sage: fix attrname, add sagemath alias (18.09) #49249

timokau · 2018-10-27T12:20:39Z

Motivation for this change

Backport of #49248.

Things done

Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
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 nox --run "nox-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)
Fits CONTRIBUTING.md.

This is a minimal change mainly to make sure repology recognizes this package as sage. I plan a bit more refactoring later, but this is intentionally kept minimally invasive so that it won't break anything and can be backported to 18.09. (cherry picked from commit 2513747)

Sage is commonly referred to as sagemath (probably to improve searchability). Many other distors call their package sagemath. (cherry picked from commit 80833d1)

GrahamcOfBorg · 2018-10-27T12:38:37Z

No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnfree = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnfree = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-27T12:39:11Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-27T12:47:09Z

Failure on x86_64-linux (full log)

Attempted: sage

Partial log (click to expand)

collision between `/nix/store/hmwpgjpdpgli5243biliqnqf657sfcy7-python2.7-backports.shutil_get_terminal_size-unstable-2016-02-21/lib/python2.7/site-packages/backports/__init__.pyc' and `/nix/store/cn0dgc09hr9dka55mxkm5mzc92jh95ml-python2.7-backports.functools_lru_cache-1.5/lib/python2.7/site-packages/backports/__init__.pyc'
collision between `/nix/store/hmwpgjpdpgli5243biliqnqf657sfcy7-python2.7-backports.shutil_get_terminal_size-unstable-2016-02-21/lib/python2.7/site-packages/backports/__init__.py' and `/nix/store/cn0dgc09hr9dka55mxkm5mzc92jh95ml-python2.7-backports.functools_lru_cache-1.5/lib/python2.7/site-packages/backports/__init__.py'
collision between `/nix/store/xcfj6qzlklpqfw6xg9v52ymx2x8vck8d-python2.7-configparser-3.5.0/lib/python2.7/site-packages/backports/__init__.pyc' and `/nix/store/cn0dgc09hr9dka55mxkm5mzc92jh95ml-python2.7-backports.functools_lru_cache-1.5/lib/python2.7/site-packages/backports/__init__.pyc'
collision between `/nix/store/xcfj6qzlklpqfw6xg9v52ymx2x8vck8d-python2.7-configparser-3.5.0/lib/python2.7/site-packages/backports/__init__.py' and `/nix/store/cn0dgc09hr9dka55mxkm5mzc92jh95ml-python2.7-backports.functools_lru_cache-1.5/lib/python2.7/site-packages/backports/__init__.py'
created 1266 symlinks in user environment
cannot build derivation '/nix/store/qn6ba5d0x1cadnjxirbzn4ksh0ij5xg0-sage-env.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/yx4xa76kaigpg9xmnzry20b3ii3a48fx-sage-with-env-8.3.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/xbbvnnbrrx7vc0zqgaiasclncwg0b9ii-sage-tests-8.3.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/12h7bk9kz7c46a7ganfaqij0hywbipbz-sage-8.3.drv': 1 dependencies couldn't be built
error: build of '/nix/store/12h7bk9kz7c46a7ganfaqij0hywbipbz-sage-8.3.drv' failed

timokau · 2018-10-27T13:02:41Z

Curious, I cannot reproduce the failure in the R build locally.

@GrahamcOfBorg build sage

GrahamcOfBorg · 2018-10-27T13:02:55Z

No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnfree = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnfree = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-27T13:03:03Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-27T13:07:49Z

Failure on x86_64-linux (full log)

Attempted: sage

Partial log (click to expand)

make[1]: *** [Makefile.common:165: test-all-basics] Error 1
make[1]: Leaving directory '/build/R-3.4.4/tests'
make: *** [Makefile:239: check] Error 2
builder for '/nix/store/jfaspyjvp7r399myxg41rxnafk8pnkwx-R-3.4.4.drv' failed with exit code 2
cannot build derivation '/nix/store/vzlqvqbkjr4gdi0h904dk3bkkhww71ij-R-3.4.4-wrapper.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/qn6ba5d0x1cadnjxirbzn4ksh0ij5xg0-sage-env.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/yx4xa76kaigpg9xmnzry20b3ii3a48fx-sage-with-env-8.3.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/xbbvnnbrrx7vc0zqgaiasclncwg0b9ii-sage-tests-8.3.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/12h7bk9kz7c46a7ganfaqij0hywbipbz-sage-8.3.drv': 1 dependencies couldn't be built
error: build of '/nix/store/12h7bk9kz7c46a7ganfaqij0hywbipbz-sage-8.3.drv' failed

timokau · 2018-10-27T21:40:24Z

@GrahamcOfBorg build sage

Abusing borg for testing here because I still can't reproduce locally.

GrahamcOfBorg · 2018-10-27T21:40:45Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-27T21:45:28Z

No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnfree = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnfree = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-27T21:51:29Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-27T21:54:23Z

No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnfree = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnfree = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-27T21:56:21Z

Failure on x86_64-linux (full log)

Attempted: sage

Partial log (click to expand)

> stopifnot(abs(mean(r) - 1) < 0.003)
Error: abs(mean(r) - 1) < 0.003 is not TRUE
Execution halted
builder for '/nix/store/inzccvmaqsa0iznzjhk4nddpqmndiv1d-R-3.4.4.drv' failed with exit code 2
cannot build derivation '/nix/store/0p0nf43kmnrvgrx10pdizfxhhinb72im-R-3.4.4-wrapper.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/lwmsa8fc04m4by2598fvy5w97ardy0a0-sage-env.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/zy5485y2in5nfabrzjahlbzl1xwyfczi-sage-with-env-8.3.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/f62gd531wlccg8m9n4g5n1az7x31l98b-sage-tests-8.3.drv': 1 dependencies couldn't be built
cannot build derivation '/nix/store/6n44ml2181cfqzam10dgk5q11xbd5v0h-sage-8.3.drv': 1 dependencies couldn't be built
error: build of '/nix/store/6n44ml2181cfqzam10dgk5q11xbd5v0h-sage-8.3.drv' failed

timokau · 2018-10-27T22:07:00Z

@GrahamcOfBorg build R

GrahamcOfBorg · 2018-10-27T22:07:11Z

Success on x86_64-linux (full log)

Attempted: R

Partial log (click to expand)

/nix/store/hf8x5lcm2ldadrk1m05agfdshybvqfb5-R-3.5.1

GrahamcOfBorg · 2018-10-27T22:07:51Z

Success on x86_64-darwin (full log)

Attempted: R

Partial log (click to expand)

copying path '/nix/store/21n6fx4pw4c5561042pgyxmpi73xbacg-libXext-1.3.3-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/17pq23xhh0q7m6d1ngzlnpm6yjsmnw3z-libXt-1.1.5-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/633xv79wavi156knj35pr9cxs34433qv-gfortran-wrapper-7.3.0' from 'https://cache.nixos.org'...
copying path '/nix/store/nix00lgaprlpaxpcg29yrxjfx99whivz-libXft-2.3.2-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/fcs8183pyn7akshb1ykn91wxmqh412x0-cairo-1.15.12-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/0yz7i5bz64phnhp6fbvi8ljirmy4k31m-libtiff-4.0.9-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/6d2cw3g8qv1h60y83j2y10g6k5xks9n0-libXmu-1.1.2-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/nfb968h86nsrb8sc956wrbbb2zfqk587-pango-1.42.1-dev' from 'https://cache.nixos.org'...
copying path '/nix/store/g1ambq0hkc4phfvv89jiyzd4bg3mbdnc-R-3.5.1' from 'https://cache.nixos.org'...
/nix/store/g1ambq0hkc4phfvv89jiyzd4bg3mbdnc-R-3.5.1

GrahamcOfBorg · 2018-10-27T22:12:11Z

No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: R

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnfree = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnfree = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-27T23:07:40Z

Timed out, unknown build status on x86_64-linux (full log)

Attempted: sage

Partial log (click to expand)

sage -t --long /nix/store/9nix1fnsj56iqqcjavkar8gbjnic8djm-sage-src-8.3/src/sage/combinat/integer_lists/__init__.py
    [0 tests, 0.00 s]
sage -t --long /nix/store/9nix1fnsj56iqqcjavkar8gbjnic8djm-sage-src-8.3/src/sage/combinat/integer_lists/invlex.pxd
    [0 tests, 0.00 s]
sage -t --long /nix/store/9nix1fnsj56iqqcjavkar8gbjnic8djm-sage-src-8.3/src/sage/combinat/designs/group_divisible_designs.py
    [30 tests, 0.68 s]
sage -t --long /nix/store/9nix1fnsj56iqqcjavkar8gbjnic8djm-sage-src-8.3/src/sage/combinat/designs/difference_family.py
building of '/nix/store/f62gd531wlccg8m9n4g5n1az7x31l98b-sage-tests-8.3.drv' timed out after 3600 seconds
cannot build derivation '/nix/store/6n44ml2181cfqzam10dgk5q11xbd5v0h-sage-8.3.drv': 1 dependencies couldn't be built
error: build of '/nix/store/6n44ml2181cfqzam10dgk5q11xbd5v0h-sage-8.3.drv' failed

timokau · 2018-10-29T09:07:52Z

Merging for now since the R failure is unrelated and not reproducible. Lets see what hydra says. In the meantime I'm working on upgrading sage's R to the latest version, then this problem should go away.

GrahamcOfBorg · 2018-10-29T09:18:27Z

No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnfree = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnfree = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-29T09:18:41Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: sage

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-10-29T09:49:08Z

Timed out, unknown build status on x86_64-linux (full log)

Attempted: sage

Partial log (click to expand)

sage -t --long /nix/store/9nix1fnsj56iqqcjavkar8gbjnic8djm-sage-src-8.3/src/sage/matrix/matrix_generic_sparse.pyx
    [77 tests, 0.33 s]
sage -t --long /nix/store/9nix1fnsj56iqqcjavkar8gbjnic8djm-sage-src-8.3/src/sage/matrix/matrix_generic_sparse.pxd
    [0 tests, 0.00 s]
sage -t --long /nix/store/9nix1fnsj56iqqcjavkar8gbjnic8djm-sage-src-8.3/src/sage/matrix/matrix_gf2e_dense.pxd
    [0 tests, 0.00 s]
sage -t --long /nix/store/9nix1fnsj56iqqcjavkar8gbjnic8djm-sage-src-8.3/src/sage/matrix/matrix_gap.pyx
building of '/nix/store/xbbvnnbrrx7vc0zqgaiasclncwg0b9ii-sage-tests-8.3.drv' timed out after 1800 seconds
cannot build derivation '/nix/store/12h7bk9kz7c46a7ganfaqij0hywbipbz-sage-8.3.drv': 1 dependencies couldn't be built
error: build of '/nix/store/12h7bk9kz7c46a7ganfaqij0hywbipbz-sage-8.3.drv' failed

Fails transiently. See NixOS#49249. The failures look harmless and are fixed with R 3.5 which will be used in sage 8.5.

Fails transiently. See NixOS#49249. The failures look harmless and are fixed with R 3.5 which will be used in sage 8.5. (cherry picked from commit d6376bc)

Fails transiently. See #49249. The failures look harmless and are fixed with R 3.5 which will be used in sage 8.5. (cherry picked from commit d6376bc)

timokau added 2 commits October 27, 2018 14:19

sage: add sagemath alias

d9e7a83

Sage is commonly referred to as sagemath (probably to improve searchability). Many other distors call their package sagemath. (cherry picked from commit 80833d1)

timokau changed the title ~~Sage fix attrname 18.09~~ sage: fix attrname, add sagemath alias (18.09) Oct 27, 2018

GrahamcOfBorg added 10.rebuild-darwin: 0 10.rebuild-linux: 1-10 labels Oct 27, 2018

timokau force-pushed the sage-fix-attrname-18.09 branch from deeabf6 to d9e7a83 Compare October 29, 2018 09:07

timokau merged commit 8126ce7 into NixOS:release-18.09 Oct 29, 2018

timokau deleted the sage-fix-attrname-18.09 branch October 29, 2018 09:08

timokau mentioned this pull request Oct 29, 2018

R: give details on test failure #49378

Closed

9 tasks

timokau added a commit to timokau/nixpkgs that referenced this pull request Nov 28, 2018

sage: don't test the downgraded R

d6376bc

Fails transiently. See NixOS#49249. The failures look harmless and are fixed with R 3.5 which will be used in sage 8.5.

timokau added a commit to timokau/nixpkgs that referenced this pull request Nov 28, 2018

sage: don't test the downgraded R

79ba32c

Fails transiently. See NixOS#49249. The failures look harmless and are fixed with R 3.5 which will be used in sage 8.5. (cherry picked from commit d6376bc)

timokau added a commit that referenced this pull request Nov 28, 2018

sage: don't test the downgraded R (#51192)

b7747ce

Fails transiently. See #49249. The failures look harmless and are fixed with R 3.5 which will be used in sage 8.5. (cherry picked from commit d6376bc)

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sage: fix attrname, add sagemath alias (18.09) #49249

sage: fix attrname, add sagemath alias (18.09) #49249

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sage: fix attrname, add sagemath alias (18.09) #49249

sage: fix attrname, add sagemath alias (18.09) #49249

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timokau commented Oct 27, 2018

Motivation for this change

Things done

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