[med-svn] [Git][med-team/mmseqs2][master] 2 commits: Fix some includes within src to use the correct zstd library
Shayan Doust
gitlab at salsa.debian.org
Fri Jul 19 15:54:45 BST 2019
Shayan Doust pushed to branch master at Debian Med / mmseqs2
Commits:
857d7fc7 by Shayan Doust at 2019-07-19T04:21:50Z
Fix some includes within src to use the correct zstd library
- - - - -
636cb533 by Shayan Doust at 2019-07-19T14:53:39Z
Run cme on patches & fix copyright file
- - - - -
4 changed files:
- debian/copyright
- + debian/patches/fix_src_zstd_includes.patch
- debian/patches/series
- debian/patches/use_system_zstd.patch
Changes:
=====================================
debian/copyright
=====================================
@@ -58,163 +58,620 @@ License: Expat
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+ 11. Patents.
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+ 12. No Surrender of Others' Freedom.
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+ .
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+ ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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+ .
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+ END OF TERMS AND CONDITIONS
License: LGPL
This version of the GNU Lesser General Public License incorporates
@@ -262,7 +719,7 @@ License: LGPL
that uses the facility (other than as an argument passed when the
facility is invoked), then you may convey a copy of the modified
version:
- .
+ .
a) under this License, provided that you make a good faith effort to
ensure that, in the event an Application does not supply the
function or data, the facility still operates, and performs
@@ -374,6 +831,8 @@ License: LGPL
apply, that proxy's public statement of acceptance of any version is
permanent authorization for you to choose that version for the
Library.
+ .
+ A copy of this license can be found under /usr/share/common-licenses
License: public_domain
PUBLIC DOMAIN NOTICE
=====================================
debian/patches/fix_src_zstd_includes.patch
=====================================
@@ -0,0 +1,45 @@
+Description: Modify some upstream source files
+ as some of the source files have includes directly referring to the old zstd folder in lib, we now use system-wide lib
+Author: Shayan Doust <hello at shayandoust.me>
+Last-Update: 2019-07-19
+---
+
+Index: mmseqs2/src/commons/DBReader.h
+===================================================================
+--- mmseqs2.orig/src/commons/DBReader.h 2019-07-19 05:18:28.757452860 +0100
++++ mmseqs2/src/commons/DBReader.h 2019-07-19 05:18:28.749452793 +0100
+@@ -15,7 +15,7 @@
+ #include "FileUtil.h"
+
+ #define ZSTD_STATIC_LINKING_ONLY // ZSTD_findDecompressedSize
+-#include <zstd/lib/zstd.h>
++#include <zstd.h>
+
+ template <typename T>
+ class DBReader {
+Index: mmseqs2/src/commons/DBWriter.h
+===================================================================
+--- mmseqs2.orig/src/commons/DBWriter.h 2019-07-19 05:18:28.757452860 +0100
++++ mmseqs2/src/commons/DBWriter.h 2019-07-19 05:18:28.749452793 +0100
+@@ -10,7 +10,7 @@
+
+ #include <string>
+ #include <vector>
+-#include <zstd/lib/zstd.h>
++#include <zstd.h>
+ #include "DBReader.h"
+
+ template <typename T> class DBReader;
+Index: mmseqs2/src/test/TestDBReaderZstd.cpp
+===================================================================
+--- mmseqs2.orig/src/test/TestDBReaderZstd.cpp 2019-07-19 05:18:28.757452860 +0100
++++ mmseqs2/src/test/TestDBReaderZstd.cpp 2019-07-19 05:18:28.749452793 +0100
+@@ -9,7 +9,7 @@
+ #include "Clustering.h"
+ #include "SetElement.h"
+ #define ZSTD_STATIC_LINKING_ONLY // ZSTD_findDecompressedSize
+-#include <zstd/lib/zstd.h>
++#include <zstd.h>
+
+ #include "DBReader.h"
+ #include "DBWriter.h"
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+fix_src_zstd_includes.patch
fix_util_installation.patch
use_system_zstd.patch
use_system_gzstream.patch
=====================================
debian/patches/use_system_zstd.patch
=====================================
@@ -1,3 +1,4 @@
+Description: Use_system_zstd
Index: mmseqs2/CMakeLists.txt
===================================================================
--- mmseqs2.orig/CMakeLists.txt
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/b654c5ac1d161eaf56d3ec8a2c14676718924ada...636cb533cd08114d7628f033ab4463c0b6626079
--
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/b654c5ac1d161eaf56d3ec8a2c14676718924ada...636cb533cd08114d7628f033ab4463c0b6626079
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