Hi all. I’m trying to pull a derivation together for a non-NixOS binary program (VESTA, a virtual molecule visualizer), mostly by following the guide here, using patchelf to resolve library paths, which is failing to locate a library that seems to be available. This is my first attempt at packaging, so I’m probably doing something stupid. Here’s my default.nix:
{ stdenv, fontconfig, lib, gdk-pixbuf, openjdk, gtk2, gtk3, iconv,
libGLU, libGL, libglvnd, pango, xorg, glib, glibc, gcc-unwrapped,
cairo, makeWrapper, fetchurl, autoPatchelfHook }:
stdenv.mkDerivation rec {
name = "VESTA-gtk3";
version = "3.5.8";
src = fetchurl {
url = "https://jp-minerals.org/vesta/archives/${version}/VESTA-gtk3.tar.bz2";
sha256 = "sha256-eL7wJcKzHx1kycfgatKxOdJSs6aGiT7nmsdLMCGGjfg=";
};
nativeBuildInputs = [
autoPatchelfHook
fontconfig.lib
gcc-unwrapped.lib
gcc-unwrapped.libgcc
gdk-pixbuf
glib
gtk2
gtk3
iconv
libGLU
libglvnd
pango
xorg.libX11
xorg.libXxf86vm
xorg.libXtst
openjdk
];
dontConfigure = true;
dontBuild = true;
installPhase = ''
mkdir $out
cp -ar * $out
'';
preFixup = let
libPath = lib.makeLibraryPath [ cairo
fontconfig.lib
gcc-unwrapped.lib
gcc-unwrapped.libgcc
gdk-pixbuf
glib
gtk2
gtk3
iconv
libGLU
libglvnd
pango
xorg.libX11
xorg.libXxf86vm
xorg.libXtst
openjdk
];
in ''
patchelf \
--set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
--set-rpath "${libPath}" \
$out/VESTA
patchelf \
--set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
--set-rpath "${libPath}" \
$out/VESTA-core
patchelf \
--set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
--set-rpath "${libPath}" \
$out/VESTA-gui
'';
meta = with lib; {
homepage = "https://jp-minerals.org/vesta/en/";
description = "Visualization for Electronic and STructural Analysis";
license = licenses.free;
platforms = platforms.linux;
architectures = [ "amd64" ];
};
}
I first load utilities in nix-shell
$ nix-shell -p binutils stdenv nix-index stdenv.cc
and then run
$ nix-build -E '((import <nixpkgs> {}).callPackage (import ./default.nix) { })' --keep-failed --no-out-link
The output indicates all libs are resolved except for one java library: libjawt.so, which nevertheless does exist, supplied by the jdk package (and nix-locate confirms this). Here is the tail of the build log:
searching for dependencies of /nix/store/pvlf028qs680ac96l6rq5cn9czapcgbx-VESTA-gtk3/PowderPlot/libswt-awt-gtk-3346.so
libjawt.so -> not found!
setting interpreter of /nix/store/pvlf028qs680ac96l6rq5cn9czapcgbx-VESTA-gtk3/STRUCTURE_TIDY/structure_tidy
searching for dependencies of /nix/store/pvlf028qs680ac96l6rq5cn9czapcgbx-VESTA-gtk3/STRUCTURE_TIDY/structure_tidy
libgcc_s.so.1 -> found: /nix/store/5gk8zqasr9hdhm9nhl0y7g0g7bf5lvbc-gcc-12.2.0-libgcc/lib
setting RPATH to: /nix/store/5gk8zqasr9hdhm9nhl0y7g0g7bf5lvbc-gcc-12.2.0-libgcc/lib
auto-patchelf: 1 dependencies could not be satisfied
error: auto-patchelf could not satisfy dependency libjawt.so wanted by /nix/store/pvlf028qs680ac96l6rq5cn9czapcgbx-VESTA-gtk3/PowderPlot/libswt-awt-gtk-3346.so
auto-patchelf failed to find all the required dependencies.
Add the missing dependencies to --libs or use `--ignore-missing="foo.so.1 bar.so etc.so"`.
/nix/store/37p8gq9zijbw6pj3lpi1ckqiv18j2g62-stdenv-linux/setup: line 79: pop_var_context: head of shell_variables not a function context
/nix/store/37p8gq9zijbw6pj3lpi1ckqiv18j2g62-stdenv-linux/setup: line 1457: pop_var_context: head of shell_variables not a function context
/nix/store/37p8gq9zijbw6pj3lpi1ckqiv18j2g62-stdenv-linux/setup: line 1594: pop_var_context: head of shell_variables not a function context
note: keeping build directory '/tmp/nix-build-VESTA-gtk3.drv-58'
error: builder for '/nix/store/qvrryfms3ym39fzzqxii28gldfbldjgh-VESTA-gtk3.drv' failed with exit code 1;
last 10 log lines:
> searching for dependencies of /nix/store/pvlf028qs680ac96l6rq5cn9czapcgbx-VESTA-gtk3/STRUCTURE_TIDY/structure_tidy
> libgcc_s.so.1 -> found: /nix/store/5gk8zqasr9hdhm9nhl0y7g0g7bf5lvbc-gcc-12.2.0-libgcc/lib
> setting RPATH to: /nix/store/5gk8zqasr9hdhm9nhl0y7g0g7bf5lvbc-gcc-12.2.0-libgcc/lib
> auto-patchelf: 1 dependencies could not be satisfied
> error: auto-patchelf could not satisfy dependency libjawt.so wanted by /nix/store/pvlf028qs680ac96l6rq5cn9czapcgbx-VESTA-gtk3/PowderPlot/libswt-awt-gtk-3346.so
> auto-patchelf failed to find all the required dependencies.
> Add the missing dependencies to --libs or use `--ignore-missing="foo.so.1 bar.so etc.so"`.
> /nix/store/37p8gq9zijbw6pj3lpi1ckqiv18j2g62-stdenv-linux/setup: line 79: pop_var_context: head of shell_variables not a function context
> /nix/store/37p8gq9zijbw6pj3lpi1ckqiv18j2g62-stdenv-linux/setup: line 1457: pop_var_context: head of shell_variables not a function context
> /nix/store/37p8gq9zijbw6pj3lpi1ckqiv18j2g62-stdenv-linux/setup: line 1594: pop_var_context: head of shell_variables not a function context
For full logs, run 'nix log /nix/store/qvrryfms3ym39fzzqxii28gldfbldjgh-VESTA-gtk3.drv'.
Confirming the error,
$ ldd /nix/store/pvlf028qs680ac96l6rq5cn9czapcgbx-VESTA-gtk3/PowderPlot/libswt-awt-gtk-3346.so
ldd: warning: you do not have execution permission for `/nix/store/pvlf028qs680ac96l6rq5cn9czapcgbx-VESTA-gtk3/PowderPlot/libswt-awt-gtk-3346.so'
linux-vdso.so.1 (0x00007f608bf5f000)
libjawt.so => not found
libc.so.6 => /nix/store/yaz7pyf0ah88g2v505l38n0f3wg2vzdj-glibc-2.37-8/lib/libc.so.6 (0x00007f608bc1a000)
/nix/store/yaz7pyf0ah88g2v505l38n0f3wg2vzdj-glibc-2.37-8/lib64/ld-linux-x86-64.so.2 (0x00007f608bf61000)
Does anyone know why patchelf can’t seem to find this particular library (everything else it found successfully), despite the fact that libjawt.so is clearly available?