[Debian-med-packaging] Bug#939506: expected primary-expression before ‘{’ token (Was: Bug#939506: unanimity ftbfs in unstable)

Matthew Fernandez matthew.fernandez at gmail.com
Wed Jan 15 03:00:02 GMT 2020 

Hi Andreas,

This is not related to aghermann, correct? Offhand I don’t know the fix to the error message you quoted, but I just tried to reproduce the build error on Debian 10.2. This repository has multiple build systems in the root directory and no build instructions in the README, so I guessed CMake. However, this doesn’t work:

    $ mkdir build
    $ cd build
    $ cmake ..
    -- The CXX compiler identification is GNU 8.3.0
    -- The C compiler identification is GNU 8.3.0
    -- Check for working CXX compiler: /usr/bin/c++
    -- Check for working CXX compiler: /usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    -- Check for working C compiler: /usr/bin/cc
    -- Check for working C compiler: /usr/bin/cc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Detecting C compile features
    -- Detecting C compile features - done
    -- Boost version: 1.67.0
    CMake Error at cmake/uny-dependencies.cmake:21 (add_subdirectory):
      add_subdirectory given source
      "/home/matthew/unanimity/third-party/pbcopper" which is not an existing
      directory.
    Call Stack (most recent call first):
      CMakeLists.txt:38 (include)


    -- Looking for pthread.h
    -- Looking for pthread.h - found
    -- Looking for pthread_create
    -- Looking for pthread_create - not found
    -- Looking for pthread_create in pthreads
    -- Looking for pthread_create in pthreads - not found
    -- Looking for pthread_create in pthread
    -- Looking for pthread_create in pthread - found
    -- Found Threads: TRUE
    -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29")
    -- Checking for module 'zlib'
    --   Found zlib, version 1.2.11
    CMake Error at cmake/uny-dependencies.cmake:45 (add_subdirectory):
      add_subdirectory given source "/home/matthew/unanimity/third-party/pbbam"
      which is not an existing directory.
    Call Stack (most recent call first):
      CMakeLists.txt:38 (include)


    -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS
    -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success
    -- Configuring incomplete, errors occurred!
    See also "/home/matthew/unanimity/build/CMakeFiles/CMakeOutput.log".
    See also "/home/matthew/unanimity/build/CMakeFiles/CMakeError.log”.

Unfortunately without further context I don’t know how to build this program.

Thanks,
Matthew

> On Jan 14, 2020, at 12:13, Andreas Tille <andreas at fam-tille.de> wrote:
> 
> Hi Matthew,
> 
> I take the freedom to ping you personally about a bug I was asking
> for help on Debian Mentors before.  My guess is its also not such
> a hard C++ problem.
> 
> (Unfortunately when I compile unanimity from Git[1] right now I'm
> running into a different issue even before:
> 
> ...
> [ 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] Fehler 1
> ...
> 
> 
> Any help to get this package build is very welcome.
> 
> Kind regards
> 
>   Andreas.
> 
> 
> [1] https://salsa.debian.org/med-team/unanimity
> 
> ----- Forwarded message from Andreas Tille <andreas at fam-tille.de> -----
> 
> Date: Fri, 20 Dec 2019 09:05:13 +0100
> From: Andreas Tille <andreas at fam-tille.de>
> To: 939506 at bugs.debian.org, 938751 at bugs.debian.org
> Cc: Debian Mentors List <debian-mentors at lists.debian.org>
> Subject: expected primary-expression before ‘{’ token (Was: Bug#939506: unanimity ftbfs in unstable)
> 
> Hi,
> 
> I think I was able to hunt down two of the three C++ issues but I'm
> stumbling here:
> 
> ...
> [ 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:569:20: error: expected primary-expression before ‘{’ token
>  569 |             Subread{ReadId(movieNames[movieName], *holeNumber,
>      |                    ^
> make[3]: *** [src/CMakeFiles/ccs.dir/build.make:66: src/CMakeFiles/ccs.dir/main/ccs.cpp.o] Error 1
> ...
> 
> 
> I wonder whether somebody can find a fix for the issue in this code
> 
>   https://salsa.debian.org/med-team/unanimity/blob/master/src/main/ccs.cpp#L569
> 
> Thanks a lot in advance
> 
>     Andreas.
> 
> -- 
> http://fam-tille.de
> 
> ----- End forwarded message -----
> 
> -- 
> http://fam-tille.de

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