[Biojava-l] Chromatagraph reading in BioJava3?

Tue Mar 13 10:48:11 UTC 2012

Aha, solved the test problem, seems the unit tests fail under JDK 7 as
a TreeSet now fails if you add a single non-comparable object, while
before it failed only when you added a second one and a comparison was
actually needed. Since new Object() doesn't implement comparable, the
tests were failing under maven for me. I can at least locally install
1.8 now, but would be nice to have a maven repo dependency on 1.8 work
in the future!

Cheers,

Nick

On 13 March 2012 10:25, Nick England <nickengland at gmail.com> wrote:
> If I try to run maven I got the following:
>
> [INFO] Building sequence analysis 0.0.1-SNAPSHOT
> [INFO] ------------------------------------------------------------------------
> Downloading: http://www.biojava.org/download/maven/org/biojava/biojava-legacy/1.8.2/biojava-legacy-1.8.2.pom
> Downloading: http://repo.maven.apache.org/maven2/org/biojava/biojava-legacy/1.8.2/biojava-legacy-1.8.2.pom
> [WARNING] The POM for org.biojava:biojava-legacy:jar:1.8.2 is missing,
> no dependency information available
> Downloading: http://www.biojava.org/download/maven/org/biojava/biojava-legacy/1.8.2/biojava-legacy-1.8.2.jar
> Downloading: http://repo.maven.apache.org/maven2/org/biojava/biojava-legacy/1.8.2/biojava-legacy-1.8.2.jar
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
>
> I get this for 1.8 and 1.8.1 as well:
>
> Could not find artifact org.biojava:biojava-legacy:jar:1.8 in
> biojava-maven-repo (http://www.biojava.org/download/maven/) -> [Help
> 1]
> Could not find artifact org.biojava:biojava-legacy:jar:1.8.1 in
> biojava-maven-repo (http://www.biojava.org/download/maven/) -> [Help
> 1]
>
> If I try to install it from source, I'm getting some class cast
> exceptions during the unit tests for some tests in core:
>
> Failed tests:
>  testGetNoteSet(org.biojavax.bio.SimpleBioEntryTest)
>  testGetRankedCrossRefs(org.biojavax.bio.SimpleBioEntryTest)
>
>
> 3.0 works fine, but lacks the class I want!.
> Presumably BioJava 1.8 hasn't always been called biojava-legacy? Since
> maven releases should be immutable, it should still be available from
> the original release maven repo?
>
> Thanks for the help,
>
> Nick
>
>
> On 12 March 2012 20:38, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> I don't think that would cause trouble as reported below, but it is
>>> odd in any case.  1.8.x shouldn't have a dependency on 3.x.
>>
>> In principle I agree, however there are historic reasons for this.  If
>> this config causes a problem then I would vote for removing it. The
>> biojava-legacy project contains no structure sources any more since it
>> was completely upgraded into the 3.X series. The API is compatible to
>> a large extent.  There is no reason for anybody to still be using a
>> 1.X version of structure.
>>
>> Andreas
>>
>>
>>
>>> Hello Nick,
>>>
>>> What kind of maven failure are you seeing?
>>>
>>>   michael
>>>
>>>
>>> On Mon, Mar 12, 2012 at 12:54 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>> I am not aware of any issues with that. Does either 1.8 or
>>>> 1.8.2-SNAPSHOT work? Depending on your IDE, you just might have to
>>>> refresh your Maven dependencies?
>>>>
>>>> Andreas
>>>>
>>>>
>>>>
>>>> On Mon, Mar 12, 2012 at 10:39 AM, Nick England <nickengland at gmail.com> wrote:
>>>>> Thanks for the help, 1.8.1 seems to have the classes I need. But I
>>>>> haven't been able to get maven to work with biojava 1.8. It works fine
>>>>> with 3.X, but when I try to use the dependency:
>>>>>                <dependency>
>>>>>                        <groupId>org.biojava</groupId>
>>>>>                        <artifactId>biojava-legacy</artifactId>
>>>>>                        <version>1.8.1</version>
>>>>>                </dependency>
>>>>> it fails, even though there appears to be the corresponding pom on the
>>>>> repository at http://www.biojava.org/download/maven/org/biojava/biojava-legacy/1.8.1/
>>>>>
>>>>> I have the repo at :
>>>>>                 <repository>
>>>>>                        <id>biojava-maven-repo</id>
>>>>>                        <name>BioJava repository</name>
>>>>>                        <url>http://www.biojava.org/download/maven/</url>
>>>>>                </repository>
>>>>>
>>>>> Am I doing something wrong, or has the release version 1.8.1 somehow
>>>>> broken on the repository?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Nick
>>>>>
>>>>> On 12 March 2012 16:43, Andreas Prlic <andreas at sdsc.edu> wrote:
>>>>>> Hi Nick,
>>>>>>
>>>>>> this feature has not been ported to biojava3 so far and you can get it
>>>>>> via biojava 1.8.1
>>>>>>
>>>>>> Andreas
>>>>>>
>>>>>> On Mon, Mar 12, 2012 at 8:04 AM, Nick England <nickengland at gmail.com> wrote:
>>>>>>> Hello all,
>>>>>>>
>>>>>>> I am trying to read some .scf files into BioJava3. I have found the
>>>>>>> example code for 1.3
>>>>>>> (http://biojava.org/wiki/BioJava:Cookbook:SeqIO:ABItoSequence) but I
>>>>>>> can't find any classes in the 3.0 API which look at all related to
>>>>>>> those ones. Is it possible, or should I downgrade to 1.3 if I want to
>>>>>>> be able to read .scf files?
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Nick
>>>>>>> _______________________________________________
>>>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>
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