Your message dated Mon, 12 Nov 2018 15:34:25 +0000
with message-id <e1gmeel-000j5z...@fasolo.debian.org>
and subject line Bug#895765: fixed in igv 2.4.14+dfsg-2
has caused the Debian Bug report #895765,
regarding igv: FTBFS with java 9
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
895765: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=895765
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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
igv_2.4.6+dfsg-1.log.gz
Description: application/gzip
--- End Message ---
--- Begin Message ---
Source: igv
Source-Version: 2.4.14+dfsg-2
We believe that the bug you reported is fixed in the latest version of
igv, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 895...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Olivier Sallou <osal...@debian.org> (supplier of updated igv package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 23 Oct 2018 14:55:18 +0200
Source: igv
Binary: igv
Architecture: source all
Version: 2.4.14+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Olivier Sallou <osal...@debian.org>
Description:
igv - Integrative Genomics Viewer
Closes: 895765
Changes:
igv (2.4.14+dfsg-2) unstable; urgency=medium
.
[ Olivier Sallou ]
fix for FTBS openjdk 11, Closes: #895765
- thanks to Markus Koschany <a...@debian.org>
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Checksums-Sha256:
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Files:
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igv_2.4.14+dfsg-2.dsc
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igv_2.4.14+dfsg-2_all.deb
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