Perhaps maven has an older version installed that is being used?
On Mon, Jul 15, 2013 at 5:04 PM, Andreas Prlic <[email protected]> wrote: > Hi David, > > I would recommend against moving 3rd party jars into jre/lib/ext in > general. This can easily lead to classpath problems and it sounds a bit > like you are having that... I'd delete the alignment.jar from there and > make sure there is no other reference to that jar in you classpath. > > Andreas > > > > > On Sun, Jul 14, 2013 at 6:21 PM, David Scott <[email protected]> > wrote: > > > Unable to run this without an Illegal Access Error even when I changed > all > > the routines > > to be public in Alignment.java > > > > I unjarred biojava3-alignment, changed access to public, and executed the > > CookbookMSA > > Profiller in the same package space. Still refers to the same access > > error: > > > > > > C:\Program > > Files\Java\jdk1.7.0_25\jre\lib\ext\biojava3-alignment-3.0.5-sources>java > > org.biojava3.alignment.CookbookMSAProfiler bones.fasta > > Loading sequences from bones.fasta... 2 sequences in 48 ms using 15872 kB > > > > Stage 1: pairwise similarity calculation... Exception in thread "main" > > java.lang.IllegalAccessError: tried to access method > > > org.biojava3.alignment.Alignments.getAllPairsScorers(Ljava/util/List;Lorg/biojava3/alignment/Alignments$PairwiseSequenceScorerType;Lorg/biojava3/alignment/template/GapPenalty;Lorg/biojava3/alignment/template/SubstitutionMatrix;)Ljava/util/List; > > from class org.biojava3.alignment.CookbookMSAProfiler at > > > org.biojava3.alignment.CookbookMSAProfiler.main(CookbookMSAProfiler.java:84) > > > > C:\Program > > Files\Java\jdk1.7.0_25\jre\lib\ext\biojava3-alignment-3.0.5-sources> > > > > Any ideas on what I'm doing wrong? > > > > I have all the BioJava jar files in the ext area. Should I be removing > > the alignment jar from the > > jre/lib/ext area so that Java uses only the recompiled Alignment.java? > Or > > is the problem somewhere > > else? > > > > Any ideas? > > > > > > Thanks, > > > > David Scott > > > > _______________________________________________ > > 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
