Bug#893409: pixelmed FTBFS with openjdk-9

[Andreas Tille]

Hi Olivier,

On Wed, Dec 19, 2018 at 06:37:04PM +0100, Olivier Sallou wrote:
> >> Adding this lib to deps should fix the pb
> 
> - I have fixed the problem, updating patch (lib needed to be added to
> other Makefile)

Cool!  Thanks a lot for your work.  Its really appreciated.
 
> - There were some other issues with an old jdk package moved to an other
> location, from JDK 9 in 2016, which is not exported [0]. Surprisingly it
> compiles anyway, but does it work as expected??

I have no idea at all.  I do not even have an expectation what the
program should do.  I simply inherited the maintenance from Mathieu
Malaterre who injected a lot of medical imaging stuff and decided to
leave the team later.  The package has quite a number of users (compared
to other specialised software) - so I expect users to report issues if
it does not work.

> It seems there is a
> new API (java.lang.ref.Cleaner) but I'm not sure it could be replaced as
> easily (and without knowing side effects), it should be updated by upstream

Upstream is dead.
 
> In the meanwhile I renamed the related package in patch.
> 
> - vecmath needed to be added as well in Makefile (done)
> 
> - javadoc generation classpath needed to be updated as well (done)
> 
> - I think that vecmath and jaxb-api jars will need to be added in
> runtime classpath (debian/DicomXX etc..) as well   (NOT done)
> 
> - 4 tests are failing (surprisingly, packaging continues)
> 
> - lintian: some errors, documentation is not in correct directory
> (libpixelmed-java-doc expects files in
> /usr/share/doc/libpixelmed-java-doc but doc is in
> /usr/share/doc/libpixelmed-java) (NOT fixed)

The latter is caused by the debhelper switch.  I'll care for this.
 
> I have pushed my updates to git (file not found , certainly a result not
> generated, but no additional info)

Thanks again.  I'll have a look tomorrow and will ask back in case
of further issues.
 
Kind regards

  Andreas.

 
> [0] https://bugs.java.com/bugdatabase/view_bug.do?bug_id=8148117

-- 
http://fam-tille.de

Bug#893409: pixelmed FTBFS with openjdk-9

[Olivier Sallou]

On 12/19/18 11:46 AM, Andreas Tille wrote:
> Hi,
>
> On Wed, Dec 19, 2018 at 10:39:55AM +0100, Olivier Sallou wrote:
>>> The missing class is in libjaxb-api-java. Just make sure it's on the
>>> CLASSPATH.
>> yeap, an other issue at java migration to openjdk 10/11
>>
>> Adding this lib to deps should fix the pb

- I have fixed the problem, updating patch (lib needed to be added to
other Makefile)

- There were some other issues with an old jdk package moved to an other
location, from JDK 9 in 2016, which is not exported [0]. Surprisingly it
compiles anyway, but does it work as expected?? It seems there is a
new API (java.lang.ref.Cleaner) but I'm not sure it could be replaced as
easily (and without knowing side effects), it should be updated by upstream

In the meanwhile I renamed the related package in patch.

- vecmath needed to be added as well in Makefile (done)

- javadoc generation classpath needed to be updated as well (done)

- I think that vecmath and jaxb-api jars will need to be added in
runtime classpath (debian/DicomXX etc..) as well   (NOT done)

- 4 tests are failing (surprisingly, packaging continues)

- lintian: some errors, documentation is not in correct directory
(libpixelmed-java-doc expects files in
/usr/share/doc/libpixelmed-java-doc but doc is in
/usr/share/doc/libpixelmed-java) (NOT fixed)



I have pushed my updates to git (file not found , certainly a result not
generated, but no additional info)


[0] https://bugs.java.com/bugdatabase/view_bug.do?bug_id=8148117

Olivier

> Thanks for the quick help.  I tried:
>
>
> diff --git a/debian/control b/debian/control
> index e0548ee..3f8b86c 100644
> --- a/debian/control
> +++ b/debian/control
> @@ -14,7 +14,8 @@ Build-Depends-Indep: default-jdk,
>   libjmdns-java,
>   libvecmath-java,
>   libpixelmed-codec-java,
> - libjsonp-java
> + libjsonp-java,
> + libjaxb-api-java
>  Standards-Version: 4.2.1
>  Vcs-Browser: https://salsa.debian.org/med-team/pixelmed
>  Vcs-Git: https://salsa.debian.org/med-team/pixelmed.git
> diff --git a/debian/patches/fixdoc.patch b/debian/patches/fixdoc.patch
> index 752b78c..1737f5f 100644
> --- a/debian/patches/fixdoc.patch
> +++ b/debian/patches/fixdoc.patch
> @@ -11,7 +11,7 @@ Index: pixelmed-20140326/Makefile
> rm -rf docs/javadoc
> javadoc \
>  -  -classpath 
> .:lib/additional/excalibur-bzip2-1.0.jar:lib/additional/hsqldb.jar:lib/additional/vecmath1.2-1.14.jar:lib/additional/commons-codec-1.3.jar:lib/additional/commons-net2.jar:lib/additional/jmdns.jar:lib/additional/jpedalSTD.jar:lib/junit/junit-4.8.1.jar
>  \
> -+  -classpath 
> .:/usr/share/java/excalibur-bzip2-1.0.jar:/usr/share/java/hsqldb.jar:/usr/share/java/vecmath.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-net2.jar:/usr/share/java/jmdns.jar:/usr/share/java/jpedalSTD.jar:/usr/share/java/junit4.jar
>  \
> ++  -classpath 
> .:/usr/share/java/excalibur-bzip2-1.0.jar:/usr/share/java/hsqldb.jar:/usr/share/java/vecmath.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-net2.jar:/usr/share/java/jmdns.jar:/usr/share/java/jpedalSTD.jar:/usr/share/java/junit4.jar:/usr/share/java/jaxb-api.jar
>  \
> -link http://download.oracle.com/javase/1.5.0/docs/api/ \
> -link http://jpedal.org/javadoc/ \
> -link http://www.hsqldb.org/doc/src/ \
> diff --git a/debian/patches/jaxb-api.patch b/debian/patches/jaxb-api.patch
> new file mode 100644
> index 000..85760dd
> --- /dev/null
> +++ b/debian/patches/jaxb-api.patch
> @@ -0,0 +1,16 @@
> +Description: For OpenJDK 11 jaxb needs to be in classpath
> +Bug-Debian: https://bugs.debian.org/893409
> +Author: Andreas Tille 
> +Last-Update: Wed, 19 Dec 2018 08:53:43 +0100
> +
> +--- a/Makefile.common.mk
>  b/Makefile.common.mk
> +@@ -65,7 +65,7 @@ JAVACOPTIONS = -O ${JAVACTARGETOPTIONS}
> + 
> + .java.class:
> +   export JAVAVERSIONTARGETJARFILE=${JAVA_HOME}/jre/lib/rt.jar; javac 
> ${JAVACOPTIONS} \
> +-  -classpath 
> ${PATHTOROOT}:${DICOMADDITIONALJARS}:${VIEWERADDITIONALJARS}:${FTPADDITIONALJARS}:${JUNITJAR}
>  \
> ++  -classpath 
> ${PATHTOROOT}:${DICOMADDITIONALJARS}:${VIEWERADDITIONALJARS}:${FTPADDITIONALJARS}:${JUNITJAR}:/usr/share/java/jaxb-api.jar
>  \
> +   -sourcepath ${PATHTOROOT} $<
> + 
> + .png.ico:
> diff --git a/debian/patches/series b/debian/patches/series
> index 10286d4..6abfc45 100644
> --- a/debian/patches/series
> +++ b/debian/patches/series
> @@ -16,3 +16,4 @@ set_java_home.patch
>  imageio.patch
>  no_Xdiags_verbose.patch
>  do_not_set_bootclasspath.patch
> +jaxb-api.patch
>
>
>
> I've pushed these changes but unfortunately it does not help. :-(
>
> Any further hints?
>
> Kind regards
>
>   Andreas.
>
>
-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE

Bug#893409: pixelmed FTBFS with openjdk-9

[Olivier Sallou]

On 12/19/18 11:46 AM, Andreas Tille wrote:
> Hi,
>
> On Wed, Dec 19, 2018 at 10:39:55AM +0100, Olivier Sallou wrote:
>>> The missing class is in libjaxb-api-java. Just make sure it's on the
>>> CLASSPATH.
>> yeap, an other issue at java migration to openjdk 10/11
>>
>> Adding this lib to deps should fix the pb
> Thanks for the quick help.  I tried:
>
>
> diff --git a/debian/control b/debian/control
> index e0548ee..3f8b86c 100644
> --- a/debian/control
> +++ b/debian/control
> @@ -14,7 +14,8 @@ Build-Depends-Indep: default-jdk,
>   libjmdns-java,
>   libvecmath-java,
>   libpixelmed-codec-java,
> - libjsonp-java
> + libjsonp-java,
> + libjaxb-api-java
>  Standards-Version: 4.2.1
>  Vcs-Browser: https://salsa.debian.org/med-team/pixelmed
>  Vcs-Git: https://salsa.debian.org/med-team/pixelmed.git
> diff --git a/debian/patches/fixdoc.patch b/debian/patches/fixdoc.patch
> index 752b78c..1737f5f 100644
> --- a/debian/patches/fixdoc.patch
> +++ b/debian/patches/fixdoc.patch
> @@ -11,7 +11,7 @@ Index: pixelmed-20140326/Makefile
> rm -rf docs/javadoc
> javadoc \
>  -  -classpath 
> .:lib/additional/excalibur-bzip2-1.0.jar:lib/additional/hsqldb.jar:lib/additional/vecmath1.2-1.14.jar:lib/additional/commons-codec-1.3.jar:lib/additional/commons-net2.jar:lib/additional/jmdns.jar:lib/additional/jpedalSTD.jar:lib/junit/junit-4.8.1.jar
>  \
> -+  -classpath 
> .:/usr/share/java/excalibur-bzip2-1.0.jar:/usr/share/java/hsqldb.jar:/usr/share/java/vecmath.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-net2.jar:/usr/share/java/jmdns.jar:/usr/share/java/jpedalSTD.jar:/usr/share/java/junit4.jar
>  \
> ++  -classpath 
> .:/usr/share/java/excalibur-bzip2-1.0.jar:/usr/share/java/hsqldb.jar:/usr/share/java/vecmath.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-net2.jar:/usr/share/java/jmdns.jar:/usr/share/java/jpedalSTD.jar:/usr/share/java/junit4.jar:/usr/share/java/jaxb-api.jar
>  \
> -link http://download.oracle.com/javase/1.5.0/docs/api/ \
> -link http://jpedal.org/javadoc/ \
> -link http://www.hsqldb.org/doc/src/ \
> diff --git a/debian/patches/jaxb-api.patch b/debian/patches/jaxb-api.patch
> new file mode 100644
> index 000..85760dd
> --- /dev/null
> +++ b/debian/patches/jaxb-api.patch
> @@ -0,0 +1,16 @@
> +Description: For OpenJDK 11 jaxb needs to be in classpath
> +Bug-Debian: https://bugs.debian.org/893409
> +Author: Andreas Tille 
> +Last-Update: Wed, 19 Dec 2018 08:53:43 +0100
> +
> +--- a/Makefile.common.mk
>  b/Makefile.common.mk
> +@@ -65,7 +65,7 @@ JAVACOPTIONS = -O ${JAVACTARGETOPTIONS}
> + 
> + .java.class:
> +   export JAVAVERSIONTARGETJARFILE=${JAVA_HOME}/jre/lib/rt.jar; javac 
> ${JAVACOPTIONS} \
> +-  -classpath 
> ${PATHTOROOT}:${DICOMADDITIONALJARS}:${VIEWERADDITIONALJARS}:${FTPADDITIONALJARS}:${JUNITJAR}
>  \
> ++  -classpath 
> ${PATHTOROOT}:${DICOMADDITIONALJARS}:${VIEWERADDITIONALJARS}:${FTPADDITIONALJARS}:${JUNITJAR}:/usr/share/java/jaxb-api.jar
>  \
> +   -sourcepath ${PATHTOROOT} $<
> + 
> + .png.ico:
> diff --git a/debian/patches/series b/debian/patches/series
> index 10286d4..6abfc45 100644
> --- a/debian/patches/series
> +++ b/debian/patches/series
> @@ -16,3 +16,4 @@ set_java_home.patch
>  imageio.patch
>  no_Xdiags_verbose.patch
>  do_not_set_bootclasspath.patch
> +jaxb-api.patch
>
>
>
> I've pushed these changes but unfortunately it does not help. :-(


I'm looking at the issue

>
> Any further hints?
>
> Kind regards
>
>   Andreas.
>
>
-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Bug#893409: pixelmed FTBFS with openjdk-9

[Andreas Tille]

Hi,

On Wed, Dec 19, 2018 at 10:39:55AM +0100, Olivier Sallou wrote:
> > The missing class is in libjaxb-api-java. Just make sure it's on the
> > CLASSPATH.
> 
> yeap, an other issue at java migration to openjdk 10/11
> 
> Adding this lib to deps should fix the pb

Thanks for the quick help.  I tried:


diff --git a/debian/control b/debian/control
index e0548ee..3f8b86c 100644
--- a/debian/control
+++ b/debian/control
@@ -14,7 +14,8 @@ Build-Depends-Indep: default-jdk,
  libjmdns-java,
  libvecmath-java,
  libpixelmed-codec-java,
- libjsonp-java
+ libjsonp-java,
+ libjaxb-api-java
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/pixelmed
 Vcs-Git: https://salsa.debian.org/med-team/pixelmed.git
diff --git a/debian/patches/fixdoc.patch b/debian/patches/fixdoc.patch
index 752b78c..1737f5f 100644
--- a/debian/patches/fixdoc.patch
+++ b/debian/patches/fixdoc.patch
@@ -11,7 +11,7 @@ Index: pixelmed-20140326/Makefile
rm -rf docs/javadoc
javadoc \
 -  -classpath 
.:lib/additional/excalibur-bzip2-1.0.jar:lib/additional/hsqldb.jar:lib/additional/vecmath1.2-1.14.jar:lib/additional/commons-codec-1.3.jar:lib/additional/commons-net2.jar:lib/additional/jmdns.jar:lib/additional/jpedalSTD.jar:lib/junit/junit-4.8.1.jar
 \
-+  -classpath 
.:/usr/share/java/excalibur-bzip2-1.0.jar:/usr/share/java/hsqldb.jar:/usr/share/java/vecmath.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-net2.jar:/usr/share/java/jmdns.jar:/usr/share/java/jpedalSTD.jar:/usr/share/java/junit4.jar
 \
++  -classpath 
.:/usr/share/java/excalibur-bzip2-1.0.jar:/usr/share/java/hsqldb.jar:/usr/share/java/vecmath.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-net2.jar:/usr/share/java/jmdns.jar:/usr/share/java/jpedalSTD.jar:/usr/share/java/junit4.jar:/usr/share/java/jaxb-api.jar
 \
-link http://download.oracle.com/javase/1.5.0/docs/api/ \
-link http://jpedal.org/javadoc/ \
-link http://www.hsqldb.org/doc/src/ \
diff --git a/debian/patches/jaxb-api.patch b/debian/patches/jaxb-api.patch
new file mode 100644
index 000..85760dd
--- /dev/null
+++ b/debian/patches/jaxb-api.patch
@@ -0,0 +1,16 @@
+Description: For OpenJDK 11 jaxb needs to be in classpath
+Bug-Debian: https://bugs.debian.org/893409
+Author: Andreas Tille 
+Last-Update: Wed, 19 Dec 2018 08:53:43 +0100
+
+--- a/Makefile.common.mk
 b/Makefile.common.mk
+@@ -65,7 +65,7 @@ JAVACOPTIONS = -O ${JAVACTARGETOPTIONS}
+ 
+ .java.class:
+   export JAVAVERSIONTARGETJARFILE=${JAVA_HOME}/jre/lib/rt.jar; javac 
${JAVACOPTIONS} \
+-  -classpath 
${PATHTOROOT}:${DICOMADDITIONALJARS}:${VIEWERADDITIONALJARS}:${FTPADDITIONALJARS}:${JUNITJAR}
 \
++  -classpath 
${PATHTOROOT}:${DICOMADDITIONALJARS}:${VIEWERADDITIONALJARS}:${FTPADDITIONALJARS}:${JUNITJAR}:/usr/share/java/jaxb-api.jar
 \
+   -sourcepath ${PATHTOROOT} $<
+ 
+ .png.ico:
diff --git a/debian/patches/series b/debian/patches/series
index 10286d4..6abfc45 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -16,3 +16,4 @@ set_java_home.patch
 imageio.patch
 no_Xdiags_verbose.patch
 do_not_set_bootclasspath.patch
+jaxb-api.patch



I've pushed these changes but unfortunately it does not help. :-(

Any further hints?

Kind regards

  Andreas.


-- 
http://fam-tille.de

Bug#893409: pixelmed FTBFS with openjdk-9

[Olivier Sallou]

On 12/19/18 10:03 AM, Markus Koschany wrote:
> Hi,
>
> Am 19.12.18 um 09:58 schrieb Andreas Tille:
> [...]
>> Any hint how to fix this?
> The missing class is in libjaxb-api-java. Just make sure it's on the
> CLASSPATH.

yeap, an other issue at java migration to openjdk 10/11

Adding this lib to deps should fix the pb


> Regards,
>
> Markus
>
>
>
> ___
> Debian-med-packaging mailing list
> debian-med-packag...@alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438



signature.asc
Description: OpenPGP digital signature

Bug#893409: pixelmed FTBFS with openjdk-9

[Markus Koschany]

Hi,

Am 19.12.18 um 09:58 schrieb Andreas Tille:
[...]
> Any hint how to fix this?

The missing class is in libjaxb-api-java. Just make sure it's on the
CLASSPATH.

Regards,

Markus




signature.asc
Description: OpenPGP digital signature

Bug#893409: pixelmed FTBFS with openjdk-9

[Andreas Tille]

Hi,

pixelmed[1] seems to be dead upstream but I've grabbed the latest commit
of somebody who saved the code base to Github now.  With this code I get:

...
warning: [options] bootstrap class path not set in conjunction with -source 7
1 warning
export JAVAVERSIONTARGETJARFILE=/usr/lib/jvm/default-java/jre/lib/rt.jar; javac 
-O -target 1.7 -source 1.7 -encoding "UTF8" -Xlint:deprecation 
-XDignore.symbol.file \
-classpath ../../..:/usr/share/java/pixelmed_codec.jar \
-sourcepath ../../.. Base64.java
warning: [options] bootstrap class path not set in conjunction with -source 7
Base64.java:25: error: package javax.xml.bind does not exist
String s = 
javax.xml.bind.DatatypeConverter.printBase64Binary(b);
 ^
Base64.java:31: error: package javax.xml.bind does not exist
byte[] b = 
javax.xml.bind.DatatypeConverter.parseBase64Binary(s);
 ^
2 errors
1 warning
make[3]: *** [Makefile:36: Base64.class] Error 1


Any hint how to fix this?

Kind regards

   Andreas.


[1] https://salsa.debian.org/med-team/pixelmed 

-- 
http://fam-tille.de

Bug#893409: pixelmed FTBFS with openjdk-9

[Andreas Tille]

Control: tags -1 help

On Sun, Mar 18, 2018 at 07:54:32PM +0200, Adrian Bunk wrote:
> Source: pixelmed
> Version: 20150917-2
> Severity: serious
> 
> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pixelmed.html
> 
> ...
> ../../../../com/pixelmed/display/SourceImage.java:1626: error: cannot find 
> symbol
>   sun.misc.Cleaner cleaner = 
> (sun.misc.Cleaner)getCleanerMethod.invoke(object,new Object[0]);
>   ^
>   symbol:   class Cleaner
>   location: package sun.misc
> ../../../../com/pixelmed/display/SourceImage.java:1626: error: cannot find 
> symbol
>   sun.misc.Cleaner cleaner = 
> (sun.misc.Cleaner)getCleanerMethod.invoke(object,new Object[0]);
>   
> ^
>   symbol:   class Cleaner
>   location: package sun.misc

Unfortunately I have no idea how to fix this.  Any hint?

Kind regards

   Andreas. 

-- 
http://fam-tille.de

Bug#893409: pixelmed FTBFS with openjdk-9

[Adrian Bunk]

Source: pixelmed
Version: 20150917-2
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pixelmed.html

...
../../../../com/pixelmed/display/SourceImage.java:1626: error: cannot find 
symbol
sun.misc.Cleaner cleaner = 
(sun.misc.Cleaner)getCleanerMethod.invoke(object,new Object[0]);
^
  symbol:   class Cleaner
  location: package sun.misc
../../../../com/pixelmed/display/SourceImage.java:1626: error: cannot find 
symbol
sun.misc.Cleaner cleaner = 
(sun.misc.Cleaner)getCleanerMethod.invoke(object,new Object[0]);

^
  symbol:   class Cleaner
  location: package sun.misc