rPackages.rJava does not build with Azul JDK

[alexvorobiev]

Describe the bug
rPackages.rJava won't install if the JDK is Azul.

To Reproduce
~/.config/nixpkgs/overlays/java.nix:

self: super:
with super; {
  jdk8 = zulu8;
  jdk = zulu8;
}

$ nix-shell -p rPackages.rJava
.....
checking Java support in R... present:
interpreter : '/nix/store/3xlg2rn1mkpypxd2xvz26xrlgfrbrmnr-zulu-8.48.0.53/jre/bin/java'
archiver    : '/nix/store/3xlg2rn1mkpypxd2xvz26xrlgfrbrmnr-zulu-8.48.0.53/bin/jar'
compiler    : '/nix/store/3xlg2rn1mkpypxd2xvz26xrlgfrbrmnr-zulu-8.48.0.53/bin/javac'
header prep.: '/nix/store/3xlg2rn1mkpypxd2xvz26xrlgfrbrmnr-zulu-8.48.0.53/bin/javah'
cpp flags   : '-I/nix/store/3xlg2rn1mkpypxd2xvz26xrlgfrbrmnr-zulu-8.48.0.53/include/'
java libs   : '-L/nix/store/3xlg2rn1mkpypxd2xvz26xrlgfrbrmnr-zulu-8.48.0.53/jre/lib/amd64/server -ljvm'
checking whether Java run-time works... yes
checking whether -Xrs is supported... yes
checking whether -Xrs will be used... yes
checking whether JVM will be loaded dynamically... no
checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details.

Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.

ERROR: configuration failed for package 'rJava'
* removing '/nix/store/d8r376x3dhgdpzpjs1c4lbmyi41z7d0w-r-rJava-0.9-13/library/rJava'
builder for '/nix/store/7g0i92kkdian0jsh9b00w4gp5whss093-r-rJava-0.9-13.drv' failed with exit code 1
error: build of '/nix/store/7g0i92kkdian0jsh9b00w4gp5whss093-r-rJava-0.9-13.drv' failed

Notify maintainers
@peti @michelk @mimame @fpletz

Metadata

 - system: `"x86_64-linux"`
 - host os: `Linux 3.10.0-1160.11.1.el7.x86_64, Red Hat Enterprise Linux Server, 7.9 (Maipo)`
 - multi-user?: `yes`
 - sandbox: `no`
 - version: `nix-env (Nix) 2.3.10`
 - channels(root): `"nixpkgs-21.03pre261451.f53c431645d"`
 - nixpkgs: `/root/.nix-defexpr/channels/nixpkgs`

Maintainer information:

# a list of nixpkgs attributes affected by the problem
attribute:
 - rPackages.rJava
# a list of nixos modules affected by the problem
module:

[nixos-discourse]

This issue has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/nix-shell-environment-to-debug-a-build-of-an-r-package/11010/1

[alexvorobiev]

Running nix-shell --pure -p rPackages.rJava --keep-failed preserved the config.log so it is clear what the issue is:

In file included from conftest.c:30:                                                                                                                                             
/nix/store/3xlg2rn1mkpypxd2xvz26xrlgfrbrmnr-zulu-8.48.0.53/include/jni.h:45:10: fatal error: jni_md.h: No such file or directory                                                 
   45 | #include "jni_md.h"                                                                                                                                                      
      |          ^~~~~~~~~~                                                                                                                                                      
compilation terminated.    

which is (partly) what #106716 is about.

So as a workaround I am using this overlay where I added the symlinks to the installPhase from https://github.com/NixOS/nixpkgs/blob/master/pkgs/development/compilers/zulu/8.nix:

self: super:
with super; {
  zulu8 = super.zulu8.overrideAttrs (attrs: {

    installPhase = ''
      mkdir -p $out
      cp -r ./* "$out/"

      jrePath="$out/jre"

      rpath=$rpath''${rpath:+:}$jrePath/lib/amd64/jli
      rpath=$rpath''${rpath:+:}$jrePath/lib/amd64/server
      rpath=$rpath''${rpath:+:}$jrePath/lib/amd64/xawt
      rpath=$rpath''${rpath:+:}$jrePath/lib/amd64

      # set all the dynamic linkers
      find $out -type f -perm -0100 \
        -exec patchelf --interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
        --set-rpath "$rpath" {} \;

      find $out -name "*.so" -exec patchelf --set-rpath "$rpath" {} \;

      mkdir -p $out/nix-support
      printWords ${setJavaClassPath} > $out/nix-support/propagated-build-inputs

      # jni.h expects jni_md.h to be in the header search path.
      ln -s $out/include/linux/*_md.h $out/include/

      # Set JAVA_HOME automatically.
      cat <<EOF >> $out/nix-support/setup-hook
      if [ -z "\''${JAVA_HOME-}" ]; then export JAVA_HOME=$out; fi
      EOF
    '';
  });
}

[taku0]

I made a PR to fix this: #110567. It is a draft because it depends on another PR #107784.

[taku0]

#110567 is now ready to merge. Could you test/review it?

[alexvorobiev]

The PR looks good to me.

[stale]

I marked this as stale due to inactivity. → More info