Commit 838929ad authored by Andreas Tille's avatar Andreas Tille
Browse files

Add open issues to changelog as todo

parent 8ac78dda

debian/changelog

+36 −0
Original line number Diff line number Diff line
@@ -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@debian.org>  Thu, 19 Dec 2019 08:17:37 +0100

debian/rules

+2 −2
Original line number Diff line number Diff line
@@ -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