[med-svn] [Git][med-team/unanimity][master] Add open issues to changelog as todo

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / unanimity


Commits:
838929ad by Andreas Tille at 2020-01-24T14:32:20+01:00
Add open issues to changelog as todo

- - - - -


2 changed files:

- debian/changelog
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -11,6 +11,42 @@ unanimity (3.4.1+git20180307.02aa264+dfsg-1) UNRELEASED; urgency=medium
     Closes: #938751
   * debian/copyright: use spaces rather than tabs to start continuation
     lines.
+  TODO:
+
+  1. With latest libpbcopper:
+[ 56%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o
+cd /build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/src && /usr/bin/c++   -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/include -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/generated -I/    build/unanimity-3.4.1+git20180307.02aa264+dfsg/src  -g -O2 -fdebug-prefix-map=/build/unanimity-3.4.1+git20180307.02aa264+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -           D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs   -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o -c /    build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/genomicconsensus/experimental/ConsensusModelFactory.cpp
+In file included from /usr/include/pbcopper/data/ReadId.h:13,
+                 from /usr/include/pbcopper/data/Read.h:19,
+                 from /usr/include/pbcopper/data/MappedRead.h:10,
+                 from /usr/include/pbbam/BamRecord.h:19,
+                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/IPoaModel.h:8,
+                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/arrow/ArrowModel.h:5,
+                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/genomicconsensus/experimental/ConsensusModelFactory.cpp:8:
+/usr/include/pbcopper/data/Interval.h:24:7: error: redefinition of ‘class PacBio::Data::Interval’
+   24 | class Interval
+      |       ^~~~~~~~
+In file included from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/ReferenceWindow.h:10,
+                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/Consensus.h:10,
+                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/WindowResult.h:7,
+                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/IConsensusModel.h:5,
+                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/ConsensusModelFactory.h:9,
+                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/genomicconsensus/experimental/ConsensusModelFactory.cpp:3:
+/build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/data/Interval.h:20:7: note: previous definition of ‘class PacBio::Data::Interval’
+   20 | class Interval
+      |       ^~~~~~~~
+make[3]: *** [src/CMakeFiles/unanimity.dir/build.make:79: src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o] Error 1
+
+  --> The definition in /include/pacbio/data/Interval.h is NOT good - we need the one of include/pacbio/data/Interval.h  !
+  
+  2. If 1. is solved
+[ 90%] Building CXX object src/CMakeFiles/ccs.dir/main/ccs.cpp.o
+cd /build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/src && /usr/bin/c++   -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/include -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/generated -I/    build/unanimity-3.4.1+git20180307.02aa264+dfsg/src  -g -O2 -fdebug-prefix-map=/build/unanimity-3.4.1+git20180307.02aa264+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -           D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs   -fPIC -std=c++14 -o CMakeFiles/ccs.dir/main/ccs.cpp.o -c /build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp
+/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp: In function ‘int Runner(const PacBio::CLI::Results&)’:
+/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:571:38: error: ‘move’ was not declared in this scope
+  571 |                     read.Sequence(), move(ipd), move(pw), read.LocalContextFlags(),
+      |                                      ^~~~
+
 
  -- Andreas Tille <tille at debian.org>  Thu, 19 Dec 2019 08:17:37 +0100
 


=====================================
debian/rules
=====================================
@@ -29,12 +29,12 @@ binary-arch: $(docs)
 	--package=unanimity \
 	--no-package=python3-consensuscore2 \
 	--buildsystem=cmake \
-	--builddirectory=build
+	--builddirectory=build --no-parallel
 	dh $@ \
 	--package=python3-consensuscore2 \
 	--no-package=unanimity \
 	--with python3 \
-	--buildsystem=pybuild
+	--buildsystem=pybuild --no-parallel
 
 # We only want to run the configure step once. If we do not do this,
 # cmake attempts to run (from the second dh invocation) in the pybuild



View it on GitLab: https://salsa.debian.org/med-team/unanimity/commit/838929ad639e69df5344752d6b9b1dba17a1eb4a

-- 
View it on GitLab: https://salsa.debian.org/med-team/unanimity/commit/838929ad639e69df5344752d6b9b1dba17a1eb4a
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