Snow Leopard Check Out Problems

[Daniel D Ence]

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  -  Biojava-l@...
http://lists.open-bio.org/mailman/listinfo/biojava-l

[Andreas Prlic-3]

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@...> 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  -  Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

_______________________________________________
Biojava-l mailing list  -  Biojava-l@...
http://lists.open-bio.org/mailman/listinfo/biojava-l

[Daniel D Ence]

I tried it again, after verifying that gzip and tar were installed on the system, and it worked this time.

Thanks for the suggestions though.


Daniel Ence

_______________________________________________
Biojava-l mailing list  -  Biojava-l@...
http://lists.open-bio.org/mailman/listinfo/biojava-l