Hi,
it turned out hat the cmake issue is a bit tricky for a MoM project so I
gave it a try myself. The current state of gatb-core packaging is in
Git[1]. I went as far as my poor cmake knowledge permits to replace the
cmake hdf5 code to use the Debian packaged code after the internal code
copy was removed. Unfortunately I failed to get the proper -I options
propagated to the compiler call since I'm ending up with:
...
[ 5%] Building CXX object
src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o
cd /build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/include
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/ include/None
-I/build/gatb-core-1.3.0+dfsg/gatb-core/src
-I/build/gatb-core-1.3.0+dfsg/gatb-core/thirdparty -g -O2
-fdebug-prefix-map=/build/gatb-core-1.3.0+dfsg=. -fstack-protector- strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2
-msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function
-Wno-format -Wno-unknown-pragmas -Wno- invalid-offsetof -o
CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o -c
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp
cd /build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/include
-I/build/gatb-core-1.3.0+dfsg/obj-x86_64-linux-gnu/ include/None
-I/build/gatb-core-1.3.0+dfsg/gatb-core/src
-I/build/gatb-core-1.3.0+dfsg/gatb-core/thirdparty -g -O2
-fdebug-prefix-map=/build/gatb-core-1.3.0+dfsg=. -fstack-protector- strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse2
-msse4.2 -mpopcnt -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function
-Wno-format -Wno-unknown-pragmas -Wno- invalid-offsetof -o
CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o -c
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp
cc1plus: error: -Wformat-security ignored without -Wformat
[-Werror=format-security]
cc1plus: error: -Wformat-security ignored without -Wformat
[-Werror=format-security]
cc1plus: error: -Wformat-security ignored without -Wformat
[-Werror=format-security]
In file included from
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:29:0,
from
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:37,
from
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.hpp:31,
from
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp:20:
/build/gatb-core-1.3.0+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:38:10:
fatal error: hdf5/hdf5.h: No such file or directory
#include <hdf5/hdf5.h>
^~~~~~~~~~~~~
cc1plus: some warnings being treated as errors
compilation terminated.
src/CMakeFiles/gatbcore-static.dir/build.make:137: recipe for target
'src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o'
failed
make[3]: ***
[src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/BankConverterAlgorithm.cpp.o]
Error 1
...
Any help to use Debian packaged hdf5 would be really appreciated.
Kind regards
Andreas.
[1] https://anonscm.debian.org/git/debian-med/gatb-core.git
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