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
