From 444bcbe26fbedcb4d1bd5266d6db1cc4d36a31de Mon Sep 17 00:00:00 2001
From: Tyson Whitehead <twhitehead@gmail.com>
Date: Wed, 18 Jul 2018 13:21:33 -0400
Subject: [PATCH] pkgs: Do all version requirements as overrides in
 all-packages

---
 pkgs/all-packages.nix     | 12 ++++++------
 pkgs/blast/default.nix    |  2 +-
 pkgs/cloudcompare.nix     |  4 ++--
 pkgs/cryptominisat.nix    |  4 ++--
 pkgs/meraculous.nix       |  9 +++------
 pkgs/octopus/octopus.nix  |  6 +++---
 pkgs/openslide/python.nix |  6 +++---
 pkgs/sumo.nix             |  4 ++--
 8 files changed, 22 insertions(+), 25 deletions(-)

diff --git a/pkgs/all-packages.nix b/pkgs/all-packages.nix
index a2a31c4..15f84f5 100644
--- a/pkgs/all-packages.nix
+++ b/pkgs/all-packages.nix
@@ -9,9 +9,9 @@ self: super: pkgs: with pkgs; {
     boost = boost162;
   };
 
-  cloudcompare = libsForQt5.callPackage ./cloudcompare.nix { };
+  cloudcompare = libsForQt5.callPackage ./cloudcompare.nix { boost = boost15x; };
 
-  cryptominisat = callPackage ./cryptominisat.nix { };
+  cryptominisat = callPackage ./cryptominisat.nix { python = python27; };
 
   #firedrake = callPackage ./firedrake { };
 
@@ -20,22 +20,22 @@ self: super: pkgs: with pkgs; {
   libxc4 = libxc404;
   libxc = libxc4;
 
-  #meraculous = callPackage ./meraculous.nix { };
+  #meraculous = callPackage ./meraculous.nix { let stdenv49 = overrideCC stdenv gcc49; in stdenv = stdenv49; boost = boost159.override { stdenv = stdenv49 }; };
 
   inherit (callPackage ./opengl/default.nix { inherit super; }) mesa_noglu;
 
-  inherit (callPackages ./octopus/octopus.nix { }) octopus72;
+  inherit (callPackages ./octopus/octopus.nix { stdenv = overrideCC stdenv gcc5; gfortran = gfortran5; }) octopus72;
   octopus7 = octopus72;
   octopus = octopus7;
 
   openfoam = callPackage ./openfoam.nix { };
 
   openslide = callPackage ./openslide { };
-  openslide-python = callPackage ./openslide/python.nix { };
+  openslide-python = callPackage ./openslide/python.nix { pythonPackages = python27Packages; };
 
   ovito = libsForQt5.callPackage ./ovito.nix { stdenv = overrideCC stdenv gcc6; };
 
-  #sumo = callPackage ./sumo.nix { };
+  #sumo = callPackage ./sumo.nix { fox = fox_1_6; };
 
   namd = callPackage ./namd.nix { };
 
diff --git a/pkgs/blast/default.nix b/pkgs/blast/default.nix
index 5fea7bd..aa0fd6e 100644
--- a/pkgs/blast/default.nix
+++ b/pkgs/blast/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, gcc5, cpio, curl
+{ stdenv, fetchurl, cpio, curl
 , python, perl, zlib, bzip2, boost }:
 
 stdenv.mkDerivation rec {
diff --git a/pkgs/cloudcompare.nix b/pkgs/cloudcompare.nix
index 61d87e9..1ea696c 100644
--- a/pkgs/cloudcompare.nix
+++ b/pkgs/cloudcompare.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchFromGitHub, cmake
-, boost15x, eigen, dxflib, gdal, flann, libLAS, LASzip
+, boost, eigen, dxflib, gdal, flann, libLAS, LASzip
 , qtbase }:
 
 stdenv.mkDerivation rec {
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     cmake
-    boost15x
+    boost
     eigen
     dxflib
     gdal
diff --git a/pkgs/cryptominisat.nix b/pkgs/cryptominisat.nix
index 267fa3b..7199163 100644
--- a/pkgs/cryptominisat.nix
+++ b/pkgs/cryptominisat.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, cmake, zlib, sqlite, boost, python27, vim }:
+{ stdenv, fetchurl, cmake, zlib, sqlite, boost, python, vim }:
 
 stdenv.mkDerivation {
   name = "cryptominisat-4.5.3";
@@ -13,7 +13,7 @@ stdenv.mkDerivation {
     zlib
     sqlite
     boost
-    python27
+    python
     vim
   ];
 
diff --git a/pkgs/meraculous.nix b/pkgs/meraculous.nix
index 17e1d5c..5090269 100644
--- a/pkgs/meraculous.nix
+++ b/pkgs/meraculous.nix
@@ -1,12 +1,9 @@
 { stdenv, overrideCC, gcc49, fetchurl, makeWrapper, gzip, cmake
-, boost159, perl, perlPackages, gnuplot }:
+, boost, perl, perlPackages, gnuplot }:
 
 # gcc 5.x c++11 requires istream to be explicitly cast to bool
 
-let
-  stdenv49 = overrideCC stdenv gcc49;
-
-in stdenv49.mkDerivation rec {
+stdenv.mkDerivation rec {
   version = "2.2.2.5_lt";
   name = "meraculous-${version}";
 
@@ -27,7 +24,7 @@ in stdenv49.mkDerivation rec {
     makeWrapper
     gzip
     cmake
-    (boost159.override { stdenv = stdenv49; })
+    boost
     perl
     perlPackages.Log4Perl
     gnuplot
diff --git a/pkgs/octopus/octopus.nix b/pkgs/octopus/octopus.nix
index 2947eeb..af6d3f3 100644
--- a/pkgs/octopus/octopus.nix
+++ b/pkgs/octopus/octopus.nix
@@ -9,12 +9,12 @@
 # nlopt (only provides libnlopt_cxx which requires c++ compiler for linking)
 #
 
-{ stdenv, fetchurl, overrideCC, gcc5, gfortran5, perl, openmpi
+{ stdenv, fetchurl, gfortran, perl, openmpi
 , libxc3, blas, liblapack, gsl, fftw, netcdffortran
 , arpack, libyaml }:
 
 let
-  common = version: sha256: (overrideCC stdenv gcc5).mkDerivation rec {
+  common = version: sha256: stdenv.mkDerivation rec {
     inherit version;
     name = "octopus-${version}";
 
@@ -24,7 +24,7 @@ let
     };
 
     buildInputs = [
-      gfortran5
+      gfortran
       perl
       openmpi
       libxc3
diff --git a/pkgs/openslide/python.nix b/pkgs/openslide/python.nix
index 8d0a7ce..415ce48 100644
--- a/pkgs/openslide/python.nix
+++ b/pkgs/openslide/python.nix
@@ -1,7 +1,7 @@
 { lib, fetchFromGitHub
-, python27Packages, openslide }:
+, pythonPackages, openslide }:
 
-python27Packages.buildPythonPackage rec {
+pythonPackages.buildPythonPackage rec {
   version = "1.1.1";
   name = "openslide-python-${version}";
 
@@ -23,7 +23,7 @@ python27Packages.buildPythonPackage rec {
   ];
 
   propagatedBuildInputs = [
-    python27Packages.pillow
+    pythonPackages.pillow
   ];
 
   meta = with lib; {
diff --git a/pkgs/sumo.nix b/pkgs/sumo.nix
index 8db8ea4..d3a4c8b 100644
--- a/pkgs/sumo.nix
+++ b/pkgs/sumo.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, unzip
 , lzma, bzip2, zlib, libjpeg, libtiff, openssl
 , mesa, xorg
-, fox_1_6, xercesc, proj, gdal, hdf5, curl }:
+, fox, xercesc, proj, gdal, hdf5, curl }:
 
 stdenv.mkDerivation rec {
   version = "0.25.0";
@@ -17,7 +17,7 @@ stdenv.mkDerivation rec {
     libjpeg libtiff
     openssl
     mesa xorg.libX11
-    fox_1_6
+    fox
     xercesc
     proj gdal
     hdf5