Re: Help for backport of seer wanted (may be libhdf5 problem?)

[Andreas Tille <tille@debian.org>]

Hi Gianfranco,

On Mon, May 30, 2016 at 09:33:05AM +0000, Gianfranco Costamagna wrote:
> Hi, a quick search on codesearch.d.n [1] shows that armadillo might be your answer :)
> 
> 
> [1] https://codesearch.debian.net/results/arma_H5T_NATIVE_DOUBLE/page_0

While this looks somehow convincing I wonder why I can easily do a local
debuild with

$ LC_ALL=C apt-cache policy libarmadillo-dev
libarmadillo-dev:
  Installed: 1:5.200.1+dfsg-1~bpo8+1
  Candidate: 1:5.200.1+dfsg-1~bpo8+1
  Version table:
     1:6.700.6+dfsg-1 0
         50 http://ftp.de.debian.org/debian/ unstable/main amd64 Packages
         90 http://ftp.de.debian.org/debian/ testing/main amd64 Packages
 *** 1:5.200.1+dfsg-1~bpo8+1 0
        501 http://ftp.de.debian.org/debian/ jessie-backports/main amd64 Packages
        100 /var/lib/dpkg/status
     1:4.450.2+dfsg-1 0
        500 http://httpredir.debian.org/debian/ jessie/main amd64 Packages

installed while a build in a Jessie+backports chroot fails.  Do you think the
solution is that simple as backporting armadillo 6.700.6+dfsg-1 ?

Kind regards

       Andreas.
 
> Il Lunedì 30 Maggio 2016 11:10, Andreas Tille <andreas@an3as.eu> ha scritto:
> Hi,
> 
> I intend to backport seer[1] but I was running into a build issue:
> 
> ...
> g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -fPIE -pie -Wl,-z,relro -Wl,-z,now  sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerFilter.o seerIO.o seerChiFilter.o seerMain.o seerCmdLine.o seerContinuousAssoc.o seerBinaryAssoc.o logitFunction.o linearFunction.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -fPIE -pie -Wl,-z,relro -Wl,-z,now -o seer
> seerIO.o: In function `int arma::hdf5_misc::get_hdf5_type<std::complex<float> >()':
> /usr/include/armadillo_bits/hdf5_misc.hpp:151: undefined reference to `arma_H5Tcreate'
> /usr/include/armadillo_bits/hdf5_misc.hpp:153: undefined reference to `arma_H5T_NATIVE_FLOAT'
> /usr/include/armadillo_bits/hdf5_misc.hpp:153: undefined reference to `arma_H5Tinsert'
> /usr/include/armadillo_bits/hdf5_misc.hpp:154: undefined reference to `arma_H5Tinsert'
> seerIO.o: In function `get_hdf5_type<double>':
> /usr/include/armadillo_bits/hdf5_misc.hpp:131: undefined reference to `arma_H5T_NATIVE_DOUBLE'
> /usr/include/armadillo_bits/hdf5_misc.hpp:131: undefined reference to `arma_H5Tcopy'
> seerIO.o: In function `arma::hdf5_misc::is_supported_arma_hdf5_type(int)':
> /usr/include/armadillo_bits/hdf5_misc.hpp:189: undefined reference to `arma_H5Tequal'
> /usr/include/armadillo_bits/hdf5_misc.hpp:190: undefined reference to `arma_H5Tclose'
> ...
> 
> 
> I wonder whether seer might need a certain libhdf5-dev version.  I was
> able to build seer once under Jessie - but this does not seem to work
> any more.  Any hint would be welcome.
> 
> Kind regards
> 
>       Andreas.
> 
> [1] https://anonscm.debian.org/git/debian-med/seer.git
> 
> -- 
> http://fam-tille.de
> 

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