[Biojava-l] error on hmmer demo
Tony Power
power3d at gmail.com
Wed Jul 25 10:15:33 UTC 2012
HI,
On Mac OSx 10, Sun Java 1.6:
Exception in thread "main" java.lang.NoClassDefFoundError: org/json/JSONObject
at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:105)
at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:41)
at biodemo.BioDemo.main(BioDemo.java:37)
Caused by: java.lang.ClassNotFoundException: org.json.JSONObject
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
... 3 more
Java Result: 1
On Win 7, Java 1.6:
java.net.UnknownHostException: hmmer.janelia.org
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:177)
at java.net.Socket.connect(Socket.java:519)
at java.net.Socket.connect(Socket.java:469)
at sun.net.NetworkClient.doConnect(NetworkClient.java:157)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)
at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)
at sun.net.www.http.HttpClient.New(HttpClient.java:306)
at sun.net.www.http.HttpClient.New(HttpClient.java:323)
at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:788)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:729)
at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:654)
at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:832)
at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:69)
at org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:41)
at biodemo.BioDemo.main(BioDemo.java:37)
I have Internet connection, for the proteins are successfully
downloaded in any of the three cases.
Thanks,
Tony
On Tue, Jul 24, 2012 at 5:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Can you try with sun-java, rather than openjdk?
> A
>
> On Tue, Jul 24, 2012 at 9:15 AM, Tony Power <power3d at gmail.com> wrote:
>> Hi again,
>>
>> Sorry about the lack of details.
>> Here it goes:
>> Debian testing;
>> Biojava from debian repository;
>> OpenJDK 7 (installed from debian rep too);
>>
>> Thanks,
>>
>> On Tue, Jul 24, 2012 at 4:19 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> Thanks for the feedback. It works in my environments, but it might have to
>>> do with the conversion of JSON->Java object.
>>>
>>> - How did you get your biojava setup? Maven? manually?
>>> - If manual setup, are you using net.sf.json-lib v. 2.3?
>>> - What is your operating system and java version?
>>>
>>> Thanks,
>>>
>>> Andreas
>>>
>>>
>>> On Tue, Jul 24, 2012 at 3:09 AM, Tony Power <power3d at gmail.com> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> When I am trying to run the demo at:
>>>> http://biojava.org/wiki/BioJava:CookBook3:HmmerService
>>>>
>>>> I get the following error:
>>>>
>>>> java.lang.ClassCastException: java.lang.Long cannot be cast to
>>>> java.lang.Integer
>>>> # Domain ACC Start End eValue
>>>> Description
>>>> at
>>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:119)
>>>> at
>>>> org.biojava3.ws.hmmer.RemoteHmmerScan.scan(RemoteHmmerScan.java:42)
>>>>
>>>> I have BioJava 3.0.4.
>>>>
>>>> Thanks,
>>>> Tony
>>>> _______________________________________________
>>>> Biojava-l mailing list - Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>>
>>>
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