Your message dated Sat, 24 Dec 2011 10:53:47 +0100
with message-id <[email protected]>
and subject line Re: Bug#650612: igv: Crashes on startup.
has caused the Debian Bug report #650612,
regarding igv: Crashes on startup.
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.
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--
650612: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650612
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Version: 2.0.30-1
Hi Shaun,
thanks for the update. It appears to have solved my problem.
Have a nice day, a merry Christmas, and a happy new year.
--
Charles
--- End Message ---
