[Debian-med-packaging] Bug#895765: igv: FTBFS with java 9
Andreas Beckmann
anbe at debian.org
Sun Apr 15 19:55:57 BST 2018
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 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/PreferenceEditorFX.java:10: error: package javafx.geometry does not exist
[javac] import javafx.geometry.Pos;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.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/prefs/PreferenceEditorFX.java:13: error: package javafx.scene.control does not exist
[javac] import javafx.scene.control.Button;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:14: error: package javafx.scene.control does not exist
[javac] import javafx.scene.control.Label;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:15: error: package javafx.scene.control does not exist
[javac] import javafx.scene.control.ScrollPane;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:16: error: package javafx.scene.control does not exist
[javac] import javafx.scene.control.TextField;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:18: error: package javafx.stage does not exist
[javac] import javafx.stage.Stage;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.java:58: error: cannot find symbol
[javac] private static void initFX(final JDialog parent, JFXPanel fxPanel, List<PreferencesManager.PreferenceGroup> preferenceGroups) {
[javac] ^
[javac] symbol: class JFXPanel
[javac] location: class PreferenceEditorFX
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/prefs/PreferenceEditorFX.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:17: error: package javafx.scene.layout does not exist
[javac] import javafx.scene.layout.*;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:4: 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/sam/mutreview/VariantReviewFX.java:5: error: package javafx.embed.swing does not exist
[javac] import javafx.embed.swing.SwingFXUtils;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:6: error: package javafx.fxml does not exist
[javac] import javafx.fxml.FXML;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:7: error: package javafx.fxml does not exist
[javac] import javafx.fxml.FXMLLoader;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:8: error: package javafx.scene does not exist
[javac] import javafx.scene.Scene;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:9: error: package javafx.scene.control does not exist
[javac] import javafx.scene.control.RadioButton;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:10: error: package javafx.scene.control does not exist
[javac] import javafx.scene.control.Toggle;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:11: error: package javafx.scene.control does not exist
[javac] import javafx.scene.control.ToggleGroup;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:13: error: package javafx.scene.layout does not exist
[javac] import javafx.scene.layout.BorderPane;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:42: error: cannot find symbol
[javac] private ToggleGroup artifactGroup; // Value injected by FXMLLoader
[javac] ^
[javac] symbol: class ToggleGroup
[javac] location: class VariantReviewFX
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:45: error: cannot find symbol
[javac] private ImageView imageView; // Value injected by FXMLLoader
[javac] ^
[javac] symbol: class ImageView
[javac] location: class VariantReviewFX
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:12: error: package javafx.scene.image does not exist
[javac] import javafx.scene.image.*;
[javac] ^
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:35: error: cannot find symbol
[javac] @FXML // ResourceBundle that was given to the FXMLLoader
[javac] ^
[javac] symbol: class FXML
[javac] location: class VariantReviewFX
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:38: error: cannot find symbol
[javac] @FXML // URL location of the FXML file that was given to the FXMLLoader
[javac] ^
[javac] symbol: class FXML
[javac] location: class VariantReviewFX
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:41: error: cannot find symbol
[javac] @FXML // fx:id="artifactGroup"
[javac] ^
[javac] symbol: class FXML
[javac] location: class VariantReviewFX
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:44: error: cannot find symbol
[javac] @FXML // fx:id="imageView"
[javac] ^
[javac] symbol: class FXML
[javac] location: class VariantReviewFX
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:47: error: cannot find symbol
[javac] @FXML
[javac] ^
[javac] symbol: class FXML
[javac] location: class VariantReviewFX
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:53: error: cannot find symbol
[javac] @FXML
[javac] ^
[javac] symbol: class FXML
[javac] location: class VariantReviewFX
[javac] /build/igv-2.4.6+dfsg/src/org/broad/igv/sam/mutreview/VariantReviewFX.java:90: error: cannot find symbol
[javac] @FXML
[javac] ^
[javac] symbol: class FXML
[javac] location: class VariantReviewFX
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] 49 errors
[javac] 1 warning
BUILD FAILED
/build/igv-2.4.6+dfsg/build.xml:194: Compile failed; see the compiler error output for details.
Total time: 24 seconds
dh_auto_build: ant -Duser.name debian returned exit code 1
make: *** [debian/rules:9: build] Error 2
Andreas
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