Bug#895765: [Debian-med-packaging] Bug#895765: IGV FTBFS with Java 11
additional remark: igv will in this case need to depend on java >= 11 as this modification for build and runtime will work only for jdk11 and above this jdk module/deprecation transition is quite a pain and make it difficult to get packages work for different jdk versions - Mail original - > De: "Markus Koschany" > À: 895...@bugs.debian.org > Envoyé: Vendredi 9 Novembre 2018 16:33:33 > Objet: [Debian-med-packaging] Bug#895765: IGV FTBFS with Java 11 > Hi, > > igv also FTBFS with Java 11 now. However the fix is trivial. The package > must build-depend on libjaxb-api-java because those classes were removed > from the JDK. Then you need to remove the > > --add-modules', 'java.xml.bind' > > line in fix_gradle.patch. > > Please find attached a patch that makes the necessary changes to the > Debian packaging without using a patch. > > 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
Bug#895765: IGV FTBFS with Java 11
Hi, igv also FTBFS with Java 11 now. However the fix is trivial. The package must build-depend on libjaxb-api-java because those classes were removed from the JDK. Then you need to remove the --add-modules', 'java.xml.bind' line in fix_gradle.patch. Please find attached a patch that makes the necessary changes to the Debian packaging without using a patch. Markus From 86feef76191c245ec314f1efc66f0f6dfba1a634 Mon Sep 17 00:00:00 2001 From: Markus Koschany Date: Fri, 9 Nov 2018 16:14:47 +0100 Subject: [PATCH 1/2] B-D on libjaxb-api-java and fix FTBFS with Java 11. --- debian/control | 1 + debian/rules | 2 ++ 2 files changed, 3 insertions(+) diff --git a/debian/control b/debian/control index 97d88d1..d406b17 100644 --- a/debian/control +++ b/debian/control @@ -17,6 +17,7 @@ Build-Depends: default-jdk, libcommons-net-java, libhttpclient-java, libhttpcore-java, + libjaxb-api-java, libjcommon-java, libjfreechart-java, libjhdf5-java, diff --git a/debian/rules b/debian/rules index 84a526b..dc61fec 100755 --- a/debian/rules +++ b/debian/rules @@ -14,6 +14,7 @@ override_dh_clean: if [ -e build_java8.gradle ] ; then mv build_java8.gradle build.gradle ; fi rm -f goby-io-igv.jar rm -f batik-codec.jar + rm -f lib/jaxb-api.jar dh_clean override_dh_auto_configure: @@ -21,3 +22,4 @@ override_dh_auto_configure: cp -a build_java9.gradle build.gradle mv src/main/java9/module-info.java src/main/java9/module-info.java.skip cp debian/log4j.xml src/main/resources/ + cp /usr/share/java/jaxb-api.jar $(CURDIR)/lib/ -- 2.19.1 signature.asc Description: OpenPGP digital signature
Bug#895765: IGV
On 10/18/2018 08:25 PM, Andreas Tille wrote: > Hi Olivier, > > On Thu, Oct 18, 2018 at 06:18:58PM +0200, Olivier Sallou wrote: >> testing with your removals, you only need to add to build gradle file >> the ref to htsjdk > I've now pushed the freshly stripped upstream version since we > both agree that a competing htsjdk is not a good idea. > >> I pushed the update on patch (but your copyright patch is not yet there) >> >> With this compile "com.github.samtools:htsjdk:debian" and htsjdk jar >> removed from upstream source, it compiles fine for me. > I confirm it compiles fine now. However: > > > $ LC_ALL=C igv > Error: Unable to initialize main class org.broad.igv.ui.Main > Caused by: java.lang.NoClassDefFoundError: > htsjdk/samtools/seekablestream/ISeekableStreamFactory I just pulled from git, rebuilt and tried with new deb, and got no issue, GUI started as expected. This kind of error suggest that it did not found in igv classpath the htsjdk.jar (not installed or not in in command classpath). > > > Sorry to admit that we seem to need another iteration to get igv out. > > Thanks a lot for your effort > > 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#895765: IGV
Hi Olivier, On Thu, Oct 18, 2018 at 06:18:58PM +0200, Olivier Sallou wrote: > > testing with your removals, you only need to add to build gradle file > the ref to htsjdk I've now pushed the freshly stripped upstream version since we both agree that a competing htsjdk is not a good idea. > I pushed the update on patch (but your copyright patch is not yet there) > > With this compile "com.github.samtools:htsjdk:debian" and htsjdk jar > removed from upstream source, it compiles fine for me. I confirm it compiles fine now. However: $ LC_ALL=C igv Error: Unable to initialize main class org.broad.igv.ui.Main Caused by: java.lang.NoClassDefFoundError: htsjdk/samtools/seekablestream/ISeekableStreamFactory Sorry to admit that we seem to need another iteration to get igv out. Thanks a lot for your effort Andreas. -- http://fam-tille.de
Bug#895765: IGV
On 10/18/2018 04:06 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Thu, Oct 18, 2018 at 01:05:12PM +0200, Olivier Sallou wrote:
>>> I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but
>>> fails with other X11 errors
>>>
>>> 2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception
>>> java.lang.IllegalArgumentException: Window must not be zero
>>> at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774)
>>> at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465)
>>> ..
>>>
>>> this is above my knowledge of gui system in java
>> in fact it seems to work. X11 error occurs when having multiple screens
>> and seems to relate to an openjdk bug [0].
>> With a single screen I could open and manipulate the GUI
>>
>> I have pushed the patch update to manage current hstjdk debian version
> Sounds good. Unfortunately I made an unfortunate observation: If I
> apply the following patch:
>
> diff --git a/debian/copyright b/debian/copyright
> index defa779..5305639 100644
> --- a/debian/copyright
> +++ b/debian/copyright
> @@ -1,31 +1,21 @@
> Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
> Source: http://www.broadinstitute.org/igv/projects/downloads
> Files-Excluded:
> -igv.jar
> -batik-codec.jar
> -igv.bat
> -igv.command
> -lib/Jama-*
> lib/batik*
> lib/commons*
> -lib/concurrent*
> lib/guava*
> -lib/jargs*
> +*/htsjdk*.jar
> lib/jcommon*
> lib/jfreechart*
> -lib/junit-*
> +*/junit-*.jar
> lib/log4j-*
> -lib/sam-*
> +*/picard-*.jar
> +*/snappy-java-*.jar
> lib/swing-layout-*
> -lib/xml-apis-*
> -lib/bcprov*
> -lib/jgrapht*
> lib/jide-oss-*
> -lib/cofoja*
> -lib/mysql-connector*
> lib/gson*
> -test/lib/ant.jar
> -test/lib/fest-assert*.jar
> +*/ant.jar
> +*/fest-Assert*.jar
> test/lib/fest-util*.jar
> test/lib/fest-reflect*.jar
> Disclaimer: This package is not part of the Debian operating system.
testing with your removals, you only need to add to build gradle file
the ref to htsjdk
diff --git a/debian/patches/fix_gradle.patch
b/debian/patches/fix_gradle.patch
index 421a147..b2a0ac4 100644
--- a/debian/patches/fix_gradle.patch
+++ b/debian/patches/fix_gradle.patch
@@ -34,7 +34,7 @@ Forwarded: no
sourceSets {
main {
java {
-@@ -45,6 +54,27 @@
+@@ -45,6 +54,28 @@
dependencies {
// Use the newer JIDE lib for Java 9 builds
compile fileTree(dir: 'lib', include: '*.jar', exclude:
'jide-oss-3.5.5.jar') + fileTree(dir: 'lib_java9', include: '*.jar')
@@ -59,10 +59,11 @@ Forwarded: no
+ compile "org.apache.logging.log4j:log4j-1.2-api:debian"
+ compile "org.apache.logging.log4j:log4j-core:debian"
+ compile "org.swinglabs:swing-layout:debian"
++ compile "com.github.samtools:htsjdk:debian"
testCompile fileTree(dir: 'test/lib', include: '*.jar')
}
-@@ -93,12 +123,13 @@
+@@ -93,12 +124,13 @@
}
compileJava {
I pushed the update on patch (but your copyright patch is not yet there)
With this compile "com.github.samtools:htsjdk:debian" and htsjdk jar
removed from upstream source, it compiles fine for me.
Olivier
>
>
> which does not mention not existing jars but more importantly removes
> those jars we **think** we don't need - specifically */htsjdk*.jar -
> recreate the tarball and try to build ... the build fails again. :-( Its
> also some htsjdk related error and I think there are more issues in this
> approach. It seems for whatever reason the build is done against the
> internal copy but the result tries somehow to take the Debian installed
> version. I'm hesitating to push my changes since than we have a broken
> IGV again.
>
> What do you suggest as next step? I might create a branch to let others
> have a look.
>
> 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#895765: IGV
On 10/18/2018 04:06 PM, Andreas Tille wrote: > Hi Olivier, > > On Thu, Oct 18, 2018 at 01:05:12PM +0200, Olivier Sallou wrote: >>> I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but >>> fails with other X11 errors >>> >>> 2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception >>> java.lang.IllegalArgumentException: Window must not be zero >>> at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774) >>> at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465) >>> .. >>> >>> this is above my knowledge of gui system in java >> in fact it seems to work. X11 error occurs when having multiple screens >> and seems to relate to an openjdk bug [0]. >> With a single screen I could open and manipulate the GUI >> >> I have pushed the patch update to manage current hstjdk debian version > Sounds good. Unfortunately I made an unfortunate observation: If I > apply the following patch: > > diff --git a/debian/copyright b/debian/copyright > index defa779..5305639 100644 > --- a/debian/copyright > +++ b/debian/copyright > @@ -1,31 +1,21 @@ > Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ > Source: http://www.broadinstitute.org/igv/projects/downloads > Files-Excluded: > -igv.jar > -batik-codec.jar > -igv.bat > -igv.command > -lib/Jama-* > lib/batik* > lib/commons* > -lib/concurrent* > lib/guava* > -lib/jargs* > +*/htsjdk*.jar oohhh, I did not see that htsjdk was part of package, though it had been removed. Explains a few things I gonna take your updates and test > lib/jcommon* > lib/jfreechart* > -lib/junit-* > +*/junit-*.jar > lib/log4j-* > -lib/sam-* > +*/picard-*.jar > +*/snappy-java-*.jar > lib/swing-layout-* > -lib/xml-apis-* > -lib/bcprov* > -lib/jgrapht* > lib/jide-oss-* > -lib/cofoja* > -lib/mysql-connector* > lib/gson* > -test/lib/ant.jar > -test/lib/fest-assert*.jar > +*/ant.jar > +*/fest-Assert*.jar > test/lib/fest-util*.jar > test/lib/fest-reflect*.jar > Disclaimer: This package is not part of the Debian operating system. > > > which does not mention not existing jars but more importantly removes > those jars we **think** we don't need - specifically */htsjdk*.jar - > recreate the tarball and try to build ... the build fails again. :-( Its > also some htsjdk related error and I think there are more issues in this > approach. It seems for whatever reason the build is done against the > internal copy but the result tries somehow to take the Debian installed > version. I'm hesitating to push my changes since than we have a broken > IGV again. > > What do you suggest as next step? I might create a branch to let others > have a look. > > 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#895765: IGV
Hi Olivier, On Thu, Oct 18, 2018 at 01:05:12PM +0200, Olivier Sallou wrote: > > I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but > > fails with other X11 errors > > > > 2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception > > java.lang.IllegalArgumentException: Window must not be zero > > at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774) > > at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465) > > .. > > > > this is above my knowledge of gui system in java > > in fact it seems to work. X11 error occurs when having multiple screens > and seems to relate to an openjdk bug [0]. > With a single screen I could open and manipulate the GUI > > I have pushed the patch update to manage current hstjdk debian version Sounds good. Unfortunately I made an unfortunate observation: If I apply the following patch: diff --git a/debian/copyright b/debian/copyright index defa779..5305639 100644 --- a/debian/copyright +++ b/debian/copyright @@ -1,31 +1,21 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://www.broadinstitute.org/igv/projects/downloads Files-Excluded: -igv.jar -batik-codec.jar -igv.bat -igv.command -lib/Jama-* lib/batik* lib/commons* -lib/concurrent* lib/guava* -lib/jargs* +*/htsjdk*.jar lib/jcommon* lib/jfreechart* -lib/junit-* +*/junit-*.jar lib/log4j-* -lib/sam-* +*/picard-*.jar +*/snappy-java-*.jar lib/swing-layout-* -lib/xml-apis-* -lib/bcprov* -lib/jgrapht* lib/jide-oss-* -lib/cofoja* -lib/mysql-connector* lib/gson* -test/lib/ant.jar -test/lib/fest-assert*.jar +*/ant.jar +*/fest-Assert*.jar test/lib/fest-util*.jar test/lib/fest-reflect*.jar Disclaimer: This package is not part of the Debian operating system. which does not mention not existing jars but more importantly removes those jars we **think** we don't need - specifically */htsjdk*.jar - recreate the tarball and try to build ... the build fails again. :-( Its also some htsjdk related error and I think there are more issues in this approach. It seems for whatever reason the build is done against the internal copy but the result tries somehow to take the Debian installed version. I'm hesitating to push my changes since than we have a broken IGV again. What do you suggest as next step? I might create a branch to let others have a look. Kind regards Andreas. -- http://fam-tille.de
Bug#895765: IGV
On 10/18/2018 12:15 PM, Olivier Sallou wrote:
>
> On 10/18/2018 12:03 PM, Olivier Sallou wrote:
>> On 10/18/2018 11:42 AM, Andreas Tille wrote:
>>> Hi Olivier,
>>>
>>> On Thu, Oct 18, 2018 at 11:13:31AM +0200, Olivier Sallou wrote:
> Unfortunately if I start the package I get the following output:
>
> $ igv
>
>
> log4j: reset attribute= "false".
> log4j: Threshold ="null".
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [org.broad.igv] additivity to [true].
> log4j: Level value for org.broad.igv is [INFO].
> log4j: org.broad.igv level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%d{-MM-dd HH:mm:ss}
> %-5p %c{1}:%L - %m%n].
> log4j: Adding appender named [console] to category [org.broad.igv].
> 2018-10-17 14:37:58 INFO DirectoryManager:179 - IGV Directory:
> /home/andreas/igv
> 2018-10-17 14:37:59 INFO Main:155 - Startup IGV Version user not_set
> 2018-10-17 14:37:59 INFO Main:156 - Java 10.0.2
> 2018-10-17 14:37:59 INFO DirectoryManager:84 - Fetching user directory...
> 2018-10-17 14:37:59 INFO Main:157 - Default User Directory: /home/andreas
> 2018-10-17 14:38:00 INFO Main:158 - OS: Linux
>
>
> 2018-10-17 14:38:00 INFO Main:208 - Unknown version: user
> 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
> java.lang.VerifyError: class
> org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final
> method htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
could be an htsjdk version issue versus what expects igv.
or getting 2 different definitions of
htsjdk.samtools.seekablestream.SeekableStream in classpath
>>> I admit I had the same idea.
>
> I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but
> fails with other X11 errors
>
> 2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception
> java.lang.IllegalArgumentException: Window must not be zero
> at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774)
> at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465)
> ..
>
> this is above my knowledge of gui system in java
in fact it seems to work. X11 error occurs when having multiple screens
and seems to relate to an openjdk bug [0].
With a single screen I could open and manipulate the GUI
I have pushed the patch update to manage current hstjdk debian version
[0] https://bugs.openjdk.java.net/browse/JDK-8204646
Olivier
>>> ...
> libhtsjdk-java - 2.16.1+dfsg-1
>>> while igv includes
>>>
>>> htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar
>> the problem is org.broad.igv.util.stream.IGVSeekableBufferedStream
>> extends a class from htsjdk but redefines a method declared as final,
>> this is forbidden.
>> Don't understand however why it compiles.
>> Recent htsjdk (as we have), includes those methods and cannot be
>> overriden. Version 2.12 did not have those methods.
>>
>> Using internal has the issue we don't have the source code for it
>> (though should match a commit). To get it work, we should simply remove
>> htsjdk related "compile" directive in build gradle file (added via our
>> patch)
>>
>>> I just realised that the Files-Excluded rules do not even remove this.
>>> I assumed this would be excluded - so what about using the internal
>>> code copy? (Unfortunately I have no idea what to change to let this
>>> happen.)
>>>
>>> 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#895765: IGV
On 10/18/2018 12:03 PM, Olivier Sallou wrote:
>
> On 10/18/2018 11:42 AM, Andreas Tille wrote:
>> Hi Olivier,
>>
>> On Thu, Oct 18, 2018 at 11:13:31AM +0200, Olivier Sallou wrote:
Unfortunately if I start the package I get the following output:
$ igv
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [org.broad.igv] additivity to [true].
log4j: Level value for org.broad.igv is [INFO].
log4j: org.broad.igv level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{-MM-dd HH:mm:ss}
%-5p %c{1}:%L - %m%n].
log4j: Adding appender named [console] to category [org.broad.igv].
2018-10-17 14:37:58 INFO DirectoryManager:179 - IGV Directory:
/home/andreas/igv
2018-10-17 14:37:59 INFO Main:155 - Startup IGV Version user not_set
2018-10-17 14:37:59 INFO Main:156 - Java 10.0.2
2018-10-17 14:37:59 INFO DirectoryManager:84 - Fetching user directory...
2018-10-17 14:37:59 INFO Main:157 - Default User Directory: /home/andreas
2018-10-17 14:38:00 INFO Main:158 - OS: Linux
2018-10-17 14:38:00 INFO Main:208 - Unknown version: user
2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
java.lang.VerifyError: class
org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method
htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
>>> could be an htsjdk version issue versus what expects igv.
>>> or getting 2 different definitions of
>>> htsjdk.samtools.seekablestream.SeekableStream in classpath
>> I admit I had the same idea.
I tried a patch to use Debian htsjdk, and pushed it. IGV ui starts, but
fails with other X11 errors
2018-10-18 10:13:25 ERROR DefaultExceptionHandler:49 - Unhandled exception
java.lang.IllegalArgumentException: Window must not be zero
at java.desktop/sun.awt.X11.XAtom.checkWindow(XAtom.java:774)
at java.desktop/sun.awt.X11.XAtom.getAtomData(XAtom.java:465)
..
this is above my knowledge of gui system in java
>>
>> ...
libhtsjdk-java - 2.16.1+dfsg-1
>> while igv includes
>>
>> htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar
> the problem is org.broad.igv.util.stream.IGVSeekableBufferedStream
> extends a class from htsjdk but redefines a method declared as final,
> this is forbidden.
> Don't understand however why it compiles.
> Recent htsjdk (as we have), includes those methods and cannot be
> overriden. Version 2.12 did not have those methods.
>
> Using internal has the issue we don't have the source code for it
> (though should match a commit). To get it work, we should simply remove
> htsjdk related "compile" directive in build gradle file (added via our
> patch)
>
>> I just realised that the Files-Excluded rules do not even remove this.
>> I assumed this would be excluded - so what about using the internal
>> code copy? (Unfortunately I have no idea what to change to let this
>> happen.)
>>
>> 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#895765: IGV
On 10/18/2018 11:42 AM, Andreas Tille wrote:
> Hi Olivier,
>
> On Thu, Oct 18, 2018 at 11:13:31AM +0200, Olivier Sallou wrote:
>>> Unfortunately if I start the package I get the following output:
>>>
>>> $ igv
>>>
>>>
>>> log4j: reset attribute= "false".
>>> log4j: Threshold ="null".
>>> log4j: Retreiving an instance of org.apache.log4j.Logger.
>>> log4j: Setting [org.broad.igv] additivity to [true].
>>> log4j: Level value for org.broad.igv is [INFO].
>>> log4j: org.broad.igv level set to INFO
>>> log4j: Class name: [org.apache.log4j.ConsoleAppender]
>>> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
>>> log4j: Setting property [conversionPattern] to [%d{-MM-dd HH:mm:ss}
>>> %-5p %c{1}:%L - %m%n].
>>> log4j: Adding appender named [console] to category [org.broad.igv].
>>> 2018-10-17 14:37:58 INFO DirectoryManager:179 - IGV Directory:
>>> /home/andreas/igv
>>> 2018-10-17 14:37:59 INFO Main:155 - Startup IGV Version user not_set
>>> 2018-10-17 14:37:59 INFO Main:156 - Java 10.0.2
>>> 2018-10-17 14:37:59 INFO DirectoryManager:84 - Fetching user directory...
>>> 2018-10-17 14:37:59 INFO Main:157 - Default User Directory: /home/andreas
>>> 2018-10-17 14:38:00 INFO Main:158 - OS: Linux
>>>
>>>
>>> 2018-10-17 14:38:00 INFO Main:208 - Unknown version: user
>>> 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
>>> java.lang.VerifyError: class
>>> org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method
>>> htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
>> could be an htsjdk version issue versus what expects igv.
>> or getting 2 different definitions of
>> htsjdk.samtools.seekablestream.SeekableStream in classpath
> I admit I had the same idea.
>
> ...
>>> libhtsjdk-java - 2.16.1+dfsg-1
> while igv includes
>
> htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar
the problem is org.broad.igv.util.stream.IGVSeekableBufferedStream
extends a class from htsjdk but redefines a method declared as final,
this is forbidden.
Don't understand however why it compiles.
Recent htsjdk (as we have), includes those methods and cannot be
overriden. Version 2.12 did not have those methods.
Using internal has the issue we don't have the source code for it
(though should match a commit). To get it work, we should simply remove
htsjdk related "compile" directive in build gradle file (added via our
patch)
>
> I just realised that the Files-Excluded rules do not even remove this.
> I assumed this would be excluded - so what about using the internal
> code copy? (Unfortunately I have no idea what to change to let this
> happen.)
>
> 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#895765: IGV
Hi Olivier,
On Thu, Oct 18, 2018 at 11:13:31AM +0200, Olivier Sallou wrote:
>
> > Unfortunately if I start the package I get the following output:
> >
> > $ igv
> >
> >
> > log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [org.broad.igv] additivity to [true].
> > log4j: Level value for org.broad.igv is [INFO].
> > log4j: org.broad.igv level set to INFO
> > log4j: Class name: [org.apache.log4j.ConsoleAppender]
> > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> > log4j: Setting property [conversionPattern] to [%d{-MM-dd HH:mm:ss}
> > %-5p %c{1}:%L - %m%n].
> > log4j: Adding appender named [console] to category [org.broad.igv].
> > 2018-10-17 14:37:58 INFO DirectoryManager:179 - IGV Directory:
> > /home/andreas/igv
> > 2018-10-17 14:37:59 INFO Main:155 - Startup IGV Version user not_set
> > 2018-10-17 14:37:59 INFO Main:156 - Java 10.0.2
> > 2018-10-17 14:37:59 INFO DirectoryManager:84 - Fetching user directory...
> > 2018-10-17 14:37:59 INFO Main:157 - Default User Directory: /home/andreas
> > 2018-10-17 14:38:00 INFO Main:158 - OS: Linux
> >
> >
> > 2018-10-17 14:38:00 INFO Main:208 - Unknown version: user
> > 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
> > java.lang.VerifyError: class
> > org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method
> > htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
>
> could be an htsjdk version issue versus what expects igv.
> or getting 2 different definitions of
> htsjdk.samtools.seekablestream.SeekableStream in classpath
I admit I had the same idea.
...
> > libhtsjdk-java - 2.16.1+dfsg-1
while igv includes
htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar
I just realised that the Files-Excluded rules do not even remove this.
I assumed this would be excluded - so what about using the internal
code copy? (Unfortunately I have no idea what to change to let this
happen.)
Kind regards
Andreas.
--
http://fam-tille.de
Bug#895765: IGV
On 10/17/2018 02:57 PM, Andreas Tille wrote:
> On Wed, Oct 17, 2018 at 02:09:10PM +0200, Olivier Sallou wrote:
in progress (not uploaded) igv packaging *should* be ok, but needs testing
>>> That's a problem for Bio-Linux 9 / Ubuntu 18.04 LTS, because the default
>>> is now Java 10 and the only other Java in the standard repo's is Java 8.
>> well, in my package env for new igv, I use Java 10, so will nto be a pb
> I can confirm that the package now builds also on my side
>
> Unfortunately if I start the package I get the following output:
>
> $ igv
>
>
> log4j: reset attribute= "false".
> log4j: Threshold ="null".
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [org.broad.igv] additivity to [true].
> log4j: Level value for org.broad.igv is [INFO].
> log4j: org.broad.igv level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%d{-MM-dd HH:mm:ss} %-5p
> %c{1}:%L - %m%n].
> log4j: Adding appender named [console] to category [org.broad.igv].
> 2018-10-17 14:37:58 INFO DirectoryManager:179 - IGV Directory:
> /home/andreas/igv
> 2018-10-17 14:37:59 INFO Main:155 - Startup IGV Version user not_set
> 2018-10-17 14:37:59 INFO Main:156 - Java 10.0.2
> 2018-10-17 14:37:59 INFO DirectoryManager:84 - Fetching user directory...
> 2018-10-17 14:37:59 INFO Main:157 - Default User Directory: /home/andreas
> 2018-10-17 14:38:00 INFO Main:158 - OS: Linux
>
>
> 2018-10-17 14:38:00 INFO Main:208 - Unknown version: user
> 2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
> java.lang.VerifyError: class
> org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method
> htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
could be an htsjdk version issue versus what expects igv.
or getting 2 different definitions of
htsjdk.samtools.seekablestream.SeekableStream in classpath
> at java.base/java.lang.ClassLoader.defineClass1(Native Method)
> at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1009)
> at
> java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
> at
> java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:801)
> at
> java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:699)
> at
> java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:622)
> at
> java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:580)
> at
> java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)
> at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
> at org.broad.igv.ui.Main.open(Main.java:282)
> at org.broad.igv.ui.Main$1.run(Main.java:109)
> at
> java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
> at
> java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
> at java.desktop/java.awt.EventQueue.access$600(EventQueue.java:97)
> at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
> at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
> at java.base/java.security.AccessController.doPrivileged(Native
> Method)
> at
> java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
> at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
> at
> java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
> at
> java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
> at
> java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
> at
> java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
> at
> java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
> at
> java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
> 2018-10-17 14:38:01 INFO ShutdownThread:46 - Shutting down
>
>
> I'm running an up to date testing system. Here is what reportbug
> generates:
>
> -- System Information:
> Debian Release: buster/sid
> APT prefers testing
> APT policy: (501, 'testing'), (50, 'buildd-unstable'), (50, 'unstable'),
> (5, 'experimental')
> Architecture: amd64 (x86_64)
> Foreign Architectures: i386
>
> Kernel: Linux 4.18.0-2-amd64 (SMP w/4 CPU cores)
> Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8),
> LAN
Bug#895765: IGV
On Wed, Oct 17, 2018 at 02:09:10PM +0200, Olivier Sallou wrote:
> >> in progress (not uploaded) igv packaging *should* be ok, but needs testing
> > That's a problem for Bio-Linux 9 / Ubuntu 18.04 LTS, because the default
> > is now Java 10 and the only other Java in the standard repo's is Java 8.
>
> well, in my package env for new igv, I use Java 10, so will nto be a pb
I can confirm that the package now builds also on my side
Unfortunately if I start the package I get the following output:
$ igv
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [org.broad.igv] additivity to [true].
log4j: Level value for org.broad.igv is [INFO].
log4j: org.broad.igv level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{-MM-dd HH:mm:ss} %-5p
%c{1}:%L - %m%n].
log4j: Adding appender named [console] to category [org.broad.igv].
2018-10-17 14:37:58 INFO DirectoryManager:179 - IGV Directory:
/home/andreas/igv
2018-10-17 14:37:59 INFO Main:155 - Startup IGV Version user not_set
2018-10-17 14:37:59 INFO Main:156 - Java 10.0.2
2018-10-17 14:37:59 INFO DirectoryManager:84 - Fetching user directory...
2018-10-17 14:37:59 INFO Main:157 - Default User Directory: /home/andreas
2018-10-17 14:38:00 INFO Main:158 - OS: Linux
2018-10-17 14:38:00 INFO Main:208 - Unknown version: user
2018-10-17 14:38:00 ERROR DefaultExceptionHandler:49 - Unhandled exception
java.lang.VerifyError: class
org.broad.igv.util.stream.IGVSeekableBufferedStream overrides final method
htsjdk.samtools.seekablestream.SeekableStream.mark(I)V
at java.base/java.lang.ClassLoader.defineClass1(Native Method)
at java.base/java.lang.ClassLoader.defineClass(ClassLoader.java:1009)
at
java.base/java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174)
at
java.base/jdk.internal.loader.BuiltinClassLoader.defineClass(BuiltinClassLoader.java:801)
at
java.base/jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull(BuiltinClassLoader.java:699)
at
java.base/jdk.internal.loader.BuiltinClassLoader.loadClassOrNull(BuiltinClassLoader.java:622)
at
java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:580)
at
java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
at org.broad.igv.ui.Main.open(Main.java:282)
at org.broad.igv.ui.Main$1.run(Main.java:109)
at
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue.access$600(EventQueue.java:97)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
at
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
2018-10-17 14:38:01 INFO ShutdownThread:46 - Shutting down
I'm running an up to date testing system. Here is what reportbug
generates:
-- System Information:
Debian Release: buster/sid
APT prefers testing
APT policy: (501, 'testing'), (50, 'buildd-unstable'), (50, 'unstable'), (5,
'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.18.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8),
LANGUAGE=de_DE.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
-- no debconf information
Ups, that's a bit less. H. no idea why that's only so few
information. Here is a bit more:
$ java --version
openjdk 10.0.2 2018-07-17
OpenJDK Runtime Environment (build 10.0.2+13-Debian-1)
OpenJDK 64-Bit Server VM
Bug#895765: igv: FTBFS with java 9
On 04/16/2018 04:38 PM, Andreas Tille wrote: > Hi Olivier, > > could you provide a patch assumed we'll stick to Java 9 and higher? I tried to add module, but javafx module is not found on system. In debian package, I found only openjfx8, no port available for java9 ? There is a bug [0] requesting version for jdk9 but it seems it is not yet available javafx is used for user interface, don't think we can remove it [0] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=850921 > > (Could you also have a look into artemis, htsjdk and picard-tools > if your time permits?) > > Kind regards > > Andreas. > > On Mon, Apr 16, 2018 at 10:17:57AM +0200, Olivier Sallou wrote: >> >> On 04/16/2018 09:32 AM, Bas Couwenberg wrote: >>> On 2018-04-16 08:18, Andreas Tille wrote: it seems something has changed with openfx since the errors below are all mentioning something like "import javafx. ...". Do you have any hint how this can be fixed? >>> There is no OpenJFX for OpenJDK 9, see: >>> >>> https://lists.debian.org/debian-java/2018/04/msg3.html >> indeed Java 9 removed some packages from *core* java and were moved to >> additional modules to add at compilation/runtime. >> Problem is this is not transparent/compatible with java <= 8. >> So, to support java 9 AND below, you need specific scripts that detect >> java version and act accordingly. This is not really cool to do and >> maintain. >> >> As proposed, either javafx can be removed from code, either we shoud >> stick to Java 9 and superior and add the javafx module. >> there is an example in biojava4 for a build.xml: >> >> >> >> >> >> . >> >> this example used java.se.ee module. >> >> For javafx, there are several modules [0]: >> >> * Base APIs for JavaFX UI Toolkit — javafx.base >> * JavaFX APIs for UI Controls — javafx.controls >> * JavaFX APIs for FXML — javafx.fxml >> * JavaFX APIs for various Graphics Tools— javafx.graphics >> * JavaFX APIs for Multimedia — javafx.media >> * JavaFX APIs for Swing-JavaFX Interoperability — javafx.swing >> * JavaFX APIs for WebView Functionality — javafx.web >> >> >> To add multiple modules, one need to separate them with comma. >> >> [0] >> https://medium.com/@afinlay/whats-new-in-java-fx-java-9-updates-a90dd3d4dbba >> >> >> >>> If the package works without JavaFX you should consider disabling that >>> for the time being. >>> >>> You can also explicitly build with OpenJDK 8, but that will just get >>> you a different RC bug because openjdk-8 will not be in buster. >>> >>> Kind Regards, >>> >>> Bas >>> >> -- >> 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 >> >> >> -- 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#895765: igv: FTBFS with java 9
Hi Olivier, could you provide a patch assumed we'll stick to Java 9 and higher? (Could you also have a look into artemis, htsjdk and picard-tools if your time permits?) Kind regards Andreas. On Mon, Apr 16, 2018 at 10:17:57AM +0200, Olivier Sallou wrote: > > > On 04/16/2018 09:32 AM, Bas Couwenberg wrote: > > On 2018-04-16 08:18, Andreas Tille wrote: > >> it seems something has changed with openfx since the errors below are > >> all mentioning something like "import javafx. ...". Do you have any > >> hint how this can be fixed? > > > > There is no OpenJFX for OpenJDK 9, see: > > > > https://lists.debian.org/debian-java/2018/04/msg3.html > > indeed Java 9 removed some packages from *core* java and were moved to > additional modules to add at compilation/runtime. > Problem is this is not transparent/compatible with java <= 8. > So, to support java 9 AND below, you need specific scripts that detect > java version and act accordingly. This is not really cool to do and > maintain. > > As proposed, either javafx can be removed from code, either we shoud > stick to Java 9 and superior and add the javafx module. > there is an example in biojava4 for a build.xml: > > > > > > . > > this example used java.se.ee module. > > For javafx, there are several modules [0]: > > * Base APIs for JavaFX UI Toolkit — javafx.base > * JavaFX APIs for UI Controls — javafx.controls > * JavaFX APIs for FXML — javafx.fxml > * JavaFX APIs for various Graphics Tools— javafx.graphics > * JavaFX APIs for Multimedia — javafx.media > * JavaFX APIs for Swing-JavaFX Interoperability — javafx.swing > * JavaFX APIs for WebView Functionality — javafx.web > > > To add multiple modules, one need to separate them with comma. > > [0] > https://medium.com/@afinlay/whats-new-in-java-fx-java-9-updates-a90dd3d4dbba > > > > > > > If the package works without JavaFX you should consider disabling that > > for the time being. > > > > You can also explicitly build with OpenJDK 8, but that will just get > > you a different RC bug because openjdk-8 will not be in buster. > > > > Kind Regards, > > > > Bas > > > > -- > 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 > > > -- http://fam-tille.de
Bug#895765: igv: FTBFS with java 9
On 04/16/2018 09:32 AM, Bas Couwenberg wrote: > On 2018-04-16 08:18, Andreas Tille wrote: >> it seems something has changed with openfx since the errors below are >> all mentioning something like "import javafx. ...". Do you have any >> hint how this can be fixed? > > There is no OpenJFX for OpenJDK 9, see: > > https://lists.debian.org/debian-java/2018/04/msg3.html indeed Java 9 removed some packages from *core* java and were moved to additional modules to add at compilation/runtime. Problem is this is not transparent/compatible with java <= 8. So, to support java 9 AND below, you need specific scripts that detect java version and act accordingly. This is not really cool to do and maintain. As proposed, either javafx can be removed from code, either we shoud stick to Java 9 and superior and add the javafx module. there is an example in biojava4 for a build.xml: . this example used java.se.ee module. For javafx, there are several modules [0]: * Base APIs for JavaFX UI Toolkit — javafx.base * JavaFX APIs for UI Controls — javafx.controls * JavaFX APIs for FXML — javafx.fxml * JavaFX APIs for various Graphics Tools— javafx.graphics * JavaFX APIs for Multimedia — javafx.media * JavaFX APIs for Swing-JavaFX Interoperability — javafx.swing * JavaFX APIs for WebView Functionality — javafx.web To add multiple modules, one need to separate them with comma. [0] https://medium.com/@afinlay/whats-new-in-java-fx-java-9-updates-a90dd3d4dbba > > If the package works without JavaFX you should consider disabling that > for the time being. > > You can also explicitly build with OpenJDK 8, but that will just get > you a different RC bug because openjdk-8 will not be in buster. > > Kind Regards, > > Bas > -- 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#895765: igv: FTBFS with java 9
On 2018-04-16 08:18, Andreas Tille wrote: it seems something has changed with openfx since the errors below are all mentioning something like "import javafx. ...". Do you have any hint how this can be fixed? There is no OpenJFX for OpenJDK 9, see: https://lists.debian.org/debian-java/2018/04/msg3.html If the package works without JavaFX you should consider disabling that for the time being. You can also explicitly build with OpenJDK 8, but that will just get you a different RC bug because openjdk-8 will not be in buster. Kind Regards, Bas
Bug#895765: igv: FTBFS with java 9
Hi,
it seems something has changed with openfx since the errors below are
all mentioning something like "import javafx. ...". Do you have any
hint how this can be fixed?
Kind regards
Andreas.
On Sun, Apr 15, 2018 at 08:55:57PM +0200, Andreas Beckmann wrote:
> Source: igv
> Version: 2.4.6+dfsg-1
> Severity: serious
> Justification: fails to build from source
>
> ...
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:7:
> error: package javafx.application does not exist
> [javac] import javafx.application.Platform;
> [javac] ^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:8:
> error: package javafx.embed.swing does not exist
> [javac] import javafx.embed.swing.JFXPanel;
> [javac] ^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:9:
> error: package javafx.geometry does not exist
> [javac] import javafx.geometry.Pos;
> [javac] ^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:10:
> error: package javafx.scene does not exist
> [javac] import javafx.scene.Node;
> [javac]^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:11:
> error: package javafx.scene does not exist
> [javac] import javafx.scene.Scene;
> [javac]^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:13:
> error: package javafx.scene.layout does not exist
> [javac] import javafx.scene.layout.GridPane;
> [javac] ^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:14:
> error: package javafx.scene.layout does not exist
> [javac] import javafx.scene.layout.StackPane;
> [javac] ^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:15:
> error: package javafx.scene.layout does not exist
> [javac] import javafx.scene.layout.VBox;
> [javac] ^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:16:
> error: package javafx.scene.paint does not exist
> [javac] import javafx.scene.paint.Color;
> [javac] ^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:17:
> error: package javafx.scene.text does not exist
> [javac] import javafx.scene.text.Text;
> [javac] ^
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:45:
> error: cannot find symbol
> [javac] static Color lightGray = new Color(0.9, 0.9, 0.9, 0.5);
> [javac]^
> [javac] symbol: class Color
> [javac] location: class Cravat
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:77:
> error: cannot find symbol
> [javac] private static void initFX(JFXPanel fxPanel, JsonObject
> jsonObject) {
> [javac]^
> [javac] symbol: class JFXPanel
> [javac] location: class Cravat
> [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:12:
> error: package javafx.scene.control does not exist
> [javac] import javafx.scene.control.*;
> [javac] ^
> [javac]
> /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:3:
> error: package javafx.application does not exist
> [javac] import javafx.application.Platform;
> [javac] ^
> [javac]
> /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:4:
> error: package javafx.beans.value does not exist
> [javac] import javafx.beans.value.ChangeListener;
> [javac] ^
> [javac]
> /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:5:
> error: package javafx.beans.value does not exist
> [javac] import javafx.beans.value.ObservableValue;
> [javac] ^
> [javac]
> /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:6:
> error: package javafx.collections does not exist
> [javac] import javafx.collections.FXCollections;
> [javac] ^
> [javac]
> /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:7:
> error: package javafx.embed.swing does not exist
> [javac] import javafx.embed.swing.JFXPanel;
> [javac] ^
> [javac]
> /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:8:
> error: package javafx.geometry does not exist
> [javac] import javafx.geometry.HPos;
> [javac] ^
> [javac]
> /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:9:
> error: package javafx.geometry does not exist
> [javac] import javafx.geometry.Insets;
> [javac] ^
> [javac]
> /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/Prefer
Bug#895765: igv: FTBFS with java 9
Source: igv Version: 2.4.6+dfsg-1 Severity: serious Justification: fails to build from source Hi, igv FTBFS with openjdk-9 as the default jdk: debian/rules build dh build --with javahelper dh_update_autotools_config dh_autoreconf dh_auto_configure jh_linkjars dh_auto_build ant -Duser.name debian Buildfile: /build/igv-2.4.6+dfsg/build.xml clean: init: [mkdir] Created dir: /build/igv-2.4.6+dfsg/tmp [mkdir] Created dir: /build/igv-2.4.6+dfsg/testtmp [copy] Copying 133 files to /build/igv-2.4.6+dfsg/tmp [copy] Copied 115 empty directories to 61 empty directories under /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/AbsoluteLayout.jar into /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/goby-io-igv__V1.0.jar into /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/htsjdk-2.12.0-18-g20ee53e-SNAPSHOT.jar into /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/jlfgr-1_0.jar into /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/mongo-java-driver-2.11.3.jar into /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/na12878kb-utils.jar into /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/ojdbc6.jar into /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/picard-lib.jar into /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/snappy-java-1.1.4.jar into /build/igv-2.4.6+dfsg/tmp [unjar] Expanding: /build/igv-2.4.6+dfsg/lib/sqlitejdbc-v056.jar into /build/igv-2.4.6+dfsg/tmp prepare: [echo] Target File: /build/igv-2.4.6+dfsg/tmp/resources/about.properties [echo] Version user [echo] Build 0 rewrite-log: compile: [javac] Compiling 910 source files to /build/igv-2.4.6+dfsg/tmp [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.8 WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by com.google.java.contract.core.apt.AnnotationProcessor (file:/usr/share/java/cofoja.jar) to method com.sun.tools.javac.processing.JavacProcessingEnvironment.getContext() WARNING: Please consider reporting this to the maintainers of com.google.java.contract.core.apt.AnnotationProcessor WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:7: error: package javafx.application does not exist [javac] import javafx.application.Platform; [javac] ^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:8: error: package javafx.embed.swing does not exist [javac] import javafx.embed.swing.JFXPanel; [javac] ^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:9: error: package javafx.geometry does not exist [javac] import javafx.geometry.Pos; [javac] ^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:10: error: package javafx.scene does not exist [javac] import javafx.scene.Node; [javac]^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:11: error: package javafx.scene does not exist [javac] import javafx.scene.Scene; [javac]^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:13: error: package javafx.scene.layout does not exist [javac] import javafx.scene.layout.GridPane; [javac] ^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:14: error: package javafx.scene.layout does not exist [javac] import javafx.scene.layout.StackPane; [javac] ^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:15: error: package javafx.scene.layout does not exist [javac] import javafx.scene.layout.VBox; [javac] ^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:16: error: package javafx.scene.paint does not exist [javac] import javafx.scene.paint.Color; [javac] ^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:17: error: package javafx.scene.text does not exist [javac] import javafx.scene.text.Text; [javac] ^ [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:45: error: cannot find symbol [javac] static Color lightGray = new Color(0.9, 0.9, 0.9, 0.5); [javac]^ [javac] symbol: class Color [javac] location: class Cravat [javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/mupit/Cravat.java:77: error: cannot find symbol [javac] private static
