Hi Daniel, I am also on Snow Leopard and can't confirm this problem.
When I do a jar xvf biojava-1.7-all.jar it all extracts fine. Are you sure your dowload has fully completed before you expand the file? Another thought: in order for gzip and tar to get installed on my system I had to manually install some optional packages from the Snow Leopard installation disk. Perhaps that is related somehow? Andreas On Mon, Sep 14, 2009 at 1:25 PM, Daniel D Ence <[email protected]> wrote: > Hi, > > I just discovered the BioJava project today when I searched to see if anyone > else had written a Nexus file parser in java. I was excited to discover that > this is part of what you guys are doing. I am trying to get > biojava1.7-all.jar for some phylogenetics software I am writing. If I > understood correctly, I download the "all" jar file and extract it using jar > ("jar xf file.jar"). I am doing this from a bash terminal on MAC-OS X 10.6 on > an Intel Core Duo chip. > > However, when doing this command, "jar xf file.jar", I get the following > error: > > java.io.EOFException: Unexpected end of ZLIB input stream > at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:223) > at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:141) > at java.util.zip.ZipInputStream.read(ZipInputStream.java:146) > at sun.tools.jar.Main.extractFile(Main.java:849) > at sun.tools.jar.Main.extract(Main.java:776) > at sun.tools.jar.Main.run(Main.java:211) > at sun.tools.jar.Main.main(Main.java:1044) > > A folder titled "biojava-1.7" is created which contains two jar files, > "apps-1.7.jar" and "biojava-1.7.jar" and a folder "apps". The apps folder > contains the following nested folders org->biojava->app. App contains two > java files, BioFlatIndex.java and BioGetSeq.java. > > It would appear that the EOF exception interrupts the extraction and I only > get those two files. > > I don't know if this is a jar issue on snow leopard or what. I guess it is > possible that I am the first person to download a new copy of biojava since > the Snow leopard release less than three weeks ago. The next thing I will try > is to get the source code and the supporting jar files listed on the download > pages and just compile it myself. > > Any help you could offer on this would be appreciated. > > > Thanks, > > Daniel Ence > > > > _______________________________________________ > 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
