[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/

[Martin Mokrejs]

commit:     ef30e8a1e8ba6e56b365f8dbaddd1b4812306392
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec  2 23:27:56 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec  2 23:27:56 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ef30e8a1

sci-biology/ncbi-tools++: fix bug #579248#c by disabling more tests

This will likely also fix the #579248 bug in rmblast (untested).

Our $FILESDIR/disable-testsuite-compilation.txt only excludes test
applications from usingboost, not the support library. Hence the above
bug.

We could either add --without-boost to the configuration command line
to disable the bosost-related code in support library or, which is the
path we take in this commit, we disable building of the yet escaping
unit_tests which needed boost.

Upstream further said:

The C++ Toolkit makes very little use of Boost outside of unit tests,
but that's a fair question.  The simplest fix preserving other uses of
Boost would be to edit .../src/corelib/Makefile.in and remove test_boost
from LIB_PROJ.  (You'll still also need to exclude building the tests by
adding '-.*/unit_tests' to the $FILESDIR/disable-testsuite-compilation.txt
file.)

Package-Manager: portage-2.3.2

 .../ncbi-tools++/files/disable-testsuite-compilation.txt      |  1 +
 .../files/ncbi-tools++-12.0.0-never_build_test_boost.patch    | 11 +++++++++++
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild           |  1 +
 3 files changed, 13 insertions(+)

diff --git a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
index aeaf75e..8df346f 100644
--- a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
+++ b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt
@@ -1,3 +1,4 @@
 .*
 -.*/test
 -.*/unit_test
+-.*/unit_tests

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch
new file mode 100644
index 0000000..68baea0
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori	2016-12-01 20:28:33.239758102 +0100
++++ ncbi_cxx--12_0_0/src/corelib/Makefile.in	2016-12-01 20:28:46.330110659 +0100
+@@ -7,7 +7,7 @@
+ #################################
+ 
+ USR_PROJ = precompile
+-LIB_PROJ = corelib test_mt test_boost
++LIB_PROJ = corelib test_mt
+ SUB_PROJ = test
+ PROJ_TAG = core
+ 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index c9f6911..1236c13 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -120,6 +120,7 @@ src_prepare() {
 		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
 		"${FILESDIR}"/${P}-fix-install.patch
 		"${FILESDIR}"/${P}-bdb6.patch
+		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
 		)
 #       "${FILESDIR}"/${P}-as-needed.patch
 #       "${FILESDIR}"/${P}-fix-creaders-linking.patch