Re: C++ help needed for psortb

On Wed, Apr 19, 2017 at 4:20 PM, Andreas Tille wrote: > Hi Bastien, > > On Wed, Apr 19, 2017 at 01:32:43PM +, Bastien Roucaries wrote: >> >> Le 19 avril 2017 08:09:11 GMT+02:00, Andreas Tille a >> écrit : >> > >> >Psortb[1] was using header files from

Re: C++ help needed for psortb

Hi Bastien, On Wed, Apr 19, 2017 at 01:32:43PM +, Bastien Roucaries wrote: > > Le 19 avril 2017 08:09:11 GMT+02:00, Andreas Tille a écrit > : > > > >Psortb[1] was using header files from biosquid[2] and hmmer2[3] but did > >not shipped the according library code. No idea

Re: C++ help needed for psortb

Le 19 avril 2017 08:09:11 GMT+02:00, Andreas Tille a écrit : >Hi Christian, > >On Tue, Apr 18, 2017 at 11:07:03PM +0200, Christian Seiler wrote: >> > >> > which is probably due to the fact that I did not changed hmmer2 to >> > create a shared rather than a static library and

Re: C++ help needed for psortb

Hi Christian, On Tue, Apr 18, 2017 at 11:07:03PM +0200, Christian Seiler wrote: > > > > which is probably due to the fact that I did not changed hmmer2 to > > create a shared rather than a static library and lhmmer is not compiled > > with -fPIC. What might be the less stressful way to solve

Re: C++ help needed for psortb

On 04/18/2017 11:01 PM, Andreas Tille wrote: > x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/psortb-3.0.4+dfsg=. > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro > -shared -L/usr/local/lib -fstack-protector-strong HMM.o hmm-binding.o -o >

Re: C++ help needed for psortb

Hi Walter, On Tue, Apr 18, 2017 at 01:26:58PM -0700, Walter Landry wrote: > > hmm-binding.cpp: In member function ‘void HMM::init(char*, int, int)’: > > hmm-binding.cpp:245:20: error: ‘CUT_NONE’ was not declared in this scope > >thresh.autocut = CUT_NONE; > > ^~~~ > >

Re: C++ help needed for psortb

Hi Andreas, On 04/18/2017 10:15 PM, Andreas Tille wrote: > The definition of the structure threshold_s can be found in > /usr/include/hmmer2/structs.h (of package libhmmer2-dev) and > looks like > > struct threshold_s { > float globT; /* T parameter: keep only hits > globT

Re: C++ help needed for psortb

Andreas Tille wrote: > hmm-binding.cpp: In member function ‘void HMM::init(char*, int, int)’: > hmm-binding.cpp:245:20: error: ‘CUT_NONE’ was not declared in this scope >thresh.autocut = CUT_NONE; > ^~~~ > Makefile:346: recipe for target

C++ help needed for psortb

Hi, I intend to package psortb in Debian Med team[1]. To successfully build this package I needed to re-arrange the package layout of biosquid and hmmer2 since psortb is using code from those project but only provides the according header files. This was solved by proper -dev packages -