Re: [Savannah-hackers] submission of BioDB - savannah.nongnu.org

[Dan Bolser]

Sorry for the delay, the gcc upgrade that I needed in order to get java
compiling properly caused a total software meltdown on my system (I fouled
up the deps for that upgrade).

Anyway, I have upgraded my whole system (as I couldn't work out how to
recover), and naturally enough, the new system had some teething
problems...

Anyway, I am going to try compiling the code with gcc again soon, so
please give me a bit more time on that.

All the best,
Dan.

On Tue, 2 Nov 2004, Michael Casadevall wrote:

>I haven't gotten any messages from you for over a week, so please 
>contact me ASAP. I'm going to remove your project registration if I 
>don't hear back from you, but you can reregister it after that point.
>Michael
>
>On Oct 24, 2004, at 10:42 AM, Michael Casadevall wrote:
>
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>> MySQL is dual licensed, and it's GPL license makes it free, so you can 
>> use it as a dependency.
>> Michael
>>
>> On Oct 24, 2004, at 10:30 AM, Dan Bolser wrote:
>>
>>>
>>> Thanks very much, this is all clear now.
>>>
>>> Is MySQL free software?
>>>
>>> Cheers,
>>> Dan.
>>>
>>> On Sat, 23 Oct 2004, Michael Casadevall wrote:
>>>
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>>>> The requirements for Savannah hosting for Java projects is that the
>>>> project must be free software and be licensed under a GPL-compatiable
>>>> license, and that everything the project requires can be used in a 
>>>> free
>>>> environment. Sun's Java license does not constitute a free (as in
>>>> speech) license. Basically, you must be able to compile and install 
>>>> in
>>>> a free environment. This also includes all JAR files your project 
>>>> uses.
>>>> If you can't compile the dependencies, error reports should be sent 
>>>> to
>>>> both the GCJ and the project's administrators.
>>>> Michael
>>>>
>>>> On Oct 23, 2004, at 1:36 PM, Dan Bolser wrote:
>>>>
>>>>>
>>>>> I think I emailed you the src code (for building the SCOP
>>>>> database) already?
>>>>>
>>>>> I have a question about the .jar files included with the Prova
>>>>> installation (not necessarily essential for this project). 
>>>>> Basically I
>>>>> would like to know if each .jar is OK to use at Savannah, i.e. if 
>>>>> it is
>>>>> 'free software'...
>>>>>
>>>>> Aside from looking for these (or equivalent) .jar files under the
>>>>> Classpath project, is there a way to rapidly determine if the
>>>>> dependencies
>>>>> are free software or not? i.e. compatible for use with a Savannah
>>>>> project
>>>>> or not?
>>>>>
>>>>> I count 84 .jar files in total, including...
>>>>>
>>>>> ant.jar
>>>>> commons-collections-2.1.jar
>>>>> junit-3.8.1.jar
>>>>> biojava.jar
>>>>> j2ssh-core.jar
>>>>> jade.jar
>>>>> jms.jar
>>>>> joram.jar
>>>>> mandarax.jar
>>>>>
>>>>> Given what you have said below, would I have to check that every 
>>>>> piece
>>>>> of
>>>>> java code packaged with the project is compile-able using GCJ and
>>>>> runnable
>>>>> under Kaffe (or equivalent free JVM)?
>>>>>
>>>>> Also I would like to know about how to deal with GCJ compile 
>>>>> problems.
>>>>> Should I report the problem to the specific code vendor 
>>>>> (org/mandarax
>>>>> in
>>>>> this case) or to GCJ mailing lists?
>>>>>
>>>>> Thanks very much for your help, and sorry for my lack of experience 
>>>>> in
>>>>> these issues,
>>>>>
>>>>> All the best,
>>>>> Dan.
>>>>>
>>>>> On Tue, 19 Oct 2004, Michael McTails wrote:
>>>>>
>>>>>> I'm evaluating the project you submitted for approval in Savannah.
>>>>>>
>>>>>> You must determine whether your project and it's dependencies
>>>>>> can run on a Free Software Java suite (see
>>>>>> http://www.gnu.org/software/java/
>>>>>> for more information).
>>>>>>
>>>>>> We recommend you to test your project using GCJ and GNU Classpath, 
>>>>>> and
>>>>>> ensure that your Java code runs on this Free Software Java suite.
>>>>>>
>>>>>> GCJ is the GNU Compiler for Java, part of the GCC (GNU Compiler
>>>>>> Collection).  The Classpath project aims to develop a free and
>>>>>> portable
>>>>>> implementation of the Java API (the classes in the 'java' package).
>>>>>>
>>>>>> More information is available at http://gcc.gnu.org/ and
>>>>>> http://www.gnu.org/software/classpath/,
>>>>>>
>>>>>> Furthermore, please include an (perhaps temporary)
>>>>>> URL pointing to the source code. We wish to review your source 
>>>>>> code,
>>>>>> even if it is not functional, to catch potential legal issues 
>>>>>> early.
>>>>>> The description you gave whenregistering will not be read by the
>>>>>> general public.
>>>>>> If you are still concerned with privacy, however, you can forward 
>>>>>> the
>>>>>> code to me by email
>>>>>> address@hidden
>>>>>>
>>>>>> Please provide us with more information about this point.
>>>>>>
>>>>>>> A package was submitted to savannah.nongnu.org
>>>>>>> This mail was sent to address@hidden,
>>>>>>> address@hidden
>>>>>>>
>>>>>>>
>>>>>>> Dan Bolser <address@hidden> described the package as
>>>>>>> follows:
>>>>>>> License: gpl
>>>>>>> Other License:
>>>>>>> Package: BioDB
>>>>>>> System name: biodb
>>>>>>> Type: non-GNU
>>>>>>>
>>>>>>> Description:
>>>>>>> This project aims to produce very simple software to produce and
>>>>>>> maintain a set
>>>>>>> of biological databases in relational form. The software will
>>>>>>> download
>>>>>>> text
>>>>>>> versions of various databases, and produce a 'standardized'
>>>>>>> relational
>>>>>>> version
>>>>>>> of that database in tab delimited form, suitable for loading into 
>>>>>>> any
>>>>>>> relational database system (such as mysql).
>>>>>>>
>>>>>>> The standard versions of these databases can then form components 
>>>>>>> of
>>>>>>> other
>>>>>>> projects.
>>>>>>>
>>>>>>> First, the SCOP databases will be 'processed'
>>>>>>> (http://scop.mrc-lmb.cam.ac.uk/scop/) which is open access.
>>>>>>>
>>>>>>> We will then consider looking at ENZYME
>>>>>>> (http://www.expasy.org/enzyme/),
>>>>>>> SwissProt (http://us.expasy.org/sprot/) and GO
>>>>>>> (http://www.geneontology.org/),
>>>>>>> based on the evaluation of the licence.
>>>>>>>
>>>>>>> Initally Perl will be used.
>>>>>>>
>>>>>>> This rather simple project may form a test bed for the new
>>>>>>> experimental
>>>>>>> software language, Prova.
>>>>>>> http://osdn.dl.sourceforge.net/sourceforge/mandarax/
>>>>>>> prova_all_1.7.1.zip
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Other Software Required:
>>>>>>> Mandarax (http://mandarax.sourceforge.net/)
>>>>>>> Prova (http://comas.soi.city.ac.uk/prova/)
>>>>>>>
>>>>>>> Other Comments:
>>>>>>> I previously submitted this project some time last year. SCOP is
>>>>>>> freely
>>>>>>> available and open source (the old licence has elapsed). Prova is
>>>>>>> LPGL. The
>>>>>>> code is trivial.
>>>>>
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