[Biojava-l] error on hmmer demo

[Tony Power]

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
>>>
>>>
>>>