[med-svn] [Git][med-team/mmseqs2][master] 4 commits: Accept the patch from Alberto, thanks!

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / mmseqs2


Commits:
50930473 by Michael R. Crusoe at 2020-05-04T17:29:59+02:00
Accept the patch from Alberto, thanks!

- - - - -
f409350a by Michael R. Crusoe at 2020-05-04T17:30:25+02:00
routine-update: Add salsa-ci file

- - - - -
2c4db8b6 by Michael R. Crusoe at 2020-05-04T17:30:25+02:00
routine-update: Rules-Requires-Root: no

- - - - -
e038c1d3 by Michael R. Crusoe at 2020-05-04T17:33:24+02:00
release 11-e1a1c+ds-3 to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/fix-ftbfs-gcc10.patch
- debian/patches/series
- + debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,6 +1,20 @@
-mmseqs2 (11-e1a1c+ds-2) unstable; urgency=medium
+mmseqs2 (11-e1a1c+ds-3) unstable; urgency=medium
 
   * Team upload.
+
+  [ Alberto Garcia ]
+  * debian/patches/fix-ftbfs-gcc10.patch:
+    - Fix FTBFS with GCC 10 (Closes: #957552).
+
+  [ Michael R. Crusoe ]
+  * Accept the patch from Alberto, thanks!
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  Mon, 04 May 2020 17:30:26 +0200
+
+mmseqs2 (11-e1a1c+ds-2) unstable; urgency=medium
+
   * Install binaries only in the mmseqs2 binary package, not also the
     mmseqs2-examples binary package
   * Report the Debian package version instead of "GITDIR-NOTFOUND"


=====================================
debian/control
=====================================
@@ -4,22 +4,23 @@ Uploaders: Shayan Doust <hello at shayandoust.me>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12)
-Build-Depends-arch: cmake,
+Build-Depends-Arch: cmake,
                     libgzstream-dev,
                     libzstd-dev,
                     zlib1g-dev,
                     libbz2-dev,
-                    libsimde-dev (>= 0.0.0.git.20200424)
+                    libsimde-dev
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/mmseqs2
 Vcs-Git: https://salsa.debian.org/med-team/mmseqs2.git
 Homepage: https://github.com/soedinglab/MMseqs2
+Rules-Requires-Root: no
 
 Package: mmseqs2
 Architecture: any
-Built-Using: ${simde:Built-Using}
 Depends: ${shlibs:Depends},
          ${misc:Depends}
+Built-Using: ${simde:Built-Using}
 Description: ultra fast and sensitive protein search and clustering
  MMseqs2 (Many-against-Many sequence searching) is a software suite to
  search and cluster huge proteins/nucleotide sequence sets. MMseqs2 is


=====================================
debian/patches/fix-ftbfs-gcc10.patch
=====================================
@@ -0,0 +1,24 @@
+Author: Milot Mirdita <milot at mirdita.de>
+Subject: Fix FTBFS with GCC 10
+Bug-Debian: https://bugs.debian.org/957552
+Origin: https://github.com/soedinglab/MMseqs2/commit/f6f001c8cc5820e50b33b355877664f7ca66cdb1
+--- mmseqs2.orig/src/commons/Sequence.cpp
++++ mmseqs2/src/commons/Sequence.cpp
+@@ -154,7 +154,7 @@
+             for(size_t i = 0; i < kmerSize; i++){
+                 pattern[i]=1;
+             }
+-            return std::make_pair<const char *, unsigned int>((const char *) pattern, static_cast<unsigned int>(kmerSize));
++            return std::make_pair<const char *, unsigned int>(const_cast<const char*>(pattern), static_cast<unsigned int>(kmerSize));
+ 
+ //            Debug(Debug::ERROR) << "Did not find spaced pattern for kmerSize: " << kmerSize << ". \n";
+ //            Debug(Debug::ERROR) << "Please report this bug to the developer\n";
+@@ -165,7 +165,7 @@
+     if (pair.second > 0) {
+         memcpy(pattern, pair.first, pair.second * sizeof(char));
+     }
+-    return std::make_pair<const char *, unsigned int>(pattern, static_cast<unsigned int>(pair.second));
++    return std::make_pair<const char *, unsigned int>(const_cast<const char*>(pattern), static_cast<unsigned int>(pair.second));
+ #undef CASE
+ }
+ 


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ fix_util_installation.patch
 use_system_zstd.patch
 use_system_gzstream.patch
 simde
+fix-ftbfs-gcc10.patch


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml



View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/c274189adac033cda0e895146c1f92b6996df313...e038c1d3117000b13e9bea1c775403c1b85fee7c

-- 
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/c274189adac033cda0e895146c1f92b6996df313...e038c1d3117000b13e9bea1c775403c1b85fee7c
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