symphony: init at 5.7.2 and rPackages.Rsymphony

[b-rodrigues]

Description of changes

EDIT: 2024-04-20 thanks to the help of @jbedo and @Kupac , this works now! Tested with example from documentation:

library(Rsymphony)

obj <- c(2, 4, 3)
mat <- matrix(c(3, 2, 1, 4, 1, 3, 2, 1, 2), nrow = 3)
dir <- c("<=", "<=", "<=")
rhs <- c(60, 40, 80)
max <- TRUE
Rsymphony_solve_LP(obj, mat, dir, rhs, max = max)

This PR contains two commits: one that adds the Symphony solver, and another that fixes the build for the R package.

Original message:
Trying to fix rPackages.Rsymphony. I've first added the symphony software in pkgs/by-name/sy/symphony/package.nix and this builds successfully. I'm able to drop in a shell and execute it with:

nix-shell -I nixpkgs=. -p symphony

When building it, the following message appears:

Libraries have been installed in:
   /nix/store/r11wx6bcf8kxfdkigspbbdzgg4mvq6yf-symphony-5.7.2/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,--rpath -Wl,LIBDIR' linker flag

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.

Trying to build the R packages, rPackages.Rsymphony doesn't succeed, so I tried to add:

    Rsymphony = old.Rsymphony.overrideAttrs (attrs: {
      preConfigure = ''
        export LD_RUN_PATH="${lib.getLib pkgs.symphony}/lib/"
      '';
    });

but trying to build results in the following error:

error: builder for '/nix/store/n310bh4kfhakzdzwrccgygh4b9d5vl3n-r-Rsymphony-0.1-33.drv' failed with exit code 1;
       last 10 log lines:
       > Running phase: buildPhase
       > Running phase: checkPhase
       > Running phase: installPhase
       > * installing *source* package 'Rsymphony' ...
       > ** package 'Rsymphony' successfully unpacked and MD5 sums checked
       > ** using staged installation
       > Cannot find SYMPHONY libraries and headers.
       > See <https://projects.coin-or.org/SYMPHONY>.
       > ERROR: configuration failed for package 'Rsymphony'
       > * removing '/nix/store/hfivzzxh1pw5rgfzc53mzxshra5wixva-r-Rsymphony-0.1-33/library/Rsymphony'
       For full logs, run 'nix log /nix/store/n310bh4kfhakzdzwrccgygh4b9d5vl3n-r-Rsymphony-0.1-33.drv'.

Any ideas?

By the way, I don't know if this should be an issue instead of a draft PR, so let me know if I should close this and open it as an issue instead.

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 24.05 Release Notes (or backporting 23.05 and 23.11 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

---

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[jbedo]

I don't think you need your override, just add the missing dependencies for symphony (cgl & clp) to buildInputs. May as well move pkg-config to nativeBuildInputs too.

[b-rodrigues]

I don't think you need your override, just add the missing dependencies for symphony (cgl & clp) to buildInputs. May as well move pkg-config to nativeBuildInputs too.

thanks for pointing out the missing deps of symphony! However, that doesn't seem to do the trick, Rsymphony still doesn't find symphony.

[jbedo]

This works for me:

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index 35c784e9f021..8dae1810745b 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -520,6 +520,7 @@ let
     Rbwa = [ pkgs.zlib.dev ];
     trackViewer = [ pkgs.zlib.dev ];
     themetagenomics = [ pkgs.zlib.dev ];
+    Rsymphony = [ pkgs.pkg-config ];
     NanoMethViz = [ pkgs.zlib.dev ];
     RcppMeCab = [ pkgs.pkg-config ];
     HilbertVisGUI = with pkgs; [ pkg-config which ];
@@ -586,7 +587,7 @@ let
     mashr = [ pkgs.gsl ];
     hadron = [ pkgs.gsl ];
     AMOUNTAIN = [ pkgs.gsl ];
-    Rsymphony = with pkgs; [ pkg-config doxygen graphviz subversion ];
+    Rsymphony = with pkgs; [ symphony doxygen graphviz subversion cgl clp ];
     tcltk2 = with pkgs; [ tcl tk ];
     tikzDevice = with pkgs; [ which texliveMedium ];
     gridGraphics = [ pkgs.which ];
@@ -1240,12 +1241,6 @@ let
     });


-    Rsymphony = old.Rsymphony.overrideAttrs (attrs: {
-      preConfigure = ''
-        export LD_RUN_PATH="${lib.getLib pkgs.symphony}/lib/"
-      '';
-    });
-
     RPostgres = old.RPostgres.overrideAttrs (attrs: {
       preConfigure = ''
         export INCLUDE_DIR=${pkgs.postgresql}/include

[jbedo]

Ah I should have looked at your commit first, I mean you needed to add it to Rsymphony not symphony.

[Sigmanificient]

@b-rodrigues did you added yourself in the maintainer list?

[b-rodrigues]

@b-rodrigues did you added yourself in the maintainer list?

yes, for symphony

[Sigmanificient]

@b-rodrigues did you added yourself in the maintainer list?

yes, for symphony

I mean this one:
https://github.com/NixOS/nixpkgs/blob/master/maintainers/maintainer-list.nix

I cant find yourself in it

[b-rodrigues]

@b-rodrigues did you added yourself in the maintainer list?

yes, for symphony

I mean this one: https://github.com/NixOS/nixpkgs/blob/master/maintainers/maintainer-list.nix

I cant find yourself in it

ops, sorry, no, first time adding a package. Should I add a commit adding myself as a maintainer to this PR?

[Sigmanificient]

Yes, you need to do it in 2 commits, one to add yourself, then one to init the package.
I recommend checking this section on how to become a maintainer & this nixpkgs manual section

[Sigmanificient]

you need to follow alphabetical order tho

maintainer brodes (line 2936) should be listed after brianmcgillion, not after b-rodrigues (line 2113)

The CI has very precise requirements

[b-rodrigues]

thank you for your patience! Hope I didn't mess anything up

[Sigmanificient]

thank you for your patience! Hope I didn't mess anything up

We are here to help, especially first contributors!
Ofborg-eval may take a bit of time

[Sigmanificient]

Can you add the Changelog file in meta attribute?

Like so

changelog = "https://github.com/coin-or/SYMPHONY/blob/${version}/CHANGELOG.md";

[b-rodrigues]

Can you add the Changelog file in meta attribute?

Like so

changelog = "https://github.com/coin-or/SYMPHONY/blob/${version}/CHANGELOG.md";

yes, done!

[Sigmanificient]

Result of nixpkgs-review pr 305301 run on x86_64-linux 1

1 package built:

• symphony

[jbedo]

@ofborg build rPackages.Rsymphony