[Biojava-l] Snow Leopard Check Out Problems

[Andreas Prlic]

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 <dence at lsu.edu> 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
>
>
>
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