[Debian-med-packaging] Bug#650612: igv: Crashes on startup.
Charles Plessy
plessy at debian.org
Thu Dec 1 08:29:27 UTC 2011
Package: igv
Version: 2.0.6-1
Severity: normal
Hi Shaun,
does the IGV work for you ? On my mixed Squeeze/Wheezy/Sid system, it
crashes with files that version 1.5.14-1 takes without hickups.
log4j:ERROR Could not find value for key log4j.appender.R
log4j:ERROR Could not instantiate appender named "R".
INFO [2011-12-01 17:27:08,939] [Main.java:95] [main] Startup IGV Version 2.0.6 (860)07/23/2011 12:05 AM
INFO [2011-12-01 17:27:09,111] [Main.java:96] [main] Default User Directory: /home/charles
java.lang.IllegalStateException: Failure initializing default SSL context
at org.apache.http.conn.ssl.SSLSocketFactory.createDefaultSSLContext(SSLSocketFactory.java:211)
at org.apache.http.conn.ssl.SSLSocketFactory.<init>(SSLSocketFactory.java:333)
at org.apache.http.conn.ssl.SSLSocketFactory.getSocketFactory(SSLSocketFactory.java:165)
at org.apache.http.impl.conn.SchemeRegistryFactory.createDefault(SchemeRegistryFactory.java:45)
at org.apache.http.impl.conn.tsccm.ThreadSafeClientConnManager.<init>(ThreadSafeClientConnManager.java:98)
at org.broad.igv.util.IGVHttpClientUtils.createClient(IGVHttpClientUtils.java:90)
at org.broad.igv.util.IGVHttpClientUtils.<clinit>(IGVHttpClientUtils.java:80)
at org.broad.igv.ui.Main.initApplication(Main.java:113)
at org.broad.igv.ui.Main.main(Main.java:70)
Caused by: java.security.ProviderException: Could not initialize NSS
at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:201)
at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:103)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
at sun.security.jca.ProviderConfig$3.run(ProviderConfig.java:262)
at sun.security.jca.ProviderConfig$3.run(ProviderConfig.java:244)
at java.security.AccessController.doPrivileged(Native Method)
at sun.security.jca.ProviderConfig.doLoadProvider(ProviderConfig.java:244)
at sun.security.jca.ProviderConfig.getProvider(ProviderConfig.java:224)
at sun.security.jca.ProviderList.getProvider(ProviderList.java:232)
at sun.security.jca.ProviderList.getService(ProviderList.java:330)
at sun.security.jca.GetInstance.getInstance(GetInstance.java:157)
at java.security.Security.getImpl(Security.java:696)
at java.security.AlgorithmParameters.getInstance(AlgorithmParameters.java:130)
at sun.security.x509.AlgorithmId.decodeParams(AlgorithmId.java:121)
at sun.security.x509.AlgorithmId.<init>(AlgorithmId.java:114)
at sun.security.x509.AlgorithmId.parse(AlgorithmId.java:381)
at sun.security.x509.X509Key.parse(X509Key.java:168)
at sun.security.x509.CertificateX509Key.<init>(CertificateX509Key.java:75)
at sun.security.x509.X509CertInfo.parse(X509CertInfo.java:705)
at sun.security.x509.X509CertInfo.<init>(X509CertInfo.java:169)
at sun.security.x509.X509CertImpl.parse(X509CertImpl.java:1747)
at sun.security.x509.X509CertImpl.<init>(X509CertImpl.java:196)
at sun.security.provider.X509Factory.engineGenerateCertificate(X509Factory.java:107)
at java.security.cert.CertificateFactory.generateCertificate(CertificateFactory.java:322)
at sun.security.provider.JavaKeyStore.engineLoad(JavaKeyStore.java:763)
at sun.security.provider.JavaKeyStore$JKS.engineLoad(JavaKeyStore.java:55)
at java.security.KeyStore.load(KeyStore.java:1201)
at sun.security.ssl.TrustManagerFactoryImpl.getCacertsKeyStore(TrustManagerFactoryImpl.java:221)
at sun.security.ssl.TrustManagerFactoryImpl.engineInit(TrustManagerFactoryImpl.java:51)
at javax.net.ssl.TrustManagerFactory.init(TrustManagerFactory.java:247)
at org.apache.http.conn.ssl.SSLSocketFactory.createSSLContext(SSLSocketFactory.java:190)
at org.apache.http.conn.ssl.SSLSocketFactory.createDefaultSSLContext(SSLSocketFactory.java:209)
... 8 more
Caused by: java.io.FileNotFoundException: /usr/lib/libnss3.so
at sun.security.pkcs11.Secmod.initialize(Secmod.java:186)
at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:197)
... 42 more
ERROR [2011-12-01 17:27:09,218] [DefaultExceptionHandler.java:42] [main] Unhandled exception
java.lang.ExceptionInInitializerError
at org.broad.igv.ui.Main.initApplication(Main.java:113)
at org.broad.igv.ui.Main.main(Main.java:70)
Caused by: java.lang.NullPointerException
at org.broad.igv.util.IGVHttpClientUtils.<clinit>(IGVHttpClientUtils.java:81)
... 2 more
ERROR [2011-12-01 17:27:09,227] [DefaultExceptionHandler.java:42] [Thread-4] Unhandled exception
java.lang.RuntimeException: IGV has not been initialized. Must call createInstance(Frame) first
at org.broad.igv.ui.IGV.getInstance(IGV.java:132)
at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:56)
Cheers,
-- System Information:
Debian Release: wheezy/sid
APT prefers stable
APT policy: (910, 'stable'), (900, 'testing'), (800, 'unstable'), (500, 'stable-updates'), (1, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.39-bpo.2-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages igv depends on:
ii default-jre [java- 1:1.6-40 Standard Java or Java compatible R
ii gcj-4.4-jre [java- 4.4.6-11 Java runtime environment using GIJ
ii gcj-jre [java-runt 4:4.4.5-1 Java runtime environment using GIJ
ii libbatik-java 1.7-6 xml.apache.org SVG Library
ii libcommons-logging 1.1.1-8 commmon wrapper interface for seve
ii libcommons-math-ja 2.1-1 Java lightweight mathematics and s
ii libcommons-net-jav 1.4.1-2 internet protocol suite Java libra
ii libconcurrent-java 1.3.4-4 utility classes for concurrent jav
ii libhttpclient-java 4.1.1-1 HTTP/1.1 compliant HTTP agent impl
ii libhttpcore-java 4.1-1 set of low level HTTP transport co
ii libjama-java 1.0.2-3 a basic linear algebra library for
ii libjargs-java 1.0.0-2 Command-line argument parsing for
ii libjaxp1.3-java 1.3.05-1 Java XML parser and transformer AP
ii libjcommon-java 1.0.16-1 General Purpose library for Java
ii libjfreechart-java 1.0.13-3 Chart library for Java
ii libjhdf5-java 2.6.1-1+b1 Java HDF5 Object Package
ii libjlibeps-java 0.1+2-1 Java library to create EPS images
ii liblog4j1.2-java 1.2.15-11 Logging library for java
ii libsam-java 1.46-1 Java library to manipulate SAM and
ii libswing-layout-ja 1.0.4-1 Extensions to Swing layout
ii libxml-commons-ext 1.3.05-2 XML Commons external code - DOM, S
ii openjdk-6-jre [jav 6b18-1.8.7-2~squeeze1 OpenJDK Java runtime, using Hotspo
igv recommends no packages.
igv suggests no packages.
-- no debconf information
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