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 <andr...@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 <andr...@fam-tille.de> -----
>
> Date: Fri, 20 Dec 2019 09:05:13 +0100
> From: Andreas Tille <andr...@fam-tille.de>
> To: 939...@bugs.debian.org, 938...@bugs.debian.org
> Cc: Debian Mentors List <debian-ment...@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
