[med-svn] [Git][med-team/salmon][master] 2 commits: Fix the build by adding a missing include

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / salmon


Commits:
511c139b by Michael R. Crusoe at 2020-07-28T14:49:08+02:00
Fix the build by adding a missing include

- - - - -
4f68e184 by Michael R. Crusoe at 2020-07-28T14:50:58+02:00
release 1.3.0+ds1-2

- - - - -


10 changed files:

- debian/changelog
- debian/patches/0008-Remove-salmon_core-lib.patch
- debian/patches/add_MEM_F_SELF_OVLP.patch
- debian/patches/disable-version-check.patch
- + debian/patches/include_fix
- debian/patches/pufferfish
- debian/patches/series
- debian/patches/spelling
- debian/patches/use-system-pkg-config-tbb.patch
- debian/patches/use_debian_packaged_libs.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+salmon (1.3.0+ds1-2) unstable; urgency=medium
+
+  * Fix the build by adding a missing include.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Tue, 28 Jul 2020 14:50:48 +0200
+
 salmon (1.3.0+ds1-1) unstable; urgency=medium
 
   * Add a patch for portable pausing in spinlocks.


=====================================
debian/patches/0008-Remove-salmon_core-lib.patch
=====================================
@@ -1,6 +1,7 @@
 From: Kevin Murray <spam at kdmurray.id.au>
 Date: Sat, 30 Jan 2016 18:06:52 +0200
 Subject: Remove salmon_core lib
+Forwarded: not-needed
 Remark: This patch is deactivated
  Upstream code has changed a lot and it is not documented why
  salmon_core lib was removed.  Before breaking anything the


=====================================
debian/patches/add_MEM_F_SELF_OVLP.patch
=====================================
@@ -4,6 +4,7 @@ Description: redefine MEM_F_SELF_OVLP
  definition to fix an FTBFS.
 Remark: This patch is deactivated since current source code
  builds nicely without it.
+Forwarded: not-needed
 Author: Sascha Steinbiss <sascha at steinbiss.name>
 --- a/src/SalmonQuantify.cpp
 +++ b/src/SalmonQuantify.cpp


=====================================
debian/patches/disable-version-check.patch
=====================================
@@ -1,5 +1,6 @@
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Author: Michael R. Crusoe <crusoe at debian.org>
 Description: Disable the newer version check
+Forwarded: not-needed
 --- salmon.orig/src/Salmon.cpp
 +++ salmon/src/Salmon.cpp
 @@ -214,13 +214,6 @@


=====================================
debian/patches/include_fix
=====================================
@@ -0,0 +1,13 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: add missing include
+Forwarded: https://github.com/COMBINE-lab/salmon/pull/552
+--- salmon.orig/include/BAMUtils.hpp
++++ salmon/include/BAMUtils.hpp
+@@ -9,6 +9,7 @@
+ }
+ 
+ #include <unordered_map>
++#include <string>
+ 
+ namespace salmon {
+   namespace bam_utils {


=====================================
debian/patches/pufferfish
=====================================
@@ -1,5 +1,6 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
 Description: Use local copy of pufferfish source for now
+Forwarded: not-needed
 --- salmon.orig/CMakeLists.txt
 +++ salmon/CMakeLists.txt
 @@ -297,11 +297,7 @@


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ disable-version-check.patch
 # 0008-Remove-salmon_core-lib.patch
 # add_MEM_F_SELF_OVLP.patch
 spelling
+include_fix


=====================================
debian/patches/spelling
=====================================
@@ -1,4 +1,4 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
 Subject: fix typos
 Forwarded: https://github.com/COMBINE-lab/salmon/pull/548/
 --- salmon.orig/include/BAMQueue.tpp


=====================================
debian/patches/use-system-pkg-config-tbb.patch
=====================================
@@ -4,7 +4,8 @@ Remark: This patch is deactivated for the moment.
         and there is no point to fiddle around now any more.
         However, may be this is more elegant and the patch is
         left as documentation.
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Author: Michael R. Crusoe <crusoe at debian.org>
+Forwarded: not-needed
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
 @@ -287,6 +287,9 @@ endif()


=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -1,7 +1,7 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Update: Tue, 11 Dec 2018 19:29:39 +0100
 Description: Use Debian packaged libraries and make sure these are linked dynamically
-
+Forwarded: not-needed
 --- salmon.orig/src/CMakeLists.txt
 +++ salmon/src/CMakeLists.txt
 @@ -1,6 +1,6 @@



View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554

-- 
View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/432a1944beaa0b5f28f73c99d669d06e63a20672...4f68e1844b6e12c5e882460b4164b4e983f9a554
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200728/086ace5c/attachment-0001.html>