gentoo Easter resync : 12.04.2020

3 files changed, 161 insertions, 0 deletions

diff --git a/sci-mathematics/glpk/files/glpk-4.65-debundle-system-libs.patch b/sci-mathematics/glpk/files/glpk-4.65-debundle-system-libs.patch
new file mode 100644
index 000000000000..78af8b8d9431
--- /dev/null
+++ b/sci-mathematics/glpk/files/glpk-4.65-debundle-system-libs.patch
@@ -0,0 +1,91 @@
+diff --git a/configure.ac b/configure.ac
+index 96c4cc5..29e11f9 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -69,6 +69,11 @@ AC_PROG_LIBTOOL
+ 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 --git a/src/Makefile.am b/src/Makefile.am
+index eb5dc1b..b814627 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -6,10 +6,8 @@ lib_LTLIBRARIES = libglpk.la
+ 
+ libglpk_la_CPPFLAGS = \
+ -I$(srcdir) \
+--I$(srcdir)/amd \
+ -I$(srcdir)/api \
+ -I$(srcdir)/bflib \
+--I$(srcdir)/colamd \
+ -I$(srcdir)/draft \
+ -I$(srcdir)/env \
+ -I$(srcdir)/intopt \
+@@ -18,8 +16,7 @@ libglpk_la_CPPFLAGS = \
+ -I$(srcdir)/mpl \
+ -I$(srcdir)/npp \
+ -I$(srcdir)/proxy \
+--I$(srcdir)/simplex \
+--I$(srcdir)/zlib
++-I$(srcdir)/simplex
+ 
+ libglpk_la_LDFLAGS = \
+ -version-info 43:0:3 \
+@@ -27,18 +24,6 @@ libglpk_la_LDFLAGS = \
+ ${NOUNDEFINED}
+ 
+ libglpk_la_SOURCES = \
+-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 \
+@@ -104,7 +89,6 @@ bflib/scf.c \
+ bflib/scfint.c \
+ bflib/sgf.c \
+ bflib/sva.c \
+-colamd/colamd.c \
+ draft/bfd.c \
+ draft/bfx.c \
+ draft/glpapi06.c \
+@@ -202,21 +186,6 @@ simplex/spxprim.c \
+ 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-4.65-fix-mysql-include-prefix.patch b/sci-mathematics/glpk/files/glpk-4.65-fix-mysql-include-prefix.patch
new file mode 100644
index 000000000000..4dd6583d6dea
--- /dev/null
+++ b/sci-mathematics/glpk/files/glpk-4.65-fix-mysql-include-prefix.patch
@@ -0,0 +1,47 @@
+From 5cff695e9eb8405efbdfa976f1fad965c55436e8 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Fri, 6 Mar 2020 16:24:10 -0500
+Subject: [PATCH 1/1] configure.ac: attempt mysql_config to find the MySQL
+ headers.
+
+When building with MySQL support, the configure script guesses that
+the path to the MySQL headers is /usr/include/mysql. That is usually
+correct, but when people install MySQL to a nonstandard location such
+as /home/mjo/usr, it falls over. Fortunately, MySQL usually provides
+an executable called "mysql_config" that can output the location of
+its headers.
+
+In such a "local" installation, if I prepend /home/mjo/usr/bin to my
+PATH, then running "mysql_config" will execute the mysql_config from
+/home/mjo/usr/bin and will therefore output -I/home/mjo/usr/include as
+the preprocessor flag that glpk needs. That's the right thing to do,
+and it works just as well for a system install under /usr or
+/usr/local.
+
+This commit attempts to find the headers using mysql_config first,
+and falls back to the location /usr/include/mysql.
+
+Gentoo-bug: https://bugs.gentoo.org/597620
+---
+ configure.ac | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/configure.ac b/configure.ac
+index 96c4cc5..d20a6ef 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -145,7 +145,10 @@ if test "$enable_mysql" = "yes"; then
+       AC_MSG_ERROR([--enable-mysql requires --enable-dl])
+    fi
+    AC_MSG_RESULT([yes])
+-   CPPFLAGS="-I/usr/include/mysql $CPPFLAGS"
++   # Guess at the include directory if mysql_config isn't in our PATH.
++   MYSQL_INCLUDE=$(mysql_config --include 2>/dev/null)
++   test -z "${MYSQL_INCLUDE}" && MYSQL_INCLUDE="-I/usr/include/mysql"
++   CPPFLAGS="${MYSQL_INCLUDE} $CPPFLAGS"
+    AC_DEFINE_UNQUOTED([MYSQL_DLNAME], ["$LIBMYSQL"], [N/A])
+ else
+    AC_MSG_RESULT([no])
+-- 
+2.24.1
+
diff --git a/sci-mathematics/glpk/files/glpk-4.65-longstep_verbosity.patch b/sci-mathematics/glpk/files/glpk-4.65-longstep_verbosity.patch
new file mode 100644
index 000000000000..1b78ece3e695
--- /dev/null
+++ b/sci-mathematics/glpk/files/glpk-4.65-longstep_verbosity.patch
@@ -0,0 +1,23 @@
+http://lists.gnu.org/archive/html/bug-glpk/2018-03/msg00000.html
+
+diff --git a/src/draft/glpios03.c b/src/draft/glpios03.c
+index 21d6a00..eb34ad0 100644
+--- a/src/draft/glpios03.c
++++ b/src/draft/glpios03.c
+@@ -920,13 +920,10 @@ int ios_driver(glp_tree *T)
+ #if 0
+       ((glp_iocp *)T->parm)->msg_lev = GLP_MSG_DBG;
+ #endif
+-#if 1 /* 16/III-2016 */
++#if 1 /* 01/III-2018 */
+       if (((glp_iocp *)T->parm)->flip)
+-#if 0 /* 20/I-2018 */
+-         xprintf("WARNING: LONG-STEP DUAL SIMPLEX WILL BE USED\n");
+-#else
+-         xprintf("Long-step dual simplex will be used\n");
+-#endif
++         if (T->parm->msg_lev >= GLP_MSG_ALL)
++            xprintf("Long-step dual simplex will be used\n");
+ #endif
+       /* on entry to the B&B driver it is assumed that the active list
+          contains the only active (i.e. root) subproblem, which is the