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Re: New version of ncbi-blast+

For info, there is a remaining hardening lintian warning:

I: ncbi-blast+: hardening-no-fortify-functions usr/lib/ncbi-blast+/libxutil.so

As it is the only one, I suspect that compilation flags are not the same than other libs, it might worth checking this upstream.
I upload the package however in the meanwhile.

Olivier


2014-06-07 0:39 GMT+02:00 Aaron M. Ucko <amu@alum.mit.edu>:
Please try adding submit to DLL_LIB in src/objtools/readers/Makefile.xobjread.lib.


On June 6, 2014 5:46:50 PM EDT, olivier sallou <olivier.sallou@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@gmail.com>:


Le 6 juin 2014 21:57, "Aaron M. Ucko" <ucko@debian.org> a écrit :


>
> Andreas Tille <andreas@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




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