[fink:package-submissions] #4975 fix pymol-py build for Xcode 9 on 10.13

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** [package-submissions:#4975] fix pymol-py build for Xcode 9 on 10.13**

**Status:** open
**Group:** Undergoing_Validation
**Created:** Mon Aug 21, 2017 10:13 AM UTC by Jack Howarth
**Last Updated:** Mon Aug 21, 2017 10:13 AM UTC
**Owner:** nobody


The attached revised pymol-py.patch and info file solve compile errors on 10.13 with Xcode 9 beta 5. The Xcode 9 clang compilers handle addtional inclusions of -I/usr/include entries in the search path differently than the Xcode 9 clang compilers on 10.12 or the llvm.org 6.0.0svn clang compilers on 10.13. In both of the later cases, the clang compiler demotes the additional -I/usr/inclcude so that it appears after the c++/v1 search path entriy. The new behavior breaks the build of pymol because the duplicated headers like math.h in c++/v1 aren't found before those in /usr/include leading to c++ compile errrors. The changes to the Info file are...

~~~
Index: pymol-py.info
===================================================================
RCS file: /cvsroot/fink/dists/10.9-libcxx/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.7
diff -u -r1.7 pymol-py.info
--- pymol-py.info	11 Mar 2017 15:44:09 -0000	1.7
+++ pymol-py.info	21 Aug 2017 10:10:04 -0000
@@ -14,7 +14,7 @@
 Source3: http://www.weizmann.ac.il/ISPC/eMovie_rigimol.inp
 Source3-MD5: 7f61fc224103aa24a92f1a03f985ce49
 PatchFile: pymol-py.patch
-PatchFile-MD5: eb9a025c1952c2bc132d89e82ab4ead1
+PatchFile-MD5: acbe3539c4837e41aba2e078ea01ce9c
 PatchFile2: pymol-py-gl.patch
 PatchFile2-MD5: 6e45a30ca2c47122951f6f92659da221 
 PatchFile3: pymol-py-unused.patch
@@ -23,7 +23,8 @@
 SourceDirectory: pymol
 # Avoid including headers from fink before source directories
 NoSetCPPFLAGS: true
-SetCFLAGS: -Wno-c++11-extensions
+SetCFLAGS: -Wno-c++11-extensions -Wno-nullability-completeness
+SetCXXFLAGS: -Wno-c++11-extensions -Wno-nullability-completeness
 Depends: <<
 	blt-shlibs,
 	freeglut2-shlibs,
~~~

and the change to the pymol-py.patch is...

~~~
Index: pymol-py.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.9-libcxx/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.2
diff -u -r1.2 pymol-py.patch
--- pymol-py.patch	30 Aug 2016 22:37:46 -0000	1.2
+++ pymol-py.patch	21 Aug 2017 10:10:04 -0000
@@ -38,7 +38,7 @@
  
  # can be changed with environment variable PREFIX_PATH
 -prefix_path = ["/usr", "/usr/X11"]
-+prefix_path = ["@FINKPREFIX@", "/usr", "@X11DIR@"]
++prefix_path = ["@FINKPREFIX@", "@X11DIR@"]
  
  pymol_src_dirs = [
      "ov/src",
~~~

Tested on 10.13 with 'fink -m'.


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