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 <[email protected]> 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 <[email protected]> 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 <[email protected]> --- a/src/SalmonQuantify.cpp +++ b/src/SalmonQuantify.cpp ===================================== debian/patches/disable-version-check.patch ===================================== @@ -1,5 +1,6 @@ -Author: Michael R. Crusoe <[email protected]> +Author: Michael R. Crusoe <[email protected]> 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 <[email protected]> +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 <[email protected]> +Author: Michael R. Crusoe <[email protected]> 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 <[email protected]> +From: Michael R. Crusoe <[email protected]> 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 <[email protected]> +Author: Michael R. Crusoe <[email protected]> +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 <[email protected]> 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.
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