[Biojava-dev] build problem

[George Waldon]

Thanks to all for the fixing.

The build took 19 minutes and 33 seconds, of which 16 min and 32 s were for the structure modules! This sounds a bit long to me. Is-this expected?

George

>----- ------- Original Message ------- -----
>From: Andreas Prlic <andreas at sdsc.edu>
>To: George Waldon <gwaldon at geneinfinity.org>
>Sent: Mon, 9 Aug 2010 12:35:56
>
>If you update the class, this should be fixed now.
>Was a problem with
>a hard coded /tmp path...
>
>Andreas
>
>
>
>On Mon, Aug 9, 2010 at 12:26 PM, George Waldon
><gwaldon at geneinfinity.org> wrote:
>> Hi,
>>
>> I am getting the following failures in
>org.biojava.bio.structure.align.benchmark.MultipleA
>lignmentTest:
>>
>> Fetching
>ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb
>/pdb1hcy.ent.gz
>> writing to \tmp\hc\pdb1hcy.ent.gz
>> java.io.FileNotFoundException:
>\tmp\hc\pdb1hcy.ent.gz (The system cannot find the
>path specified)
>> ...
>>
>> and
>>
>> Fetching
>ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb
>/pdb1nls.ent.gz
>> writing to \tmp\nl\pdb1nls.ent.gz
>> java.io.FileNotFoundException:
>\tmp\nl\pdb1nls.ent.gz (The system cannot find the
>path specified)
>> at java.io.FileOutputStream.open(Native Method)
>> at
>java.io.FileOutputStream.<init>(FileOutputStream.ja
>va:179)
>> at
>java.io.FileOutputStream.<init>(FileOutputStream.ja
>va:131)
>> at
>org.biojava.bio.structure.io.PDBFileReader.download
>PDB(PDBFileReader.java:430)
>> ...
>>
>> Does anyone has a solution for this? I am
>building from within NetBeans.
>>
>> Thanks,
>> George
>>
>
>
>
>-- 
>---------------------------------------------------
>--------------------
>Dr. Andreas Prlic
>Senior Scientist, RCSB PDB Protein Data Bank
>University of California, San Diego
>(+1) 858.246.0526
>---------------------------------------------------
>--------------------