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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> >>>> 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 <[email protected]> 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 <[email protected]> >>>>>> 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 - [email protected] >>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list - [email protected] >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
