Question: minia 2.0.3 problem building from source - hdf5/hdf5.h missing?
0
gravatar for Torst
18 months ago by
Torst840
Australia
Torst840 wrote:

Is this some issue with assumption of hdf5 library being installed at system level instead of using bundled one?

cd /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/build/ext/gatb-core/src && /bio/linuxbrew/bin/g++-5 -Os -w -pipe -march=core2 -I/tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/build/ext/gatb-core/include -I/tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src -I/tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/thirdparty -O3 -DINT128_FOUND -DWITH_LAMBDA_EXPRESSION -std=c++0x -DWITH_MPHF -DDONT_USE_TR1 -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o -c /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp In file included from /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp:33:0, from /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageTools.hpp:34, from /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp:21: /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp:34:23: fatal error: hdf5/hdf5.h: No such file or directory compilation terminated.

minia • 558 views
ADD COMMENTlink modified 18 months ago by Rayan Chikhi1.2k • written 18 months ago by Torst840
0
gravatar for Rayan Chikhi
18 months ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k wrote:

Hmm, could you please give some more details on the system and the commands you typed to compile? Users do not need hdf5 to be preinstalled, it is packaged with minia sources.

I cannot reproduce the problem locally using these commands; minia builds correctly for me.

wget http://gatb-tools.gforge.inria.fr/versions/src/minia-2.0.3-Source.tar.gz

tar xf minia-2.0.3-Source.tar.gz

cd minia-2.0.3-Source

mkdir build

cd build

cmake .. && make -j 4
ADD COMMENTlink modified 18 months ago • written 18 months ago by Rayan Chikhi1.2k
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