[Debian-med-packaging] New version of ncbi-blast+

[olivier sallou]

Hi Aaron,
I tried to compile ncbi-blast 2.2.29 to prepare the package.
I updated the patches to match the new release, but it fails to compile at
makemblindex:

/usr/bin/g++  -std=gnu++11 -Wl,--enable-new-dtags -rdynamic -pthread
-fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--as-needed  -O  -fPIE
-pie main.o mkindex_app.o   -Wl,-rpath,/usr/lib/ncbi-blast+
-Wl,-rpath-link,/home/osallou/Desktop/DEBIAN-MED/ncbi-blast+/ncbi-blast+/ncbi-blast-2.2.29+-src/c++/BUILD/lib
-L/home/osallou/Desktop/DEBIAN-MED/ncbi-blast+/ncbi-blast+/ncbi-blast-2.2.29+-src/c++/BUILD/lib
-lxalgoblastdbindex -lblast -lcomposition_adjustment -lseqdb -lblastdb
-lxobjread -lvariation -lcreaders -lsubmit -lxobjutil -ltables -lxconnect
-lxobjmgr -lgenome_collection -lseqedit -lseqset -lseq -lseqcode -lsequtil
-lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -lz  -lbz2
-lnsl -ldl -lm  -lpthread -o makembindex
/home/osallou/Desktop/DEBIAN-MED/ncbi-blast+/ncbi-blast+/ncbi-blast-2.2.29+-src/c++/BUILD/lib/libxobjread.so:
undefined reference to
`ncbi::objects::CSeq_submit_Base::SetSub(ncbi::objects::CSubmit_block&)'
/home/osallou/Desktop/DEBIAN-MED/ncbi-blast+/ncbi-blast+/ncbi-blast-2.2.29+-src/c++/BUILD/lib/libxobjread.so:
undefined reference to `ncbi::objects::CSeq_submit_Base::ResetData()'
/home/osallou/Desktop/DEBIAN-MED/ncbi-blast+/ncbi-blast+/ncbi-blast-2.2.29+-src/c++/BUILD/lib/libxobjread.so:
undefined reference to `ncbi::objects::CSubmit_block_Base::GetTypeInfo()'
/home/osallou/Desktop/DEBIAN-MED/ncbi-blast+/ncbi-blast+/ncbi-blast-2.2.29+-src/c++/BUILD/lib/libxobjread.so:
undefined reference to
`ncbi::objects::CSeq_submit_Base::C_Data::DoSelect(ncbi::objects::CSeq_submit_Base::C_Data::E_Choice,
ncbi::CObjectMemoryPool*)'
/home/osallou/Desktop/DEBIAN-MED/ncbi-blast+/ncbi-blast+/ncbi-blast-2.2.29+-src/c++/BUILD/lib/libxobjread.so:
undefined reference to `ncbi::objects::CSeq_submit_Base::CSeq_submit_Base()'
/home/osallou/Desktop/DEBIAN-MED/ncbi-blast+/ncbi-blast+/ncbi-blast-2.2.29+-src/c++/BUILD/lib/libxobjread.so:
undefined reference to
`ncbi::objects::CSeq_submit_Base::C_Data::ResetSelection()'
/home/osallou/Desktop/DEBIAN-MED/ncbi-blast+/ncbi-blast+/ncbi-blast-2.2.29+-src/c++/BUILD/lib/libxobjread.so:
undefined reference to `vtable for ncbi::objects::CSeq_submit'
....

Do you have any idea of what is missing?

Thanks for your help

Olivier



2014-06-06 22:24 GMT+02:00 olivier sallou <olivier.sallou at gmail.com>:

>
> Le 6 juin 2014 21:57, "Aaron M. Ucko" <ucko at debian.org> a écrit :
>
> >
> > Andreas Tille <andreas at an3as.eu> writes:
> >
> > > Hi Aaron,
> >
> > Hi, Andreas.
> >
> > > since some time there is a new version of ncbi-blast+.  Do you intend
> to
> > > update the Debian package?  Just tell us if we should step in for
> > > whatever reason.
> >
> > I thought Olivier was still the package's primary maintainer (as he's
> > certainly welcome to be), but I can step in if necessary.  Thanks for
> > asking!
> Hi
> I still manage updates. In fact, without any other request, I was waiting
> for a pending bug fix as i did not see any major modification in this
> release.
>
> But i can upload this release this week-end.
>
> Olivier
>
> >
> > --
> > Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
> > http://www.mit.edu/~amu/ |
> http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu
>
>


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