commit:     2f68c7a59f7e94579b72450618e1e7e799fcffe4
Author:     Nicholas Vinson <nvinson234 <AT> gmail <DOT> com>
AuthorDate: Thu Jan 12 14:28:07 2017 +0000
Commit:     Lars Wendler <polynomial-c <AT> gentoo <DOT> org>
CommitDate: Fri Jan 13 16:13:39 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2f68c7a5

sci-biology/mira: Update flex-2.6.3 fix; add cmath header

    Another round of testing discovered that caf_flexer.cc is also a
    pre-generated lexer.  The commit updates the ebuild to remove that
    file as well.  The file abs.C fails to find the pow() function.
    Modern versions of C++ store the header for that function in cmath.
    The file is updated to include that header.

    Gentoo-bug: 585942

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3442

 sci-biology/mira/files/mira-4.0.2-cmath.patch | 14 ++++++++++++++
 sci-biology/mira/mira-4.0.2.ebuild            |  6 ++++--
 2 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/sci-biology/mira/files/mira-4.0.2-cmath.patch 
b/sci-biology/mira/files/mira-4.0.2-cmath.patch
new file mode 100644
index 00000000..a4a0201
--- /dev/null
+++ b/sci-biology/mira/files/mira-4.0.2-cmath.patch
@@ -0,0 +1,14 @@
+--- mira-4.0.2/src/mira/ads.C
++++ mira-4.0.2/src/mira/ads.C
+@@ -31,10 +31,11 @@
+  * Routines for computing scores and some other classification number are
+  *  provided, too.
+  *
+  */
+ 
++#include <cmath>
+ 
+ #include "ads.H"
+ 
+ #include "errorhandling/errorhandling.H"
+ #include "util/dptools.H"

diff --git a/sci-biology/mira/mira-4.0.2.ebuild 
b/sci-biology/mira/mira-4.0.2.ebuild
index 3814d2d..758e30b 100644
--- a/sci-biology/mira/mira-4.0.2.ebuild
+++ b/sci-biology/mira/mira-4.0.2.ebuild
@@ -41,7 +41,8 @@ src_prepare() {
        find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 
's/flex++/flex -+/' || die
        epatch \
                "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
-               "${FILESDIR}"/${P}-cout.patch
+               "${FILESDIR}"/${P}-cout.patch \
+               "${FILESDIR}"/${P}-cmath.patch
 
        sed \
                -e "s:-O[23]::g" \
@@ -50,9 +51,10 @@ src_prepare() {
 
        eautoreconf
 
-       # Remove C++ source files that were built with flex by upstream.
+       # Remove C++ source files that upstream built with flex.
        local f
        local PREBUILT_CXX_LEXER_FILES=(
+               "$S"/src/caf/caf_flexer.cc
                "$S"/src/io/exp_flexer.cc
                "$S"/src/mira/parameters_flexer.cc
        )

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