[Debian-med-packaging] cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.

[Andreas Tille]

Hi Gianfranco,

On Thu, Dec 17, 2015 at 05:45:19PM +0000, Gianfranco Costamagna wrote:
> I remember something ghc related
> 
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=787227
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=773768

Seems to be the same consequence as I've drawn below.  I checked in the
pbuilder chroot

diff --git a/debian/rules b/debian/rules
index 8916f38..3fdf167 100755
--- a/debian/rules
+++ b/debian/rules
@@ -63,6 +63,7 @@ endif
        /bin/sh debian/bin/python_fix.sh
 
 override_dh_auto_build:
+       if mount | grep "^proc " ; then echo "proc mounted - fine"; else mount proc /proc -t proc ; fi
        cd build ; make
        cp NEWS.txt changelog



and I was able to make the api_java_doc target successfully.

Since I have not seen things like this in the ghc source I wonder if
this should be really the suggested solution to the problem.

Comments?

Kind regards

       Andreas.


> --------------------------------------------
> Gio 17/12/15, Andreas Tille <andreas at fam-tille.de> ha scritto:
> 
>  Oggetto: Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.
>  A: "Debian Mentors List" <debian-mentors at lists.debian.org>
>  Cc: "Debian Med Packaging Team" <debian-med-packaging at lists.alioth.debian.org>, "Ivo Maintz" <ivo at maintz.de>
>  Data: Giovedì 17 dicembre 2015, 17:26
>  
>  Hi Kevin,
>  
>  On Thu, Dec 17, 2015 at 10:44:40PM +1100, Kevin Murray
>  wrote:
>  > 
>  > I have pushed a possible fix to the branch
>  'daube/possible-cmake-fix'. I am not
>  > sure of the overall effects, the build is taking ages
>  on my laptop, but it seems
>  > to have fixed the immediate error.
>  
>  Thanks a lot for this first and very helpful step. 
>  Following this
>  strategy I was even able to work around another issue with
>  Java bindings
>  which was also solved by setting a variable accordingly.
>  
>  Finally after 1-2 hours of building I went into
>  
>  ...
>  make[4]: Entering directory
>  '/build/libsbml-5.12.0+dfsg/build'
>  [100%] Generate Java-API Documentation
>  /usr/bin/javac: error while loading shared libraries:
>  libjli.so: cannot open shared object file: No such file or
>  directory
>  docs/CMakeFiles/api_docs_java.dir/build.make:61: recipe for
>  target '../docs/formatted/java-api/index.html' failed
>  make[4]: *** [../docs/formatted/java-api/index.html] Error
>  127
>  make[4]: Leaving directory
>  '/build/libsbml-5.12.0+dfsg/build'
>  CMakeFiles/Makefile2:1123: recipe for target
>  'docs/CMakeFiles/api_docs_java.dir/all' failed
>  make[3]: *** [docs/CMakeFiles/api_docs_java.dir/all] Error
>  2
>  make[3]: Leaving directory
>  '/build/libsbml-5.12.0+dfsg/build'
>  ...
>  
>  
>  When I trow the error message above in a web search it comes
>  up with the
>  log of bug #548729 which says:
>  
>  
>      This is most likely a lack of
>  /proc.  Some ld.so features require
>      /proc/self/exe.
>      
>      $ readelf -d /usr/bin/java  | grep
>  ORIGIN
>       0x000000000000000f
>  (RPATH)             
>  Library rpath:
>  [$ORIGIN/../lib/amd64/jli:$ORIGIN/../jre/lib/amd64/jli]
>       0x000000006ffffffb
>  (FLAGS_1)            Flags:
>  ORIGIN
>      
>      AFAIK, a mounted /proc is close to
>  mandatory these days.  The error
>      message could be nicer, but this is a
>  libc bug.
>  
>  
>  If I try inside the pbuilder chroot:
>  
>  1|root at wr-linux01:/ #
>  mount               
>                 
>                 
>                 
>                 
>                 
>                 
>                 
>                 
>                 
>                 
>        
>  mount: failed to read mtab: No such file or directory
>  2|root at wr-linux01:/ #
>  readelf -d /usr/bin/java  | grep ORIGIN
>   0x000000000000000f (RPATH)       
>        Library rpath:
>  [$ORIGIN/../lib/amd64/jli:/usr/local/jre/lib/amd64/jli:$ORIGIN/../lib/amd64:/usr/local/lib/amd64:$ORIGIN/../jre/lib/amd64:/usr/local/jre/lib/amd64]
>  
>  
>  I can confirm that /proc is not mounted.  Any idea how
>  to approach this
>  to finally build libsbml successfully (at least passing the
>  step to
>  Generate Java-API Documentation?
>  
>  Kind regards
>  
>         Andreas.
>  
>  -- 
>  http://fam-tille.de
>  
> 

-- 
http://fam-tille.de