[Debian-med-packaging] Bug#814875: libsis-jhdf5-java: FTBFS: jni.h:45:20: fatal error: jni_md.h: No such file or directory

Tue Feb 16 10:19:03 UTC 2016

Hi,

I think this issue occured since the change of default-jdk from
openjdk-7-jdk to openjdk-8-jdk.  Looking at

$ apt-file search jni_md.h | grep "^openjdk-[78]-jdk"
openjdk-7-jdk: /usr/lib/jvm/java-7-openjdk-amd64/include/jni_md.h
openjdk-7-jdk: /usr/lib/jvm/java-7-openjdk-amd64/include/linux/jni_md.h
openjdk-8-jdk: /usr/lib/jvm/java-8-openjdk-amd64/include/linux/jni_md.h

I wonder whether this might be a missing symlink or so inside
openjdk-8-jdk?

Any hint would be welcome

     Andreas.

On Tue, Feb 16, 2016 at 09:17:12AM +0100, Chris Lamb wrote:
> Source: libsis-jhdf5-java
> Version: 14.12.1-1
> Severity: serious
> Justification: fails to build from source
> User: reproducible-builds at lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org
> 
> Dear Maintainer,
> 
> libsis-jhdf5-java fails to build from source in unstable/amd64:
> 
>   [..]
> 
>      jh_linkjars
>      debian/rules override_dh_auto_build
>   make[1]: Entering directory '/home/lamby/temp/cdt.20160216090302.IWEuAiIzzC/libsis-jhdf5-java-14.12.1'
>   # C build
>   cd source/c && \
>   	cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro  -shared -fPIC -Wl,--exclude-libs,ALL \
>   	-I/usr/lib/jvm/default-java/include/ -I/usr/include/hdf5/serial \
>          	jhdf5/*.c hdf-java/*.c -o libsis-jhdf5.so -lz -lhdf5_serial
>   In file included from jhdf5/exceptionImpJHDF5.c:24:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5ConstantsJHDF5.c:17:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5ImpJHDF5.c:28:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5aImpJHDF5.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5dImpJHDF5.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5fImpJHDF5.c:29:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5gImpJHDF5.c:40:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5iImpJHDF5.c:28:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5lImpJHDF5.c:41:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5oImpJHDF5.c:40:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5pImpJHDF5.c:40:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5rImpJHDF5.c:28:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5sImpJHDF5.c:28:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5tImpJHDF5.c:28:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/h5zImpJHDF5.c:28:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from jhdf5/strcpyJHDF5.c:3:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5Constants.c:18:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5Imp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5aImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5dImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5eImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5fImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5gImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5iImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5lImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5oImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5pImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5rImp.c:28:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5sImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5tImp.c:30:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5util.c:24:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/h5zImp.c:28:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   In file included from hdf-java/nativeData.c:35:0:
>   /usr/lib/jvm/default-java/include/jni.h:45:20: fatal error: jni_md.h: No such file or directory
>   compilation terminated.
>   debian/rules:32: recipe for target 'override_dh_auto_build' failed
>   make[1]: *** [override_dh_auto_build] Error 1
>   make[1]: Leaving directory '/home/lamby/temp/cdt.20160216090302.IWEuAiIzzC/libsis-jhdf5-java-14.12.1'
>   debian/rules:14: recipe for target 'build' failed
>   make: *** [build] Error 2
> 
>   [..]
> 
> The full build log is attached.
> 
> 
> Regards,
> 
> -- 
>       ,''`.
>      : :'  :     Chris Lamb
>      `. `'`      lamby at debian.org / chris-lamb.co.uk
>        `-

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