[med-svn] [Git][med-team/unanimity][master] Fix some issues in gcc9

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / unanimity


Commits:
8ac78dda by Andreas Tille at 2019-12-20T07:57:36Z
Fix some issues in gcc9

- - - - -


2 changed files:

- + debian/patches/gcc9.patch
- debian/patches/series


Changes:

=====================================
debian/patches/gcc9.patch
=====================================
@@ -0,0 +1,34 @@
+Description: Fix some issues in gcc-9
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 19 Dec 2019 08:14:41 +0100
+
+--- a/src/main/ccs.cpp
++++ b/src/main/ccs.cpp
+@@ -10,6 +10,7 @@
+ #include <sstream>
+ #include <string>
+ #include <vector>
++#include <iomanip>
+ 
+ #include <boost/algorithm/string.hpp>
+ #include <boost/algorithm/string/join.hpp>
+@@ -468,7 +469,7 @@ static int Runner(const PacBio::CLI::Res
+             std::make_unique<BamWriter>(outputFile, PrepareHeader(args.InputCommandLine(), ds));
+         const string pbiFileName = outputFile + ".pbi";
+         auto ccsPbi = std::make_unique<PbiBuilder>(pbiFileName);
+-        writer = async(launch::async, BamWriterThread, ref(workQueue), move(ccsBam), move(ccsPbi),
++        writer = async(launch::async, BamWriterThread, ref(workQueue), std::move(ccsBam), move(ccsPbi),
+                        settings);
+ 
+         // Always generate pbi file
+@@ -567,8 +568,8 @@ static int Runner(const PacBio::CLI::Res
+         chunk->back().Reads.emplace_back(
+             Subread{ReadId(movieNames[movieName], *holeNumber,
+                            Interval(read.QueryStart(), read.QueryEnd())),
+-                    read.Sequence(), move(ipd), move(pw), read.LocalContextFlags(),
+-                    read.ReadAccuracy(), SNR(read.SignalToNoise()), move(chem)});
++                    read.Sequence(), std::move(ipd), std::move(pw), read.LocalContextFlags(),
++                    read.ReadAccuracy(), SNR(read.SignalToNoise()), std::move(chem)});
+     }
+ 
+     // run the remaining tasks


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ git-version.patch
 no-static-linking.patch
 do_not_refer_to_non-existing_images.patch
 2to3.patch
+gcc9.patch



View it on GitLab: https://salsa.debian.org/med-team/unanimity/commit/8ac78dda0954c3d1e1b68a255675f0da1a655af0

-- 
View it on GitLab: https://salsa.debian.org/med-team/unanimity/commit/8ac78dda0954c3d1e1b68a255675f0da1a655af0
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