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Problems building libsbml

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  Problems building libsbml Andreas Tille <andreas@an3as.eu> - 2018-05-14 14:30 +0200
    Re: Problems building libsbml Markus Koschany <apo@debian.org> - 2018-05-14 15:10 +0200
      Re: Problems building libsbml Andreas Tille <tille@debian.org> - 2018-05-14 16:00 +0200
        Re: Problems building libsbml Markus Koschany <apo@debian.org> - 2018-05-15 13:40 +0200

#10496 — Problems building libsbml

Hi,

when trying to rebuild libsbml[1] (to fix #896531) I get

...
make[4]: Entering directory '/build/libsbml-5.16.0+dfsg/build'
[100%] Generate Java-API Documentation
/build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java:112: error: package com.sun.tools.doclets.standard is not visible
import com.sun.tools.doclets.standard.Standard;
                            ^
  (package com.sun.tools.doclets.standard is declared in module jdk.javadoc, which does not export it)
Note: /build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: /build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 error
make[4]: *** [docs/CMakeFiles/api_docs_java.dir/build.make:62: ../docs/formatted/java-api/index.html] Error 1
make[4]: Leaving directory '/build/libsbml-5.16.0+dfsg/build'
...



I've tried to fix this with a patch[2] but that way I'm running into

...
[100%] Generate Java-API Documentation
/build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java:112: error: package com.sun.tools.doclets.standard is not visible
import com.sun.tools.doclets.standard.Standard;
                            ^
  (package com.sun.tools.doclets.standard is declared in module jdk.javadoc, which does not export it)
/build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java:129: error: no interface expected here
public class SBMLDoclet extends Doclet
                                ^
/build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java:163: error: no interface expected here
        extends Doclet
                ^
/build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java:171: error: cannot find symbol
        public static boolean start(RootDoc root)
                                    ^
  symbol:   class RootDoc
  location: class FileExclusionDoclet
/build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java:197: error: cannot find symbol
                                           DocErrorReporter reporter)
                                           ^
  symbol:   class DocErrorReporter
  location: class FileExclusionDoclet
/build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java:337: error: no interface expected here
        extends Doclet
                ^
/build/libsbml-5.16.0+dfsg/docs/src/SBMLDoclet.java:339: error: cannot find symbol
        private static RootDoc the_root;
                       ^
  symbol:   class RootDoc
  location: class SBMLProcessingDoclet
...



I'm not sure how this should be interpreted in the context of the
patch[3] by Markus Koschany which deals with not-existing doc.  May be
that error existed before but was treated as warning but is turned into
an error now.

Any hint would be welcome

     Andreas.


[1] https://salsa.debian.org/med-team/libsbml
[2] https://salsa.debian.org/med-team/libsbml/blob/master/debian/patches/javadoc.patch
[3] https://salsa.debian.org/med-team/libsbml/blob/master/debian/patches/javadoc_java9.patch

-- 
http://fam-tille.de

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#10497

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Am 14.05.2018 um 14:27 schrieb Andreas Tille:
> package com.sun.tools.doclets.standard is declared in module jdk.javadoc, which does not export it

Hello,

com.sun.tools.doclets was superseded by jdk.javadoc.doclet and the
errors you see are due to the new module system since Java 9 and
probably some other API changes. In short: The code should ideally be
ported to the new jdk.javadoc API. For now it should be possible to work
around it by exporting the jdk.javadoc module as it is mentioned in this
bug report.

https://bugs.openjdk.java.net/browse/JDK-8154399

Maybe this one might give you some hints as well

https://bugs.openjdk.java.net/browse/JDK-8179488

Though you should expect that this will also stop working eventually. I
would also consider to drop the documentation from the package completely.

Here are some more information what has changed in Java 10.

http://www.oracle.com/technetwork/java/javase/10-relnote-issues-4108729.html

Removal of Old (JDK 6, JDK 7, and JDK 8 Era) Standard Doclet

The old (JDK 6, JDK 7 and JDK 8 era) standard doclet, which outputs HTML
content, and which has been superseded by a replacement, has been
removed in this release. The underlying javadoc API (see com.sun.javadoc
in the API documentation) has been deprecated, but is still available
for the time being, for use by user-provided doclets.

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#10498

Hi Markus,

On Mon, May 14, 2018 at 03:00:44PM +0200, Markus Koschany wrote:
> Though you should expect that this will also stop working eventually. I
> would also consider to drop the documentation from the package completely.

Could you suggest a safe way to do this reliably?  (Unfortunately I'm not
comfortable with Java stuff to know where to turn the lever to reach this.)

Thanks for your fast help

       Andreas.

-- 
http://fam-tille.de

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#10499

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Hi,

Am 14.05.2018 um 15:57 schrieb Andreas Tille:
> Hi Markus,
> 
> On Mon, May 14, 2018 at 03:00:44PM +0200, Markus Koschany wrote:
>> Though you should expect that this will also stop working eventually. I
>> would also consider to drop the documentation from the package completely.
> 
> Could you suggest a safe way to do this reliably?  (Unfortunately I'm not
> comfortable with Java stuff to know where to turn the lever to reach this.)

It depends on your build system. In this case libsbml is built with
CMake hence I suggest to patch docs/CMakeLists.txt and remove all code
related to building the Java documentation. You could also try to only
remove Java classes that fail to build, SBMLDoclet.java, and then remove
the code in docs/CMakeLists.txt that references it. I presume a custom
Java doclet is expendable.

Regards,

Markus

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