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

[Gianfranco Costamagna]

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

Cheers

G.

--------------------------------------------
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