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suitesparse: 4.4.4 -> 5.3.0 #35213

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merged 1 commit into from Oct 20, 2018
Merged

suitesparse: 4.4.4 -> 5.3.0 #35213

merged 1 commit into from Oct 20, 2018

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jluttine
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@jluttine jluttine commented Feb 20, 2018 •
edited

Motivation for this change

This is work in progress, do not merge.

EDIT: Ready for review and merge now.

Upgrading SuiteSparse to 5.3.0. However, the build failed and I was a bit lost with all the complexity of the package. I thought I'd put it here if someone wants to help and/or that it's public so there wouldn't be overlapping efforts done.

Error log

cc: @ttuegel Perhaps you, as a maintainer, know better how to upgrade this package?

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-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/)
  • Fits CONTRIBUTING.md.

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jluttine commented Feb 21, 2018 •
edited

I modified the derivation quite heavily. Someone should check that it still makes sense. Anyway, the build is almost successful now. At the very end, at post-installation fixup phase, I get the following error:

/nix/store/4gc1xjghbqfwc498cidj53dk5ynwr0zz-suitesparse-5.1.2/share/doc/suitesparse-5.1.2/cholmod/getproto: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
/nix/store/4gc1xjghbqfwc498cidj53dk5ynwr0zz-suitesparse-5.1.2/share/doc/suitesparse-5.1.2/cholmod/getmproto: interpreter directive changed from "/bin/sh" to "/nix/store/i0ay05pqkbnvpfijm52mmlrp6kmkl80c-bash-4.4-p12/bin/sh"
checking for references to /tmp/nix-build-suitesparse-5.1.2.drv-0 in /nix/store/4gc1xjghbqfwc498cidj53dk5ynwr0zz-suitesparse-5.1.2...
RPATH of binary /nix/store/4gc1xjghbqfwc498cidj53dk5ynwr0zz-suitesparse-5.1.2/lib/libspqr.so.2.0.8 contains a forbidden reference to /tmp/nix-build-suitesparse-5.1.2.drv-0
builder for ‘/nix/store/1wzlj7r2ppmqg6biibjsny9ijj6jdcwg-suitesparse-5.1.2.drv’ failed with exit code 1

Not yet sure how to fix it.

@jluttine jluttine changed the title suitesparse: 4.4.4 -> 5.1.2 [WIP] suitesparse: 4.4.4 -> 5.1.2 Jun 30, 2018
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This built now on my machine. I think someone should review this as I'm not too confident about my changes.

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Hmm.. nox-review failing.

@jluttine jluttine force-pushed the suitesparse-5.1.2 branch 2 times, most recently from 31b9789 to 498f72f Compare June 30, 2018 15:56
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@GrahamcOfBorg build julia

@jluttine jluttine changed the title suitesparse: 4.4.4 -> 5.1.2 suitesparse: 4.4.4 -> 5.2.0 Jul 2, 2018
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jluttine commented Jul 2, 2018

@GrahamcOfBorg build suitesparse

@jluttine jluttine changed the title suitesparse: 4.4.4 -> 5.2.0 suitesparse: 4.4.4 -> 5.3.0 Oct 7, 2018
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jluttine commented Oct 7, 2018 •
edited

I changed the updated version from 5.2.0 to 5.3.0. Build succeeds, but nox review fails:

error: build of '/nix/store/f8p1b61nwdamwyx9ff897d9ps4i4p8ly-sage-wrapper-8.3.drv', '/nix/store/rjfqbak8b89123zbzwir1ich9pc1yfyb-sage-wrapper-8.3.drv', '/nix/store/s0cwmcvix092b8fh518ck18zv479mnxg-julia-0.6.4.drv' failed
The invocation of "nix-build -A suitesparse -A sageWithDoc -A python36Packages.cvxopt -A python27Packages.cvxopt -A sage -A julia -A suitesparse_4_4 /etc/nixpkgs" failed

Probably they fail because of this kind of warnings/errors:

WARNING: Error during initialization of module CHOLMOD:
ErrorException("could not load symbol "SuiteSparse_config":
/nix/store/wamgmpfa2lcqd4nmj0j8g99jjb0lnlhn-suitesparse-5.3.0/lib/libsuitesparse.so: undefined symbol: SuiteSparse_config")

@jluttine jluttine force-pushed the suitesparse-5.1.2 branch 2 times, most recently from c76ded7 to a2fd8ba Compare October 7, 2018 13:32
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jluttine commented Oct 7, 2018

Fixed the symbol loading issue, but still nox review failing.

error: build of '/nix/store/9rpg8fnlw5gd3c9m9lrdw635xj0jznw3-julia-0.6.4.drv', '/nix/store/ibmnf9qxqm1w4g510d3vzk11gm6z8znx-sage-wrapper-8.3.drv', '/nix/store/xaj5bqv6rhm2jq4vm834bx0kqvdpcrm1-sage-wrapper-8.3.drv' failed
The invocation of "nix-build -A suitesparse -A sageWithDoc -A python27Packages.cvxopt -A python36Packages.cvxopt -A sage -A julia -A suitesparse_4_4 /etc/nixpkgs" failed

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jluttine commented Oct 7, 2018 •
edited

I tried building julia without this pull request on nixos-unstable but it didn't build. I got the same error. So, I suppose that package is broken despite this change. Looking into sage next..

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jluttine commented Oct 7, 2018

Actually, sage seems to build just fine. I built it separately and it took a looooong time but it was successful. I suppose nox review just errored when julia failed and then it reported every unfinished build also as failed.

So, in my opinion, nox review succeeds in practice and I guess this is ready for review or merge.

@ttuegel You're the maintainer of the package. Do you want to review or who should I ask?

@ttuegel ttuegel self-requested a review October 8, 2018 13:57
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ttuegel reviewed Oct 8, 2018
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pkgs/development/libraries/science/math/suitesparse/default.nix
};

dontUseCmakeConfigure = true;
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What is the dependency on cmake for if not calling cmake?

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Can't say I understand much about these, but if cmake is not a build input, it fails to build GraphBLAS.

pkgs/development/libraries/science/math/suitesparse/default.nix Show resolved Hide resolved
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jluttine commented Oct 8, 2018 via email

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Ok, that should be fixed now. For some reason, I had added -llapack build flag and liblapack as a build dependency. These weren't compatible with openblas, which contains its own lapack anyway, so I just removed lapack as it had been before. As far as I can tell, this should be working now. Any other comments, @ttuegel?

@ttuegel ttuegel merged commit 2e4397f into NixOS:master Oct 20, 2018
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ttuegel commented Oct 20, 2018

Thanks!

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