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

[olivier sallou]

2014-06-07 0:39 GMT+02:00 Aaron M. Ucko <amu at alum.mit.edu>:

> Please try adding submit to DLL_LIB in
> src/objtools/readers/Makefile.xobjread.lib.
>
> Thanks it worked. I tried to do this but I did not know on which
Makefile....

>
> On June 6, 2014 5:46:50 PM EDT, olivier sallou <olivier.sallou at gmail.com>
> wrote:
>>
>> 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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>>
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>>
>>
> --
> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>



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