[Biojava-dev] build problem

[Andreas Prlic]

That seems like a very long time... on the automated build server the
times look like below:

If the structure module takes so much time, I wonder if you are behind
a very slow network? Some of the junit tests fetch PDB files from a
public ftp server and I wonder if there is a networking issue. Having
said this, the two slowest modules are structure and protmod. We will
try to cut down the time spent on those tests...

Andreas


INFO] biojava ............................................... SUCCESS [21.430s]
[INFO] bytecode .............................................. SUCCESS [44.778s]
[INFO] core .................................................. SUCCESS
[4:54.691s]
[INFO] alignment ............................................. SUCCESS [48.048s]
[INFO] blast ................................................. SUCCESS
[1:20.263s]
[INFO] biojava3-structure .................................... SUCCESS
[8:12.412s]
[INFO] das ................................................... SUCCESS
[1:13.103s]
[INFO] sequence .............................................. SUCCESS [18.176s]
[INFO] sequence-core ......................................... SUCCESS [47.424s]
[INFO] sequence-rna .......................................... SUCCESS [28.770s]
[INFO] sequence-biosql ....................................... SUCCESS [47.032s]
[INFO] sequence-fasta ........................................ SUCCESS [29.075s]
[INFO] sequence-blastxml ..................................... SUCCESS [44.392s]
[INFO] sequencing ............................................ SUCCESS [49.520s]
[INFO] phylo ................................................. SUCCESS [48.459s]
[INFO] biosql ................................................ SUCCESS [57.503s]
[INFO] gui ................................................... SUCCESS [58.610s]
[INFO] biojava3-core ......................................... SUCCESS
[1:05.398s]
[INFO] biojava3-phylo ........................................ SUCCESS [46.623s]
[INFO] biojava3-structure-gui ................................ SUCCESS
[1:06.737s]
[INFO] biojava3-alignment .................................... SUCCESS [54.682s]
[INFO] biojava3-genome ....................................... SUCCESS [49.844s]
[INFO] biojava3-protmod ...................................... SUCCESS
[10:05.171s]
[INFO] biojava3-ws ........................................... SUCCESS [44.379s]


On Mon, Aug 9, 2010 at 1:52 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
> 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
>>---------------------------------------------------
>>--------------------
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------