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