[Biojava-dev] build problem

Mon Aug 9 22:20:27 UTC 2010

Here is my summary and some of the timings are pretty good (simple HP laptop with a dual core):

------------------------------------------------------------------------
Reactor Summary:
------------------------------------------------------------------------
biojava ............................................... SUCCESS [3.820s]
bytecode .............................................. SUCCESS [6.022s]
core .................................................. SUCCESS [52.822s]
alignment ............................................. SUCCESS [4.332s]
blast ................................................. SUCCESS [27.453s]
biojava3-structure .................................... SUCCESS [7:33.228s]
das ................................................... SUCCESS [18.456s]
sequence .............................................. SUCCESS [0.122s]
sequence-core ......................................... SUCCESS [3.974s]
sequence-rna .......................................... SUCCESS [0.313s]
sequence-biosql ....................................... SUCCESS [2.735s]
sequence-fasta ........................................ SUCCESS [0.324s]
sequence-blastxml ..................................... SUCCESS [3.339s]
sequencing ............................................ SUCCESS [5.637s]
phylo ................................................. SUCCESS [5.084s]
biosql ................................................ SUCCESS [6.344s]
gui ................................................... SUCCESS [6.552s]
biojava3-core ......................................... SUCCESS [8.477s]
biojava3-phylo ........................................ SUCCESS [3.596s]
biojava3-structure-gui ................................ SUCCESS [8.283s]
biojava3-alignment .................................... SUCCESS [6.002s]
biojava3-genome ....................................... SUCCESS [3.933s]
biojava3-protmod ...................................... SUCCESS [8:59.048s]
biojava3-ws ........................................... SUCCESS [1.367s]
------------------------------------------------------------------------
------------------------------------------------------------------------
BUILD SUCCESSFUL
------------------------------------------------------------------------
Total time: 19 minutes 33 seconds
Finished at: Mon Aug 09 13:48:00 PDT 2010
Final Memory: 116M/363M
------------------------------------------------------------------------

The long time comes apparently from fetching all these files. I tried the build last week on a different network after removing the faulty test as suggested by Scott and I had similar timing. This could be an issue with NetBeans in fact. If someone has experienced such long delays, it would be interesting to know in which conditions this occurred.

Thanks again,

George

>----- ------- Original Message ------- -----
>From: Andreas Prlic <andreas at sdsc.edu>
>To: George Waldon <gwaldon at geneinfinity.org>
>Sent: Mon, 9 Aug 2010 14:27:27
>
>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.Multipl
>eA
>>>lignmentTest:
>>>>
>>>> Fetching
>>>ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/p
>db
>>>/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/p
>db
>>>/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.downlo
>ad
>>>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
>---------------------------------------------------
>--------------------