reinit the tree, so we can have metadata

5 files changed, 371 insertions, 0 deletions

diff --git a/sci-mathematics/glpk/files/glpk-4.52.1-mariadb-5.5.patch b/sci-mathematics/glpk/files/glpk-4.52.1-mariadb-5.5.patch
new file mode 100644
index 000000000000..06aa8e5de95c
--- /dev/null
+++ b/sci-mathematics/glpk/files/glpk-4.52.1-mariadb-5.5.patch
@@ -0,0 +1,11 @@
+--- glpk-4.52.1/src/glpsql.c.orig	2014-02-05 22:14:21.487843989 +0100
++++ glpk-4.52.1/src/glpsql.c	2014-02-05 22:14:32.764510562 +0100
+@@ -1106,8 +1106,6 @@
+ #define byte_defined 1
+ #endif
+ 
+-#include <my_global.h>
+-#include <my_sys.h>
+ #include <mysql.h>
+ 
+ struct db_mysql
diff --git a/sci-mathematics/glpk/files/glpk-4.54-debundle-system-libs.patch b/sci-mathematics/glpk/files/glpk-4.54-debundle-system-libs.patch
new file mode 100644
index 000000000000..a3140341a483
--- /dev/null
+++ b/sci-mathematics/glpk/files/glpk-4.54-debundle-system-libs.patch
@@ -0,0 +1,86 @@
+Remove suitesparse (camd,colamd) and zlib bundles
+bicatali - apr 2014
+
+--- configure.ac.orig	2014-04-05 14:18:56.045148287 -0700
++++ configure.ac	2014-04-05 14:23:24.878803309 -0700
+@@ -59,6 +59,11 @@
+ dnl Check for math library
+ AC_CHECK_LIB([m], [exp])
+ 
++AC_CHECK_LIB([amd], [amd_1])
++AC_CHECK_LIB([colamd], [colamd])
++AC_CHECK_HEADER([amd.h])
++AC_CHECK_LIB([z], [gzopen])
++
+ dnl Check for <sys/time.h> header
+ AC_CHECK_HEADER([sys/time.h],
+    AC_DEFINE([HAVE_SYS_TIME_H], [1], [N/A]))
+--- src/Makefile.am.orig	2014-04-05 14:19:16.401273769 -0700
++++ src/Makefile.am	2014-04-05 14:21:56.696259485 -0700
+@@ -6,15 +6,12 @@
+ 
+ libglpk_la_CPPFLAGS = \
+ -I$(srcdir) \
+--I$(srcdir)/amd \
+ -I$(srcdir)/bflib \
+ -I$(srcdir)/cglib \
+--I$(srcdir)/colamd \
+ -I$(srcdir)/env \
+ -I$(srcdir)/minisat \
+ -I$(srcdir)/misc \
+--I$(srcdir)/proxy \
+--I$(srcdir)/zlib
++-I$(srcdir)/proxy
+ 
+ libglpk_la_LDFLAGS = \
+ -version-info 37:1:1 \
+@@ -92,18 +89,6 @@
+ glpssx02.c \
+ glptsp.c \
+ lux.c \
+-amd/amd_1.c \
+-amd/amd_2.c \
+-amd/amd_aat.c \
+-amd/amd_control.c \
+-amd/amd_defaults.c \
+-amd/amd_dump.c \
+-amd/amd_info.c \
+-amd/amd_order.c \
+-amd/amd_post_tree.c \
+-amd/amd_postorder.c \
+-amd/amd_preprocess.c \
+-amd/amd_valid.c \
+ bflib/btf.c \
+ bflib/btfint.c \
+ bflib/fhv.c \
+@@ -117,7 +102,6 @@
+ bflib/sva.c \
+ cglib/cfg.c \
+ cglib/cfg1.c \
+-colamd/colamd.c \
+ env/alloc.c \
+ env/dlsup.c \
+ env/env.c \
+@@ -150,21 +134,6 @@
+ misc/wclique.c \
+ misc/wclique1.c \
+ proxy/proxy.c \
+-proxy/proxy1.c \
+-zlib/adler32.c \
+-zlib/compress.c \
+-zlib/crc32.c \
+-zlib/deflate.c \
+-zlib/gzclose.c \
+-zlib/gzlib.c \
+-zlib/gzread.c \
+-zlib/gzwrite.c \
+-zlib/inffast.c \
+-zlib/inflate.c \
+-zlib/inftrees.c \
+-zlib/trees.c \
+-zlib/uncompr.c \
+-zlib/zio.c \
+-zlib/zutil.c
++proxy/proxy1.c
+ 
+ ## eof ##
diff --git a/sci-mathematics/glpk/files/glpk-4.57-debundle-system-libs.patch b/sci-mathematics/glpk/files/glpk-4.57-debundle-system-libs.patch
new file mode 100644
index 000000000000..d9efff2bb5f5
--- /dev/null
+++ b/sci-mathematics/glpk/files/glpk-4.57-debundle-system-libs.patch
@@ -0,0 +1,88 @@
+Remove suitesparse (camd,colamd) and zlib bundles
+bicatali - apr 2014
+Updated for 4.57 by soap (Jan 2016)
+
+--- glpk-4.57/configure.ac
++++ glpk-4.57/configure.ac
+@@ -59,6 +59,11 @@
+ dnl Check for math library
+ AC_CHECK_LIB([m], [exp])
+ 
++AC_CHECK_LIB([amd], [amd_1])
++AC_CHECK_LIB([colamd], [colamd])
++AC_CHECK_HEADER([amd.h])
++AC_CHECK_LIB([z], [gzopen])
++
+ dnl Check for <sys/time.h> header
+ AC_CHECK_HEADER([sys/time.h],
+    AC_DEFINE([HAVE_SYS_TIME_H], [1], [N/A]))
+--- glpk-4.57/src/Makefile.am
++++ glpk-4.57/src/Makefile.am
+@@ -6,16 +6,13 @@
+ 
+ libglpk_la_CPPFLAGS = \
+ -I$(srcdir) \
+--I$(srcdir)/amd \
+ -I$(srcdir)/bflib \
+ -I$(srcdir)/cglib \
+--I$(srcdir)/colamd \
+ -I$(srcdir)/env \
+ -I$(srcdir)/minisat \
+ -I$(srcdir)/misc \
+ -I$(srcdir)/proxy \
+--I$(srcdir)/simplex \
+--I$(srcdir)/zlib
++-I$(srcdir)/simplex
+ 
+ libglpk_la_LDFLAGS = \
+ -version-info 38:0:2 \
+@@ -90,18 +87,6 @@
+ glpssx01.c \
+ glpssx02.c \
+ lux.c \
+-amd/amd_1.c \
+-amd/amd_2.c \
+-amd/amd_aat.c \
+-amd/amd_control.c \
+-amd/amd_defaults.c \
+-amd/amd_dump.c \
+-amd/amd_info.c \
+-amd/amd_order.c \
+-amd/amd_post_tree.c \
+-amd/amd_postorder.c \
+-amd/amd_preprocess.c \
+-amd/amd_valid.c \
+ bflib/btf.c \
+ bflib/btfint.c \
+ bflib/fhv.c \
+@@ -115,7 +100,6 @@
+ bflib/sva.c \
+ cglib/cfg.c \
+ cglib/cfg1.c \
+-colamd/colamd.c \
+ env/alloc.c \
+ env/dlsup.c \
+ env/env.c \
+@@ -158,21 +142,6 @@
+ simplex/spxprob.c \
+ simplex/spychuzc.c \
+ simplex/spychuzr.c \
+-simplex/spydual.c \
+-zlib/adler32.c \
+-zlib/compress.c \
+-zlib/crc32.c \
+-zlib/deflate.c \
+-zlib/gzclose.c \
+-zlib/gzlib.c \
+-zlib/gzread.c \
+-zlib/gzwrite.c \
+-zlib/inffast.c \
+-zlib/inflate.c \
+-zlib/inftrees.c \
+-zlib/trees.c \
+-zlib/uncompr.c \
+-zlib/zio.c \
+-zlib/zutil.c
++simplex/spydual.c
+ 
+ ## eof ##
diff --git a/sci-mathematics/glpk/files/glpk-4.60-debundle-system-libs.patch b/sci-mathematics/glpk/files/glpk-4.60-debundle-system-libs.patch
new file mode 100644
index 000000000000..8790de5414fd
--- /dev/null
+++ b/sci-mathematics/glpk/files/glpk-4.60-debundle-system-libs.patch
@@ -0,0 +1,92 @@
+Remove suitesparse (camd,colamd) and zlib bundles
+bicatali - apr 2014
+Updated for 4.57 by soap (Jan 2016)
+Updated for 4.60 by bicatali (Dec 2016)
+
+--- glpk-4.60/configure.ac
++++ glpk-4.60/configure.ac
+@@ -59,6 +59,11 @@
+ dnl Check for math library
+ AC_CHECK_LIB([m], [exp])
+ 
++AC_CHECK_LIB([amd], [amd_1])
++AC_CHECK_LIB([colamd], [colamd])
++AC_CHECK_HEADER([amd.h])
++AC_CHECK_LIB([z], [gzopen])
++
+ dnl Check for <sys/time.h> header
+ AC_CHECK_HEADER([sys/time.h],
+    AC_DEFINE([HAVE_SYS_TIME_H], [1], [N/A]))
+
+--- glpk-4.60/src/Makefile.am
++++ glpk-4.60/src/Makefile.am
+@@ -6,18 +6,15 @@
+ 
+ libglpk_la_CPPFLAGS = \
+ -I$(srcdir) \
+--I$(srcdir)/amd \
+ -I$(srcdir)/api \
+ -I$(srcdir)/bflib \
+ -I$(srcdir)/cglib \
+--I$(srcdir)/colamd \
+ -I$(srcdir)/env \
+ -I$(srcdir)/minisat \
+ -I$(srcdir)/misc \
+ -I$(srcdir)/mpl \
+ -I$(srcdir)/proxy \
+--I$(srcdir)/simplex \
+--I$(srcdir)/zlib
++-I$(srcdir)/simplex
+ 
+ libglpk_la_LDFLAGS = \
+ -version-info 41:0:1 \
+@@ -63,18 +60,6 @@
+ glpssx02.c \
+ lux.c \
+ spv.c \
+-amd/amd_1.c \
+-amd/amd_2.c \
+-amd/amd_aat.c \
+-amd/amd_control.c \
+-amd/amd_defaults.c \
+-amd/amd_dump.c \
+-amd/amd_info.c \
+-amd/amd_order.c \
+-amd/amd_post_tree.c \
+-amd/amd_postorder.c \
+-amd/amd_preprocess.c \
+-amd/amd_valid.c \
+ api/advbas.c \
+ api/asnhall.c \
+ api/asnlp.c \
+@@ -142,7 +127,6 @@
+ cglib/gmicut.c \
+ cglib/gmigen.c \
+ cglib/mirgen.c \
+-colamd/colamd.c \
+ env/alloc.c \
+ env/dlsup.c \
+ env/env.c \
+@@ -195,21 +179,6 @@
+ simplex/spxprob.c \
+ simplex/spychuzc.c \
+ simplex/spychuzr.c \
+-simplex/spydual.c \
+-zlib/adler32.c \
+-zlib/compress.c \
+-zlib/crc32.c \
+-zlib/deflate.c \
+-zlib/gzclose.c \
+-zlib/gzlib.c \
+-zlib/gzread.c \
+-zlib/gzwrite.c \
+-zlib/inffast.c \
+-zlib/inflate.c \
+-zlib/inftrees.c \
+-zlib/trees.c \
+-zlib/uncompr.c \
+-zlib/zio.c \
+-zlib/zutil.c
++simplex/spydual.c
+ 
+ ## eof ##
diff --git a/sci-mathematics/glpk/files/glpk-4.63-debundle-system-libs.patch b/sci-mathematics/glpk/files/glpk-4.63-debundle-system-libs.patch
new file mode 100644
index 000000000000..e836219d0add
--- /dev/null
+++ b/sci-mathematics/glpk/files/glpk-4.63-debundle-system-libs.patch
@@ -0,0 +1,94 @@
+Remove suitesparse (camd,colamd) and zlib bundles
+bicatali - apr 2014
+Updated for 4.57 by soap (Jan 2016)
+Updated for 4.60 by bicatali (Dec 2016)
+Updated for 4.63 by bicatali (Jul 2017)
+
+diff -Nuar --exclude '*.orig' --exclude '*.rej' --exclude '*~' glpk-4.63.orig/configure.ac glpk-4.63/configure.ac
+--- glpk-4.63.orig/configure.ac	2017-07-25 00:00:00.000000000 -0700
++++ glpk-4.63/configure.ac	2017-07-27 14:10:47.986520907 -0700
+@@ -69,6 +69,11 @@
+ dnl Check for math library
+ AC_CHECK_LIB([m], [exp])
+ 
++AC_CHECK_LIB([amd], [amd_1])
++AC_CHECK_LIB([colamd], [colamd])
++AC_CHECK_HEADER([amd.h])
++AC_CHECK_LIB([z], [gzopen])
++
+ dnl Check for <sys/time.h> header
+ AC_CHECK_HEADER([sys/time.h],
+    AC_DEFINE([HAVE_SYS_TIME_H], [1], [N/A]))
+diff -Nuar --exclude '*.orig' --exclude '*.rej' --exclude '*~' glpk-4.63.orig/src/Makefile.am glpk-4.63/src/Makefile.am
+--- glpk-4.63.orig/src/Makefile.am	2017-07-25 00:00:00.000000000 -0700
++++ glpk-4.63/src/Makefile.am	2017-07-27 14:11:30.841536062 -0700
+@@ -6,18 +6,15 @@
+ 
+ libglpk_la_CPPFLAGS = \
+ -I$(srcdir) \
+--I$(srcdir)/amd \
+ -I$(srcdir)/api \
+ -I$(srcdir)/bflib \
+ -I$(srcdir)/cglib \
+--I$(srcdir)/colamd \
+ -I$(srcdir)/env \
+ -I$(srcdir)/minisat \
+ -I$(srcdir)/misc \
+ -I$(srcdir)/mpl \
+ -I$(srcdir)/proxy \
+--I$(srcdir)/simplex \
+--I$(srcdir)/zlib
++-I$(srcdir)/simplex
+ 
+ libglpk_la_LDFLAGS = \
+ -version-info 42:2:2 \
+@@ -57,18 +54,6 @@
+ glpssx01.c \
+ glpssx02.c \
+ lux.c \
+-amd/amd_1.c \
+-amd/amd_2.c \
+-amd/amd_aat.c \
+-amd/amd_control.c \
+-amd/amd_defaults.c \
+-amd/amd_dump.c \
+-amd/amd_info.c \
+-amd/amd_order.c \
+-amd/amd_post_tree.c \
+-amd/amd_postorder.c \
+-amd/amd_preprocess.c \
+-amd/amd_valid.c \
+ api/advbas.c \
+ api/asnhall.c \
+ api/asnlp.c \
+@@ -142,7 +127,6 @@
+ cglib/gmigen.c \
+ cglib/mirgen.c \
+ cglib/spv.c \
+-colamd/colamd.c \
+ env/alloc.c \
+ env/dlsup.c \
+ env/env.c \
+@@ -196,21 +180,6 @@
+ simplex/spxprob.c \
+ simplex/spychuzc.c \
+ simplex/spychuzr.c \
+-simplex/spydual.c \
+-zlib/adler32.c \
+-zlib/compress.c \
+-zlib/crc32.c \
+-zlib/deflate.c \
+-zlib/gzclose.c \
+-zlib/gzlib.c \
+-zlib/gzread.c \
+-zlib/gzwrite.c \
+-zlib/inffast.c \
+-zlib/inflate.c \
+-zlib/inftrees.c \
+-zlib/trees.c \
+-zlib/uncompr.c \
+-zlib/zio.c \
+-zlib/zutil.c
++simplex/spydual.c
+ 
+ ## eof ##