Re: Problems linking hdf5, gzstream, boost_program_options due to usage of simple Makefile

2016-03-30 Thread Andreas Tille
Hi Jakub, On Tue, Mar 29, 2016 at 10:01:51PM +0200, Jakub Wilk wrote: > > https://github.com/johnlees/seer links to: > http://www.cs.unc.edu/Research/compgeom/gzstream/ > > AFAICT, this is not packaged for Debian. (Although we have multiple embedded > code copies[0]. Yay...) See #819532. Kind

Re: Problems linking hdf5, gzstream, boost_program_options due to usage of simple Makefile

2016-03-29 Thread Peter Colberg
Hi Andreas, On Tue, Mar 29, 2016 at 09:18:50PM +0200, Andreas Tille wrote: > I'm trying to package seer[1] for the Debian Med team. Upstream provides a > simple Makefile which is probably the cause why the libraries for linking > are not found properly so it ends up in > > ... > g++ -g -O2 -fsta

Re: Problems linking hdf5, gzstream, boost_program_options due to usage of simple Makefile

2016-03-29 Thread Andrey Rahmatullin
On Tue, Mar 29, 2016 at 09:18:50PM +0200, Andreas Tille wrote: > Hi, > > I'm trying to package seer[1] for the Debian Med team. Upstream provides a > simple Makefile which is probably the cause why the libraries for linking > are not found properly so it ends up in > > ... > g++ -g -O2 -fstack-p

Re: Problems linking hdf5, gzstream, boost_program_options due to usage of simple Makefile

2016-03-29 Thread Jakub Wilk
* Ghislain Vaillant , 2016-03-29, 20:47: No idea what is gzstream and which package provides it. https://github.com/johnlees/seer links to: http://www.cs.unc.edu/Research/compgeom/gzstream/ AFAICT, this is not packaged for Debian. (Although we have multiple embedded code copies[0]. Yay...)

Re: Problems linking hdf5, gzstream, boost_program_options due to usage of simple Makefile

2016-03-29 Thread Ghislain Vaillant
Hey Andreas On 29/03/16 20:18, Andreas Tille wrote: Hi, I'm trying to package seer[1] for the Debian Med team. Upstream provides a simple Makefile which is probably the cause why the libraries for linking are not found properly so it ends up in ... g++ -g -O2 -fstack-protector-strong -Wformat

Re: Problems linking hdf5, gzstream, boost_program_options due to usage of simple Makefile

2016-03-29 Thread Gianfranco Costamagna
Hi, >g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 >-std=c++11 -I/nonexistent/software/include -I../gzstream -I../dlib -D >>DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -Wl,-z,relro >sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerE

Problems linking hdf5, gzstream, boost_program_options due to usage of simple Makefile

2016-03-29 Thread Andreas Tille
Hi, I'm trying to package seer[1] for the Debian Med team. Upstream provides a simple Makefile which is probably the cause why the libraries for linking are not found properly so it ends up in ... g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -I/nonex