Imported io-lib, a Staden library

[Charles Plessy-12]

Le Tue, Jul 08, 2008 at 04:55:32PM +0100, James Bonfield a écrit :
> Maybe I should just give up and embrace the libtool abomination like
> the rest of the planet! It probably now works properly on the few
> remaining systems that anyone still supports.

Hello,

I posted a very naive patch for this on sourceforge. I would like to
apply something like this for Debian, so that I can then dynamically
link other programs (such as srf.sourceforge.net) againt libread.

https://sourceforge.net/tracker/index.php?func=detail&aid=2082376&group_id=100316&atid=627060

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan


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[Charles Plessy-12]

Le Tue, Jul 08, 2008 at 02:07:58PM +0100, James Bonfield a écrit :
>
> Agreed on the io_lib name too - it's pretty atrocious, but I'm
> assuming the name was picked (it predates my work on it) as it was
> originally just an internal part of a larger package and not
> distributed separately.

Hello again,

I just realised while browsing the WWW that in Fedora libread was
renamed libstaden-read.

http://rpmfind.net/linux/RPM/fedora/updates/testing/8/x86_64/staden-io_lib-devel-1.11.2.1-2.fc8.i386.html

What is your opinion about this name. Would you agree if we used the
same in Debian ?

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan


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[James Bonfield]

On Fri, Aug 29, 2008 at 10:04:39PM +0900, Charles Plessy wrote:
> I just realised while browsing the WWW that in Fedora libread was
> renamed libstaden-read.
>
> http://rpmfind.net/linux/RPM/fedora/updates/testing/8/x86_64/staden-io_lib-devel-1.11.2.1-2.fc8.i386.html
>
> What is your opinion about this name. Would you agree if we used the
> same in Debian ?

That's not a bad idea. The existing name is hideous frankly and it's
just "getting around to it" that's prevented me picking something
else. libstaden-read I like as it has a namespace I can use for others too.

James

--
James Bonfield (jkb@...) | Hora aderat briligi. Nunc et Slythia Tova
                                  | Plurima gyrabant gymbolitare vabo;
  A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi.


--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.


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[Andreas Tille]

On Fri, 29 Aug 2008, James Bonfield wrote:

> On Fri, Aug 29, 2008 at 10:04:39PM +0900, Charles Plessy wrote:
>> I just realised while browsing the WWW that in Fedora libread was
>> renamed libstaden-read.
>>
>> http://rpmfind.net/linux/RPM/fedora/updates/testing/8/x86_64/staden-io_lib-devel-1.11.2.1-2.fc8.i386.html
>>
>> What is your opinion about this name. Would you agree if we used the
>> same in Debian ?
>
> That's not a bad idea. The existing name is hideous frankly and it's
> just "getting around to it" that's prevented me picking something
> else. libstaden-read I like as it has a namespace I can use for others too.

When I read the first mail of Charles I've thought "Oh no, not 'libread'".
So I really agree with libstaden-read and it is good to know that other
distributors tried a reasonable rename.  Lets try to stick compatible with
these - and perhaps we could release this upstream soon.

Kind regards

         Andreas.

--
http://fam-tille.de


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[Tim Cutts]

On 2 Sep 2008, at 10:50 am, Andreas Tille wrote:

> On Fri, 29 Aug 2008, James Bonfield wrote:
>
>> On Fri, Aug 29, 2008 at 10:04:39PM +0900, Charles Plessy wrote:
>>> I just realised while browsing the WWW that in Fedora libread was
>>> renamed libstaden-read.
>>>
>>> http://rpmfind.net/linux/RPM/fedora/updates/testing/8/x86_64/staden-io_lib-devel-1.11.2.1-2.fc8.i386.html
>>>
>>> What is your opinion about this name. Would you agree if we used the
>>> same in Debian ?
>>
>> That's not a bad idea. The existing name is hideous frankly and it's
>> just "getting around to it" that's prevented me picking something
>> else. libstaden-read I like as it has a namespace I can use for  
>> others too.
>
> When I read the first mail of Charles I've thought "Oh no, not  
> 'libread'".
> So I really agree with libstaden-read and it is good to know that  
> other
> distributors tried a reasonable rename.  Lets try to stick  
> compatible with
> these - and perhaps we could release this upstream soon.

Wow - stop the presses.  Everyone agrees with each other.  This has to  
be some sort of record in any Debian-related community.  :-)

Oh, and for the record, libstaden-read gets the thumbs up from me, too.

Tim


--
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 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.


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[Charles Plessy-12]

Le Tue, Sep 02, 2008 at 01:37:09PM +0100, Tim Cutts a écrit :
>
> Wow - stop the presses.  Everyone agrees with each other.  This has to  
> be some sort of record in any Debian-related community.  :-)

Hmmm, this goes too well. Here is a licence issue to syphon this
enthousiasm ;)

In the latest versions I noticed that the following files:
open_trace_file.c and sff.c, contain portions of code that have the
following licenses:

/*
 * Portions of this code have been derived from 454 Life Sciences Corporation's
 * getsff.c code (specifically the WriteSFFFile function.
 * It bears the following copyright notice:
 *
 * ------------------------------------------------------------
 * Copyright (c)[2001-2005] 454 Life Sciences Corporation. All Rights Reserved.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 *
 * IN NO EVENT SHALL LICENSOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE.
 * ------------------------------------------------------------
 *
 * The remainder is Copyright Genome Research Limited (GRL) and is also
 * provided "AS IS" without warranty.
 */


/*
 * 454 sorted format (.srt) index searching for SFF files.
 * Uses a binary search.
 * This function and getuint4_255 above are taken with permission
 * from 454's getsff.c with the following licence:
 *
 * Copyright (c)[2001-2005] 454 Life Sciences Corporation. All Rights Reserved.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 *
 * IN NO EVENT SHALL LICENSOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE.
 */


I am affraid that our archive administrators will object that this licence
does not give the right to redistribute (not to mention to copy and modify),
and that there is no sign that the permission given to the upstream authors is
also given to Debian. If my worries are justified, is it possible to clarify
this with 454 Life Sciences Corporation?


This issue will leave us some time to polish the package. I will commit
tomorrow an update in our SVN that provides a dynamic library, but I did not
manage to get the soname right.

Have a nice day,


--
Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan


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[James Bonfield]

On Tue, Sep 02, 2008 at 11:08:09PM +0900, Charles Plessy wrote:
> I am affraid that our archive administrators will object that this licence
> does not give the right to redistribute (not to mention to copy and modify),
> and that there is no sign that the permission given to the upstream authors is
> also given to Debian. If my worries are justified, is it possible to clarify
> this with 454 Life Sciences Corporation?

Well spotted. I searched back through my email where I asked if I may
use this code (the SFF format had feedback from many people, including
myself, but at least I did take the effort to check that the code to
read it was public). I had a response of "Feel free to take the code
from getsff.c to support the sorted index. There are no licensing
restrictions on that source code." from Jim Knight at 454.com.

I'll contact him again to clarify the redistribution, copy and
modification clauses.

James

--
James Bonfield (jkb@...) | Hora aderat briligi. Nunc et Slythia Tova
                                  | Plurima gyrabant gymbolitare vabo;
  A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi.


--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.


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