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]
>
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
