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qualimap add fonts requirement #19041

Merged
merged 1 commit into from
Dec 3, 2019
Merged

qualimap add fonts requirement #19041

merged 1 commit into from
Dec 3, 2019

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bernt-matthias
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Without the fonts it fails (on minimal systems) with

|  Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
|  at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
|  at java.base/java.security.AccessController.doPrivileged(Native Method)
|  at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
|  at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
|  at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
|  at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
|  at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
|  at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
|  at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
|  at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
|  at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
|  at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
|  at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
|  at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
|  at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
|  at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
|  at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
|  at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
|  at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
|  at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
|  at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
|  at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
|  at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
|  Caused by: java.lang.reflect.InvocationTargetException
|  at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
|  at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
|  at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
|  at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
|  at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
|  ... 22 more
|  Caused by: java.lang.NullPointerException
|  at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
|  at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
|  at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
|  at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
|  at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
|  at java.base/java.security.AccessController.doPrivileged(Native Method)
|  at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
|  at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
|  at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
|  ... 27 more

see also galaxyproject/tools-iuc#2701

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Without the fonts it fails (on minimal systems) with 

```
|  Exception in thread "main" java.lang.InternalError: java.lang.reflect.InvocationTargetException
|  at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
|  at java.base/java.security.AccessController.doPrivileged(Native Method)
|  at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
|  at java.desktop/sun.font.SunFontManager.getInstance(SunFontManager.java:247)
|  at java.desktop/sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:265)
|  at java.desktop/sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:856)
|  at org.jfree.text.G2TextMeasurer.getStringWidth(G2TextMeasurer.java:79)
|  at org.jfree.text.TextUtilities.nextLineBreak(TextUtilities.java:294)
|  at org.jfree.text.TextUtilities.createTextBlock(TextUtilities.java:235)
|  at org.jfree.chart.title.TextTitle.arrangeRR(TextTitle.java:628)
|  at org.jfree.chart.title.TextTitle.arrange(TextTitle.java:497)
|  at org.jfree.chart.JFreeChart.drawTitle(JFreeChart.java:1316)
|  at org.jfree.chart.JFreeChart.draw(JFreeChart.java:1204)
|  at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1404)
|  at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1384)
|  at org.jfree.chart.JFreeChart.createBufferedImage(JFreeChart.java:1369)
|  at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.saveImages(ExportHtmlThread.java:263)
|  at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.generateAndSaveReport(ExportHtmlThread.java:189)
|  at org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread.run(ExportHtmlThread.java:158)
|  at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.exportResult(NgsSmartTool.java:297)
|  at org.bioinfo.ngs.qc.qualimap.main.BamQcTool.execute(BamQcTool.java:283)
|  at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)
|  at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)
|  Caused by: java.lang.reflect.InvocationTargetException
|  at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
|  at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
|  at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
|  at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
|  at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:84)
|  ... 22 more
|  Caused by: java.lang.NullPointerException
|  at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262)
|  at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225)
|  at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107)
|  at java.desktop/sun.awt.X11FontManager.createFontConfiguration(X11FontManager.java:719)
|  at java.desktop/sun.font.SunFontManager$2.run(SunFontManager.java:367)
|  at java.base/java.security.AccessController.doPrivileged(Native Method)
|  at java.desktop/sun.font.SunFontManager.<init>(SunFontManager.java:312)
|  at java.desktop/sun.awt.FcFontManager.<init>(FcFontManager.java:35)
|  at java.desktop/sun.awt.X11FontManager.<init>(X11FontManager.java:56)
|  ... 27 more
```

see also galaxyproject/tools-iuc#2701
@bernt-matthias bernt-matthias added the please review & merge set to ask for merge label Dec 3, 2019
@bernt-matthias bernt-matthias changed the title Update meta.yaml qualimap add fonts requirement Dec 3, 2019
@mvdbeek mvdbeek merged commit bcbdf85 into master Dec 3, 2019
@mvdbeek mvdbeek deleted the topic/qualimap-fonts-1 branch December 3, 2019 13:40
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