[Debian-med-packaging] C++ issue in latest unanimity (packaging refreshed, but may be tiny stumbling C++ stone for me)

[Olivier Sallou]

On 10/10/2018 01:36 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Wed, Oct 10, 2018 at 11:30:32AM +0200, Olivier Sallou wrote:
>>> /usr/bin/c++  -g -O2 -fdebug-prefix-map=/build/unanimity-3.1.0+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  -lpthread  -rdynamic CMakeFiles/ccs.dir/main/ccs.cpp.o  -o ../ccs -ldl libunanimity.a libcc2.a -lpbbam -Wl,-Bstatic -lpbcopper -Wl,-Bdynamic
>>> /usr/bin/ld: CMakeFiles/ccs.dir/main/ccs.cpp.o: in function `Runner(PacBio::CLI::Results const&)':
>>> ./build/src/./src/main/ccs.cpp:361: undefined reference to `PacBio::CCS::ConsensusSettings::ConsensusSettings(PacBio::CLI::Results const&)'
>> PacBio lib (pbbam) seems to not have the ConsensusSettings defined,
>> maybe this lib has been modified.. I see you uploaded a new version this
>> month (and a new upstream in september)
> I've updated libpbbam-dev and tried building unanimity using
>
> diff --git a/debian/control b/debian/control
> index 838b7c4..bb22bfc 100644
> --- a/debian/control
> +++ b/debian/control
> @@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
>                 python-numpy,
>                 libboost-dev,
>                 libhts-dev,
> -               libpbbam-dev,
> +               libpbbam-dev (>= 0.19.0~),
>                 libpbcopper-dev,
>                 libseqan2-dev,
>                 pandoc
>
> but the problem remains.  Isn't the relevant definition not inside the
> unanimity code in
>
>    include/pacbio/ccs/ConsensusSettings.h
looking a src/CmakeLists, libunanimity.a should contain all .h fields in
include dir , but looking at generated file, no pacbio/ccs/... related
symbols are found

add_library(unanimity STATIC
    ${UNANIMITY_FILES}
)

with UNANIMITY_FILES containing UNY_HEADER, which should match all
include header files (file(GLOB_RECURSE UNY_HEADER "${UNY_IncludeDir}/*.h"))
>
> ?
>
> Kind regards
>
>       Andreas.
>
>>> [1] https://salsa.debian.org/med-team/unanimity

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

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