Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.
I think a non mounted proc is a bug, so probably you should fix the autobuilders and your build environment? The other issue is because of perl transition started yesterday. I think things will be better in the next few days https://release.debian.org/transitions/html/perl.html In the meanwhile you can build from a testing environment I think. Bests G. Sent from Yahoo Mail on Android On Thu, 17 Dec, 2015 at 23:52, Andreas Tille wrote: Hi Jakub, On Thu, Dec 17, 2015 at 11:34:53PM +0100, Jakub Wilk wrote: > * Andreas Tille , 2015-12-17, 19:11: > >override_dh_auto_build: > >+ if mount | grep "^proc " ; then echo "proc mounted - fine"; else > >mount proc /proc -t proc ; fi > > Well, you need root privileges to mount /proc, so doing it in debian/rules > almost certainly won't work. > > If /proc is not mounted in your build environment, then you need to fix the > environment. There's nothing that can be done about it in debian/rules. Right, the build-hook makes you root but probably the build itself is a non-privileged user. But *how* exactly can I ensure on my machine (and autobuilders!) that /proc is mounted??? BTW, on a different build machine (running testing in contrast to the machine some hours ago running stable) I get: ... 0 packages upgraded, 558 newly installed, 0 to remove and 0 not upgraded. Need to get 146 MB/367 MB of archives. After unpacking 1183 MB will be used. The following packages have unmet dependencies: libnet-ssleay-perl : Depends: perlapi-5.20.2 which is a virtual package and is not provided by any available package. libxml-libxml-perl : Depends: perlapi-5.20.2 which is a virtual package and is not provided by any available package. libxml-parser-perl : Depends: perlapi-5.20.2 which is a virtual package and is not provided by any available package. libhtml-parser-perl : Depends: perlapi-5.20.2 which is a virtual package and is not provided by any available package. Unable to resolve dependencies! Giving up... ... This somehow sounds like #787530 but I have no idea how to fix this. Seems I have opened a can of worms with this package. :-( Kind regards Andreas. -- http://fam-tille.de
Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.
Hi Jakub, On Thu, Dec 17, 2015 at 11:34:53PM +0100, Jakub Wilk wrote: > * Andreas Tille , 2015-12-17, 19:11: > >override_dh_auto_build: > >+ if mount | grep "^proc " ; then echo "proc mounted - fine"; else > >mount proc /proc -t proc ; fi > > Well, you need root privileges to mount /proc, so doing it in debian/rules > almost certainly won't work. > > If /proc is not mounted in your build environment, then you need to fix the > environment. There's nothing that can be done about it in debian/rules. Right, the build-hook makes you root but probably the build itself is a non-privileged user. But *how* exactly can I ensure on my machine (and autobuilders!) that /proc is mounted??? BTW, on a different build machine (running testing in contrast to the machine some hours ago running stable) I get: ... 0 packages upgraded, 558 newly installed, 0 to remove and 0 not upgraded. Need to get 146 MB/367 MB of archives. After unpacking 1183 MB will be used. The following packages have unmet dependencies: libnet-ssleay-perl : Depends: perlapi-5.20.2 which is a virtual package and is not provided by any available package. libxml-libxml-perl : Depends: perlapi-5.20.2 which is a virtual package and is not provided by any available package. libxml-parser-perl : Depends: perlapi-5.20.2 which is a virtual package and is not provided by any available package. libhtml-parser-perl : Depends: perlapi-5.20.2 which is a virtual package and is not provided by any available package. Unable to resolve dependencies! Giving up... ... This somehow sounds like #787530 but I have no idea how to fix this. Seems I have opened a can of worms with this package. :-( Kind regards Andreas. -- http://fam-tille.de
Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.
* Andreas Tille , 2015-12-17, 19:11: override_dh_auto_build: + if mount | grep "^proc " ; then echo "proc mounted - fine"; else mount proc /proc -t proc ; fi Well, you need root privileges to mount /proc, so doing it in debian/rules almost certainly won't work. If /proc is not mounted in your build environment, then you need to fix the environment. There's nothing that can be done about it in debian/rules. -- Jakub Wilk
Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.
Hi Gianfranco, On Thu, Dec 17, 2015 at 05:45:19PM +, 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 ha scritto: > > Oggetto: Re: cmake issue in libsbml: Cannot generate java documentation, > please specify the Java_JAVADOC_JAR. > A: "Debian Mentors List" > Cc: "Debian Med Packaging Team" > , "Ivo Maintz" > 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 > 0x000f > (RPATH) > Library rpath: > [$ORIGIN/../lib/amd64/jli:$ORIGIN/../jre/lib/amd64/jli] > 0x6ffb > (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@wr-linux01:/ # > mount > > > > > > > > > > > > mount: failed to read mtab: No such file or directory > 2|root@wr-linux01:/ # > readelf -d /usr/bin/java | grep ORIGIN > 0x000f (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
Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.
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 ha scritto: Oggetto: Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR. A: "Debian Mentors List" Cc: "Debian Med Packaging Team" , "Ivo Maintz" 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 0x000f (RPATH) Library rpath: [$ORIGIN/../lib/amd64/jli:$ORIGIN/../jre/lib/amd64/jli] 0x6ffb (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@wr-linux01:/ # mount mount: failed to read mtab: No such file or directory 2|root@wr-linux01:/ # readelf -d /usr/bin/java | grep ORIGIN 0x000f (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
Re: cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.
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 0x000f (RPATH) Library rpath: [$ORIGIN/../lib/amd64/jli:$ORIGIN/../jre/lib/amd64/jli] 0x6ffb (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@wr-linux01:/ # mount mount: failed to read mtab: No such file or directory 2|root@wr-linux01:/ # readelf -d /usr/bin/java | grep ORIGIN 0x000f (RPATH) Library rpath: [$ORIGIN/../lib/amd64/jli:/usr/local/jre/lib/amd64/jli:$ORIGIN/../lib/amd64:/usr/local/lib/amd64:$ORIGIN/../jre/lib/amd64:/usr/local/jre/lib/amd64] I can confirm that /proc is not mounted. Any idea how to approach this to finally build libsbml successfully (at least passing the step to Generate Java-API Documentation? Kind regards Andreas. -- http://fam-tille.de
cmake issue in libsbml: Cannot generate java documentation, please specify the Java_JAVADOC_JAR.
Hi, I'm trying to fix libsbml bugs and while doing so upgrade to the latest upstream version. Since the original tarball needs to be stripped I moved the packaging from SVN to Git[1] (so please do not try debcheckout which does not lead to the latest packaging status). Unfortunately my attempt is blocked by ... CMake Error at docs/CMakeLists.txt:212 (message): Cannot generate java documentation, please specify the Java_JAVADOC_JAR. -- Configuring incomplete, errors occurred! ... even if I tried in debian/rules export JDK_PATH=$(readlink -f /usr/bin/javac | sed "s:/bin/javac::") export JAVA_INCLUDE_PATH=$(JDK_PATH)/include as well as specifying -DJDK_PATH:STRING=/usr/lib/jvm/default-java -DJAVA_INCLUDE_PATH:STRING=/usr/lib/jvm/default-java/include to the cmake call. Any help would be welcome. Kind regards Andreas. [1] git://anonscm.debian.org/debian-med/libsbml.git -- http://fam-tille.de
