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 <[email protected]>: > 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 <[email protected]> > 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 <[email protected]>: >> >>> >>> Le 6 juin 2014 21:57, "Aaron M. Ucko" <[email protected]> a écrit : >>> >>> > >>> > Andreas Tille <[email protected]> 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/[email protected] >>> >>> >> >> >> -- >> >> gpg key id: 4096R/326D8438 (keyring.debian.org) >> >> Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 >> >> > -- > Sent from my Android device with K-9 Mail. Please excuse my brevity. > -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
