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

[Andreas Tille]

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

?

Kind regards

      Andreas.

> > [1] https://salsa.debian.org/med-team/unanimity

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