[Biojava-dev] Structures test failures

[Steve Darnell]

Jules,

Thanks for the suggestion.  In the interim, I was able to work around my
Eclipse and svn problems.  It's not a fully integrated solution, but it
works.

The Subclipse svn plug-in from Tigris would fail during checkout with an
exception stating "RA layer request failed svn: REPORT of '[...]' 200
OK" for both Windows 7 and OSX 10.6.  For Windows, there are reports of
the Windows indexing service, antivirus scanners, or the Subclipse
JavaHL adapter causing svn problems.  Resolving these issues did not
help.

In the end, I used a git client on Windows to clone the biojava project
from github and then imported it into Eclipse as an existing Maven
project with the m2eclipse plug-in.  I was able to successfully build
and install biojava3-structure and its dependencies without test
failures.


To the list,

If anyone has had similar problems setting up Eclispe, I would be
grateful to hear how you resolved the problem.  If not, my solution is
good enough for now.

Regards,
Steve

-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org
[mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of Jules
Jacobsen
Sent: Tuesday, August 24, 2010 7:41 AM
To: biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] Structures test failures

Hi Steve,

Unless you're a staunch Eclipse user I can recommend Netbeans for maven 
as it works very well with it. One issue I've had is that Netbeans 6.9 
is generally slower and more cumbersome than 6.8, worse still 6.9.1 
seems incapable of connecting to the repository at all. So stick with 
6.8 and it should be fine.

I can confirm that the most recent dev version of biojava-structure does

not fail any tests, although I just tried checking out the read-only 
public version from svn://code.open-bio.org/biojava/biojava-live/trunk 
and encountered a 'rev-props' error and now I'm unable to connect at
all...

Your error isn't likely to be maven related - if everything else ran 
fine it's probably just that you have an out-of date version of the 
source as the structure module is independent of the other modules, but 
I can't tell for sure without seeing the error messages produced by the 
failed tests.

Regards,

Jules

On 23/08/2010 17:21, Steve Darnell wrote:
> Greetings,
>
> I am attempting to build biojava from the anonymous svn server at
> github; I cannot even connect to the anonymous svn server at open-bio.
> I am unable to package/install the structure module and I suspect it
is
> caused by two failures that occur in the unit tests:
>
> Failed tests:
>    testOldSecOutput(org.biojava.bio.structure.TestSECalignment)
>
testParsePairs(org.biojava.bio.structure.align.TestAlignDBSearchPairs)
>
> Tests run: 61, Failures: 2, Errors: 0, Skipped: 0
>
> The build log has no indication that the structure module was packaged
> or installed.
>
> I have yet to configure Eclipse to build biojava, so this is how I
> attempted to build it on the command line:
>
> $ svn co http://svn.github.com/biojava/biojava.git ./biojava
> $ cd biojava
> $ mvn clean install>  biojava.log&  tail -f biojava.log
> $ cd ~/.m2/repository/org/biojava
> $ ls
> % alignment
> % biojava
> % biojava3-alignment
> % biojava3-core
> % biojava3-phylo
> % blast
> % bytecode
> % core
>
> I am new to maven, so it is likely I am overlooking something obvious.
> I have reproduced this outcome on OSX 10.6.4 and Ubuntu 10.04.  I
would
> appreciate any suggestions that the dev list might have.
>
> Best regards,
> Steve Darnell
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
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