 
- 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
Copy link
Member

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
Copy link
Contributor Author

@yurrriq Thank you for testing!

ping? @joelmo

@SuperSandro2000
Copy link
Member

SuperSandro2000 commented Nov 24, 2020 •
edited

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
Copy link
Contributor Author

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
jonringer approved these changes Nov 24, 2020
View reviewed changes
Copy link
Contributor

@jonringer jonringer left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
@omasanori omasanori deleted the rpy2 branch November 24, 2020 09:27
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jonringer jonringer jonringer approved these changes

@FRidh FRidh Awaiting requested review from FRidh

@joelmo joelmo Awaiting requested review from joelmo

Assignees
No one assigned
Labels
6.topic: python 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10
Projects
None yet
Milestone
No milestone
5 participants
@omasanori @nixos-discourse @yurrriq @SuperSandro2000 @jonringer