From lennart at karssen.org  Tue Apr  2 18:29:15 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Tue, 02 Apr 2013 18:29:15 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <515446DC.6040602@karssen.org>
References: <515446DC.6040602@karssen.org>
Message-ID: <515B075B.4080502@karssen.org>

Dear list,

As I didn't get any comments to dissuade me, I've just committed a
change that sets the default behaviour of export.plink() in GenABEL to
export .tped/.tfam files. This works around bug #2055.


Best,

Lennart.

On 28/03/13 14:34, L.C. Karssen wrote:
> Dear list,
> 
> We recently got bitten by bug #2055 (ref [1]) in GenABEL's
> export.plink() again. Data was exported to .ped format and everything
> seemed to have gone well, however, we later found out that the exported
> genotypes were wrong. Exporting to .tped (export.plink(...,
> transpose=TRUE)) worked fine.
> 
> I think we should change the default for the transpose option to TRUE
> and add a warning in case someone sets it to FALSE. I'm of course
> willing to write the necessary code.
> At least this will safeguard the users from this problem until the
> actual bug is fixed.
> 
> What are you're thoughts on this?
> 
> 
> Best,
> 
> Lennart.
> 
> [1]
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
> 
> lennart at karssen.org
> http://blog.karssen.org
> 
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
> 
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From mgmaria at yandex.ru  Wed Apr  3 11:58:23 2013
From: mgmaria at yandex.ru (Maria G)
Date: Wed, 03 Apr 2013 13:58:23 +0400
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <515B075B.4080502@karssen.org>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
Message-ID: <84251364983103@web2f.yandex.ru>

Dear Lennart,

that's really helpful, thank you! 

Does it mean I have to update the version of GenABEL to get read of the bug? Which version is fine?


best
Mariya

02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
> Dear list,
>
> As I didn't get any comments to dissuade me, I've just committed a
> change that sets the default behaviour of export.plink() in GenABEL to
> export .tped/.tfam files. This works around bug #2055.
>
> Best,
>
> Lennart.
>
> On 28/03/13 14:34, L.C. Karssen wrote:
>
>> ?Dear list,
>>
>> ?We recently got bitten by bug #2055 (ref [1]) in GenABEL's
>> ?export.plink() again. Data was exported to .ped format and everything
>> ?seemed to have gone well, however, we later found out that the exported
>> ?genotypes were wrong. Exporting to .tped (export.plink(...,
>> ?transpose=TRUE)) worked fine.
>>
>> ?I think we should change the default for the transpose option to TRUE
>> ?and add a warning in case someone sets it to FALSE. I'm of course
>> ?willing to write the necessary code.
>> ?At least this will safeguard the users from this problem until the
>> ?actual bug is fixed.
>>
>> ?What are you're thoughts on this?
>>
>> ?Best,
>>
>> ?Lennart.
>>
>> ?[1]
>> ?https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
>> ?--
>> ?-----------------------------------------------------------------
>> ?L.C. Karssen
>> ?Utrecht
>> ?The Netherlands
>>
>> ?lennart at karssen.org
>> ?http://blog.karssen.org
>>
>> ?Stuur mij aub geen Word of Powerpoint bestanden!
>> ?Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>> ?------------------------------------------------------------------
>>
>> ?_______________________________________________
>> ?genabel-devel mailing list
>> ?genabel-devel at lists.r-forge.r-project.org
>> ?https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
> ,
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

From yurii.aulchenko at gmail.com  Wed Apr  3 12:19:50 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 3 Apr 2013 12:19:50 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <84251364983103@web2f.yandex.ru>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
Message-ID: <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>

Hi Maria,

if my understanding is correct, the fix is now only in the devel-version on
SVN - so you would need to export and build package if you really want it
(see http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).

But the 'fix' is very simple (and is not actually fixing anything - just
trying to avoid confusion!): the default option now is set to
'transpose=TRUE'. So you can simply set this up manually when calling
'export.plink' :)

Yurii


On Wed, Apr 3, 2013 at 11:58 AM, Maria G <mgmaria at yandex.ru> wrote:

> Dear Lennart,
>
> that's really helpful, thank you!
>
> Does it mean I have to update the version of GenABEL to get read of the
> bug? Which version is fine?
>
>
> best
> Mariya
>
> 02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
> > Dear list,
> >
> > As I didn't get any comments to dissuade me, I've just committed a
> > change that sets the default behaviour of export.plink() in GenABEL to
> > export .tped/.tfam files. This works around bug #2055.
> >
> > Best,
> >
> > Lennart.
> >
> > On 28/03/13 14:34, L.C. Karssen wrote:
> >
> >>  Dear list,
> >>
> >>  We recently got bitten by bug #2055 (ref [1]) in GenABEL's
> >>  export.plink() again. Data was exported to .ped format and everything
> >>  seemed to have gone well, however, we later found out that the exported
> >>  genotypes were wrong. Exporting to .tped (export.plink(...,
> >>  transpose=TRUE)) worked fine.
> >>
> >>  I think we should change the default for the transpose option to TRUE
> >>  and add a warning in case someone sets it to FALSE. I'm of course
> >>  willing to write the necessary code.
> >>  At least this will safeguard the users from this problem until the
> >>  actual bug is fixed.
> >>
> >>  What are you're thoughts on this?
> >>
> >>  Best,
> >>
> >>  Lennart.
> >>
> >>  [1]
> >>
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
> >>  --
> >>  -----------------------------------------------------------------
> >>  L.C. Karssen
> >>  Utrecht
> >>  The Netherlands
> >>
> >>  lennart at karssen.org
> >>  http://blog.karssen.org
> >>
> >>  Stuur mij aub geen Word of Powerpoint bestanden!
> >>  Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> >>  ------------------------------------------------------------------
> >>
> >>  _______________________________________________
> >>  genabel-devel mailing list
> >>  genabel-devel at lists.r-forge.r-project.org
> >>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >
> > --
> > -----------------------------------------------------------------
> > L.C. Karssen
> > Utrecht
> > The Netherlands
> >
> > lennart at karssen.org
> > http://blog.karssen.org
> >
> > Stuur mij aub geen Word of Powerpoint bestanden!
> > Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> > ------------------------------------------------------------------
> >
> > ,
> > _______________________________________________
> > genabel-devel mailing list
> > genabel-devel at lists.r-forge.r-project.org
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From mgmaria at yandex.ru  Wed Apr  3 12:52:30 2013
From: mgmaria at yandex.ru (Maria G)
Date: Wed, 03 Apr 2013 14:52:30 +0400
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
Message-ID: <175661364986350@web10f.yandex.ru>

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From lennart at karssen.org  Wed Apr  3 13:20:32 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 03 Apr 2013 13:20:32 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
Message-ID: <515C1080.9010606@karssen.org>

Hi Yurii, Maria,

Indeed, this is more a workaround than a fix. I think we communicated
this simple workaround in the past, but I agree with Maria we should
either announce it more widely, or, probably better push a new GenABEL
release to CRAN (for those people who don't read the announcements :-)).

Yurii, what do you think? One the one hand it is not urgent (we've been
living with this bug for a while) on the other hand, the present
situation is a dangerous one... Are there any developments in GenABEL
SVN that are not ready for publishing yet?


Best,

Lennart.

On 04/03/2013 12:19 PM, Yurii Aulchenko wrote:
> Hi Maria,
> 
> if my understanding is correct, the fix is now only in the devel-version on
> SVN - so you would need to export and build package if you really want it
> (see http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).
> 
> But the 'fix' is very simple (and is not actually fixing anything - just
> trying to avoid confusion!): the default option now is set to
> 'transpose=TRUE'. So you can simply set this up manually when calling
> 'export.plink' :)
> 
> Yurii
> 
> 
> On Wed, Apr 3, 2013 at 11:58 AM, Maria G <mgmaria at yandex.ru> wrote:
> 
>> Dear Lennart,
>>
>> that's really helpful, thank you!
>>
>> Does it mean I have to update the version of GenABEL to get read of the
>> bug? Which version is fine?
>>
>>
>> best
>> Mariya
>>
>> 02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
>>> Dear list,
>>>
>>> As I didn't get any comments to dissuade me, I've just committed a
>>> change that sets the default behaviour of export.plink() in GenABEL to
>>> export .tped/.tfam files. This works around bug #2055.
>>>
>>> Best,
>>>
>>> Lennart.
>>>
>>> On 28/03/13 14:34, L.C. Karssen wrote:
>>>
>>>>  Dear list,
>>>>
>>>>  We recently got bitten by bug #2055 (ref [1]) in GenABEL's
>>>>  export.plink() again. Data was exported to .ped format and everything
>>>>  seemed to have gone well, however, we later found out that the exported
>>>>  genotypes were wrong. Exporting to .tped (export.plink(...,
>>>>  transpose=TRUE)) worked fine.
>>>>
>>>>  I think we should change the default for the transpose option to TRUE
>>>>  and add a warning in case someone sets it to FALSE. I'm of course
>>>>  willing to write the necessary code.
>>>>  At least this will safeguard the users from this problem until the
>>>>  actual bug is fixed.
>>>>
>>>>  What are you're thoughts on this?
>>>>
>>>>  Best,
>>>>
>>>>  Lennart.
>>>>
>>>>  [1]
>>>>
>> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
>>>>  --
>>>>  -----------------------------------------------------------------
>>>>  L.C. Karssen
>>>>  Utrecht
>>>>  The Netherlands
>>>>
>>>>  lennart at karssen.org
>>>>  http://blog.karssen.org
>>>>
>>>>  Stuur mij aub geen Word of Powerpoint bestanden!
>>>>  Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>>  ------------------------------------------------------------------
>>>>
>>>>  _______________________________________________
>>>>  genabel-devel mailing list
>>>>  genabel-devel at lists.r-forge.r-project.org
>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>
>>> --
>>> -----------------------------------------------------------------
>>> L.C. Karssen
>>> Utrecht
>>> The Netherlands
>>>
>>> lennart at karssen.org
>>> http://blog.karssen.org
>>>
>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>> ------------------------------------------------------------------
>>>
>>> ,
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
> 
> 
> 
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 


-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Wed Apr  3 13:20:29 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 3 Apr 2013 13:20:29 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <175661364986350@web10f.yandex.ru>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <175661364986350@web10f.yandex.ru>
Message-ID: <CAHX9t6KyiejRvnErAgH6S+bP5W7+mTBvAscga_3CPQVsurxErA@mail.gmail.com>

On Wed, Apr 3, 2013 at 12:52 PM, Maria G <mgmaria at yandex.ru> wrote:

>  Hi Yurii
>
> 03.04.2013, 14:19, "Yurii Aulchenko" <yurii.aulchenko at gmail.com>:
>
> Hi Maria,
>
> if my understanding is correct, the fix is now only in the devel-version
> on SVN - so you would need to export and build package if you really want
> it (see
> http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).
>
>
>
>
>
> But the 'fix' is very simple (and is not actually fixing anything - just
> trying to avoid confusion!): the default option now is set to
> 'transpose=TRUE'. So you can simply set this up manually when calling
> 'export.plink' :)
>
>
> yes, sure :)
> I was just also thinking about other users - How would you let everybody
> now about the simple way to 'fix'?
>
>

Good question. I am not sure this particular fix justifies wider
announcement, but in general, there are several ways we inform people about
new things:

If a bug was discussed on forum we probably need to update the topic.

Bigger things are announced as news on www.genabel.org.

We used to also put announcement as a 'sticky topic' on the forum (top
topic - 'GenABEL/ProbABEL announcements') - but I think somehow it is not
quite used.

The last way of cause is if people hang on the devel-list :)

I think everybody would benefit if someone would volunteer to update
news/announcements more systematically (now only bigger things get
occasionally in, when me or Lennart get time to put together a news story).

best wishes,
Yurii
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From yurii.aulchenko at gmail.com  Wed Apr  3 13:23:56 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 3 Apr 2013 13:23:56 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <515C1080.9010606@karssen.org>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
Message-ID: <CAHX9t6J16qok+jQ+prpxYTvGQVF+_QD4Mjt5z=bV+jxUNPeBag@mail.gmail.com>

In theory I agree :)

In practice submitting to CRAN takes from 4 hours to a full day, so I
personally would not like to submit unless strictly necessary.

As for this particular fix - I expect some more code changes still this
week, so if we decide to publish on CRAN I would wait till next week.

best wishes,
YA

On Wed, Apr 3, 2013 at 1:20 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Hi Yurii, Maria,
>
> Indeed, this is more a workaround than a fix. I think we communicated
> this simple workaround in the past, but I agree with Maria we should
> either announce it more widely, or, probably better push a new GenABEL
> release to CRAN (for those people who don't read the announcements :-)).
>
> Yurii, what do you think? One the one hand it is not urgent (we've been
> living with this bug for a while) on the other hand, the present
> situation is a dangerous one... Are there any developments in GenABEL
> SVN that are not ready for publishing yet?
>
>
> Best,
>
> Lennart.
>
> On 04/03/2013 12:19 PM, Yurii Aulchenko wrote:
> > Hi Maria,
> >
> > if my understanding is correct, the fix is now only in the devel-version
> on
> > SVN - so you would need to export and build package if you really want it
> > (see
> http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).
> >
> > But the 'fix' is very simple (and is not actually fixing anything - just
> > trying to avoid confusion!): the default option now is set to
> > 'transpose=TRUE'. So you can simply set this up manually when calling
> > 'export.plink' :)
> >
> > Yurii
> >
> >
> > On Wed, Apr 3, 2013 at 11:58 AM, Maria G <mgmaria at yandex.ru> wrote:
> >
> >> Dear Lennart,
> >>
> >> that's really helpful, thank you!
> >>
> >> Does it mean I have to update the version of GenABEL to get read of the
> >> bug? Which version is fine?
> >>
> >>
> >> best
> >> Mariya
> >>
> >> 02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
> >>> Dear list,
> >>>
> >>> As I didn't get any comments to dissuade me, I've just committed a
> >>> change that sets the default behaviour of export.plink() in GenABEL to
> >>> export .tped/.tfam files. This works around bug #2055.
> >>>
> >>> Best,
> >>>
> >>> Lennart.
> >>>
> >>> On 28/03/13 14:34, L.C. Karssen wrote:
> >>>
> >>>>  Dear list,
> >>>>
> >>>>  We recently got bitten by bug #2055 (ref [1]) in GenABEL's
> >>>>  export.plink() again. Data was exported to .ped format and everything
> >>>>  seemed to have gone well, however, we later found out that the
> exported
> >>>>  genotypes were wrong. Exporting to .tped (export.plink(...,
> >>>>  transpose=TRUE)) worked fine.
> >>>>
> >>>>  I think we should change the default for the transpose option to TRUE
> >>>>  and add a warning in case someone sets it to FALSE. I'm of course
> >>>>  willing to write the necessary code.
> >>>>  At least this will safeguard the users from this problem until the
> >>>>  actual bug is fixed.
> >>>>
> >>>>  What are you're thoughts on this?
> >>>>
> >>>>  Best,
> >>>>
> >>>>  Lennart.
> >>>>
> >>>>  [1]
> >>>>
> >>
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
> >>>>  --
> >>>>  -----------------------------------------------------------------
> >>>>  L.C. Karssen
> >>>>  Utrecht
> >>>>  The Netherlands
> >>>>
> >>>>  lennart at karssen.org
> >>>>  http://blog.karssen.org
> >>>>
> >>>>  Stuur mij aub geen Word of Powerpoint bestanden!
> >>>>  Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> >>>>  ------------------------------------------------------------------
> >>>>
> >>>>  _______________________________________________
> >>>>  genabel-devel mailing list
> >>>>  genabel-devel at lists.r-forge.r-project.org
> >>>>
> >>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>>
> >>> --
> >>> -----------------------------------------------------------------
> >>> L.C. Karssen
> >>> Utrecht
> >>> The Netherlands
> >>>
> >>> lennart at karssen.org
> >>> http://blog.karssen.org
> >>>
> >>> Stuur mij aub geen Word of Powerpoint bestanden!
> >>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> >>> ------------------------------------------------------------------
> >>>
> >>> ,
> >>> _______________________________________________
> >>> genabel-devel mailing list
> >>> genabel-devel at lists.r-forge.r-project.org
> >>>
> >>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >> _______________________________________________
> >> genabel-devel mailing list
> >> genabel-devel at lists.r-forge.r-project.org
> >>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>
> >
> >
> >
> >
> >
> > _______________________________________________
> > genabel-devel mailing list
> > genabel-devel at lists.r-forge.r-project.org
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >
>
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From pirastu at burlo.trieste.it  Wed Apr  3 13:25:59 2013
From: pirastu at burlo.trieste.it (Nicola Pirastu)
Date: Wed, 3 Apr 2013 13:25:59 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <515C1080.9010606@karssen.org>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
Message-ID: <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>

Dear all,

how about we create a FAQ page on the website or on the forum as sticky topic?


I think we are missing one and this is one of those questions which are bound to come up every once in a while (together with "ProbABEL won't work with 1000G indels imputed with IMPUTE").


Best

Nicola



Il giorno 03/apr/2013, alle ore 13:20, "L.C. Karssen" <lennart at karssen.org> ha scritto:

> Hi Yurii, Maria,
> 
> Indeed, this is more a workaround than a fix. I think we communicated
> this simple workaround in the past, but I agree with Maria we should
> either announce it more widely, or, probably better push a new GenABEL
> release to CRAN (for those people who don't read the announcements :-)).
> 
> Yurii, what do you think? One the one hand it is not urgent (we've been
> living with this bug for a while) on the other hand, the present
> situation is a dangerous one... Are there any developments in GenABEL
> SVN that are not ready for publishing yet?
> 
> 
> Best,
> 
> Lennart.
> 
> On 04/03/2013 12:19 PM, Yurii Aulchenko wrote:
>> Hi Maria,
>> 
>> if my understanding is correct, the fix is now only in the devel-version on
>> SVN - so you would need to export and build package if you really want it
>> (see http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).
>> 
>> But the 'fix' is very simple (and is not actually fixing anything - just
>> trying to avoid confusion!): the default option now is set to
>> 'transpose=TRUE'. So you can simply set this up manually when calling
>> 'export.plink' :)
>> 
>> Yurii
>> 
>> 
>> On Wed, Apr 3, 2013 at 11:58 AM, Maria G <mgmaria at yandex.ru> wrote:
>> 
>>> Dear Lennart,
>>> 
>>> that's really helpful, thank you!
>>> 
>>> Does it mean I have to update the version of GenABEL to get read of the
>>> bug? Which version is fine?
>>> 
>>> 
>>> best
>>> Mariya
>>> 
>>> 02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
>>>> Dear list,
>>>> 
>>>> As I didn't get any comments to dissuade me, I've just committed a
>>>> change that sets the default behaviour of export.plink() in GenABEL to
>>>> export .tped/.tfam files. This works around bug #2055.
>>>> 
>>>> Best,
>>>> 
>>>> Lennart.
>>>> 
>>>> On 28/03/13 14:34, L.C. Karssen wrote:
>>>> 
>>>>> Dear list,
>>>>> 
>>>>> We recently got bitten by bug #2055 (ref [1]) in GenABEL's
>>>>> export.plink() again. Data was exported to .ped format and everything
>>>>> seemed to have gone well, however, we later found out that the exported
>>>>> genotypes were wrong. Exporting to .tped (export.plink(...,
>>>>> transpose=TRUE)) worked fine.
>>>>> 
>>>>> I think we should change the default for the transpose option to TRUE
>>>>> and add a warning in case someone sets it to FALSE. I'm of course
>>>>> willing to write the necessary code.
>>>>> At least this will safeguard the users from this problem until the
>>>>> actual bug is fixed.
>>>>> 
>>>>> What are you're thoughts on this?
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Lennart.
>>>>> 
>>>>> [1]
>>>>> 
>>> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
>>>>> --
>>>>> -----------------------------------------------------------------
>>>>> L.C. Karssen
>>>>> Utrecht
>>>>> The Netherlands
>>>>> 
>>>>> lennart at karssen.org
>>>>> http://blog.karssen.org
>>>>> 
>>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>>> ------------------------------------------------------------------
>>>>> 
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>> 
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>> 
>>>> --
>>>> -----------------------------------------------------------------
>>>> L.C. Karssen
>>>> Utrecht
>>>> The Netherlands
>>>> 
>>>> lennart at karssen.org
>>>> http://blog.karssen.org
>>>> 
>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>> ------------------------------------------------------------------
>>>> 
>>>> ,
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> 
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> 
> 
> 
> -- 
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
> 
> lennart at karssen.org
> http://blog.karssen.org
> 
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel


From lennart at karssen.org  Wed Apr  3 13:26:15 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 03 Apr 2013 13:26:15 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <CAHX9t6J16qok+jQ+prpxYTvGQVF+_QD4Mjt5z=bV+jxUNPeBag@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <CAHX9t6J16qok+jQ+prpxYTvGQVF+_QD4Mjt5z=bV+jxUNPeBag@mail.gmail.com>
Message-ID: <515C11D7.5040605@karssen.org>

On 04/03/2013 01:23 PM, Yurii Aulchenko wrote:
> In theory I agree :)
> 
> In practice submitting to CRAN takes from 4 hours to a full day, so I
> personally would not like to submit unless strictly necessary.

True. It looks simple, but something always pops up.

> 
> As for this particular fix - I expect some more code changes still this
> week, so if we decide to publish on CRAN I would wait till next week.

Good. Let's wait until these changes you mention are in. One or two more
weeks won't make much of a difference, I'd say. Having more changes in
also makes for a nicer Changelog ;-).


Lennart.

> 
> best wishes,
> YA
> 
> On Wed, Apr 3, 2013 at 1:20 PM, L.C. Karssen <lennart at karssen.org> wrote:
> 
>> Hi Yurii, Maria,
>>
>> Indeed, this is more a workaround than a fix. I think we communicated
>> this simple workaround in the past, but I agree with Maria we should
>> either announce it more widely, or, probably better push a new GenABEL
>> release to CRAN (for those people who don't read the announcements :-)).
>>
>> Yurii, what do you think? One the one hand it is not urgent (we've been
>> living with this bug for a while) on the other hand, the present
>> situation is a dangerous one... Are there any developments in GenABEL
>> SVN that are not ready for publishing yet?
>>
>>
>> Best,
>>
>> Lennart.
>>
>> On 04/03/2013 12:19 PM, Yurii Aulchenko wrote:
>>> Hi Maria,
>>>
>>> if my understanding is correct, the fix is now only in the devel-version
>> on
>>> SVN - so you would need to export and build package if you really want it
>>> (see
>> http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).
>>>
>>> But the 'fix' is very simple (and is not actually fixing anything - just
>>> trying to avoid confusion!): the default option now is set to
>>> 'transpose=TRUE'. So you can simply set this up manually when calling
>>> 'export.plink' :)
>>>
>>> Yurii
>>>
>>>
>>> On Wed, Apr 3, 2013 at 11:58 AM, Maria G <mgmaria at yandex.ru> wrote:
>>>
>>>> Dear Lennart,
>>>>
>>>> that's really helpful, thank you!
>>>>
>>>> Does it mean I have to update the version of GenABEL to get read of the
>>>> bug? Which version is fine?
>>>>
>>>>
>>>> best
>>>> Mariya
>>>>
>>>> 02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
>>>>> Dear list,
>>>>>
>>>>> As I didn't get any comments to dissuade me, I've just committed a
>>>>> change that sets the default behaviour of export.plink() in GenABEL to
>>>>> export .tped/.tfam files. This works around bug #2055.
>>>>>
>>>>> Best,
>>>>>
>>>>> Lennart.
>>>>>
>>>>> On 28/03/13 14:34, L.C. Karssen wrote:
>>>>>
>>>>>>  Dear list,
>>>>>>
>>>>>>  We recently got bitten by bug #2055 (ref [1]) in GenABEL's
>>>>>>  export.plink() again. Data was exported to .ped format and everything
>>>>>>  seemed to have gone well, however, we later found out that the
>> exported
>>>>>>  genotypes were wrong. Exporting to .tped (export.plink(...,
>>>>>>  transpose=TRUE)) worked fine.
>>>>>>
>>>>>>  I think we should change the default for the transpose option to TRUE
>>>>>>  and add a warning in case someone sets it to FALSE. I'm of course
>>>>>>  willing to write the necessary code.
>>>>>>  At least this will safeguard the users from this problem until the
>>>>>>  actual bug is fixed.
>>>>>>
>>>>>>  What are you're thoughts on this?
>>>>>>
>>>>>>  Best,
>>>>>>
>>>>>>  Lennart.
>>>>>>
>>>>>>  [1]
>>>>>>
>>>>
>> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
>>>>>>  --
>>>>>>  -----------------------------------------------------------------
>>>>>>  L.C. Karssen
>>>>>>  Utrecht
>>>>>>  The Netherlands
>>>>>>
>>>>>>  lennart at karssen.org
>>>>>>  http://blog.karssen.org
>>>>>>
>>>>>>  Stuur mij aub geen Word of Powerpoint bestanden!
>>>>>>  Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>>>>  ------------------------------------------------------------------
>>>>>>
>>>>>>  _______________________________________________
>>>>>>  genabel-devel mailing list
>>>>>>  genabel-devel at lists.r-forge.r-project.org
>>>>>>
>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>
>>>>> --
>>>>> -----------------------------------------------------------------
>>>>> L.C. Karssen
>>>>> Utrecht
>>>>> The Netherlands
>>>>>
>>>>> lennart at karssen.org
>>>>> http://blog.karssen.org
>>>>>
>>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>>> ------------------------------------------------------------------
>>>>>
>>>>> ,
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>
>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>
>>
>>
>> --
>> -----------------------------------------------------------------
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>>
>> lennart at karssen.org
>> http://blog.karssen.org
>>
>> Stuur mij aub geen Word of Powerpoint bestanden!
>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>> ------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
> 
> 
> 


-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Wed Apr  3 13:33:13 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 3 Apr 2013 13:33:13 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
Message-ID: <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>

I am - in general - for it. Something like 'current bugs and workarounds'?
We will need to keep this updated (e.g. when problem gets eventually fixed,
update the entry).

Yurii

On Wed, Apr 3, 2013 at 1:25 PM, Nicola Pirastu <pirastu at burlo.trieste.it>wrote:

> Dear all,
>
> how about we create a FAQ page on the website or on the forum as sticky
> topic?
>
>
> I think we are missing one and this is one of those questions which are
> bound to come up every once in a while (together with "ProbABEL won't work
> with 1000G indels imputed with IMPUTE").
>
>
> Best
>
> Nicola
>
>
>
> Il giorno 03/apr/2013, alle ore 13:20, "L.C. Karssen" <lennart at karssen.org>
> ha scritto:
>
> > Hi Yurii, Maria,
> >
> > Indeed, this is more a workaround than a fix. I think we communicated
> > this simple workaround in the past, but I agree with Maria we should
> > either announce it more widely, or, probably better push a new GenABEL
> > release to CRAN (for those people who don't read the announcements :-)).
> >
> > Yurii, what do you think? One the one hand it is not urgent (we've been
> > living with this bug for a while) on the other hand, the present
> > situation is a dangerous one... Are there any developments in GenABEL
> > SVN that are not ready for publishing yet?
> >
> >
> > Best,
> >
> > Lennart.
> >
> > On 04/03/2013 12:19 PM, Yurii Aulchenko wrote:
> >> Hi Maria,
> >>
> >> if my understanding is correct, the fix is now only in the
> devel-version on
> >> SVN - so you would need to export and build package if you really want
> it
> >> (see
> http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).
> >>
> >> But the 'fix' is very simple (and is not actually fixing anything - just
> >> trying to avoid confusion!): the default option now is set to
> >> 'transpose=TRUE'. So you can simply set this up manually when calling
> >> 'export.plink' :)
> >>
> >> Yurii
> >>
> >>
> >> On Wed, Apr 3, 2013 at 11:58 AM, Maria G <mgmaria at yandex.ru> wrote:
> >>
> >>> Dear Lennart,
> >>>
> >>> that's really helpful, thank you!
> >>>
> >>> Does it mean I have to update the version of GenABEL to get read of the
> >>> bug? Which version is fine?
> >>>
> >>>
> >>> best
> >>> Mariya
> >>>
> >>> 02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
> >>>> Dear list,
> >>>>
> >>>> As I didn't get any comments to dissuade me, I've just committed a
> >>>> change that sets the default behaviour of export.plink() in GenABEL to
> >>>> export .tped/.tfam files. This works around bug #2055.
> >>>>
> >>>> Best,
> >>>>
> >>>> Lennart.
> >>>>
> >>>> On 28/03/13 14:34, L.C. Karssen wrote:
> >>>>
> >>>>> Dear list,
> >>>>>
> >>>>> We recently got bitten by bug #2055 (ref [1]) in GenABEL's
> >>>>> export.plink() again. Data was exported to .ped format and everything
> >>>>> seemed to have gone well, however, we later found out that the
> exported
> >>>>> genotypes were wrong. Exporting to .tped (export.plink(...,
> >>>>> transpose=TRUE)) worked fine.
> >>>>>
> >>>>> I think we should change the default for the transpose option to TRUE
> >>>>> and add a warning in case someone sets it to FALSE. I'm of course
> >>>>> willing to write the necessary code.
> >>>>> At least this will safeguard the users from this problem until the
> >>>>> actual bug is fixed.
> >>>>>
> >>>>> What are you're thoughts on this?
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Lennart.
> >>>>>
> >>>>> [1]
> >>>>>
> >>>
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
> >>>>> --
> >>>>> -----------------------------------------------------------------
> >>>>> L.C. Karssen
> >>>>> Utrecht
> >>>>> The Netherlands
> >>>>>
> >>>>> lennart at karssen.org
> >>>>> http://blog.karssen.org
> >>>>>
> >>>>> Stuur mij aub geen Word of Powerpoint bestanden!
> >>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> >>>>> ------------------------------------------------------------------
> >>>>>
> >>>>> _______________________________________________
> >>>>> genabel-devel mailing list
> >>>>> genabel-devel at lists.r-forge.r-project.org
> >>>>>
> >>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>>>
> >>>> --
> >>>> -----------------------------------------------------------------
> >>>> L.C. Karssen
> >>>> Utrecht
> >>>> The Netherlands
> >>>>
> >>>> lennart at karssen.org
> >>>> http://blog.karssen.org
> >>>>
> >>>> Stuur mij aub geen Word of Powerpoint bestanden!
> >>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> >>>> ------------------------------------------------------------------
> >>>>
> >>>> ,
> >>>> _______________________________________________
> >>>> genabel-devel mailing list
> >>>> genabel-devel at lists.r-forge.r-project.org
> >>>>
> >>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>> _______________________________________________
> >>> genabel-devel mailing list
> >>> genabel-devel at lists.r-forge.r-project.org
> >>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> genabel-devel mailing list
> >> genabel-devel at lists.r-forge.r-project.org
> >>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>
> >
> >
> > --
> > -----------------------------------------------------------------
> > L.C. Karssen
> > Utrecht
> > The Netherlands
> >
> > lennart at karssen.org
> > http://blog.karssen.org
> >
> > Stuur mij aub geen Word of Powerpoint bestanden!
> > Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> > ------------------------------------------------------------------
> >
> > _______________________________________________
> > genabel-devel mailing list
> > genabel-devel at lists.r-forge.r-project.org
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From mgmaria at yandex.ru  Wed Apr  3 13:49:36 2013
From: mgmaria at yandex.ru (Maria G)
Date: Wed, 03 Apr 2013 15:49:36 +0400
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
Message-ID: <267251364989776@web10f.yandex.ru>

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From looongdog at gmail.com  Wed Apr  3 15:47:11 2013
From: looongdog at gmail.com (Vladimir Naumov)
Date: Wed, 3 Apr 2013 17:47:11 +0400
Subject: [GenABEL-dev] patch for bug #1287
Message-ID: <75AEC73BD89E4182B0ACC541252048BE@gmail.com>

http://r-forge.r-project.org/tracker/index.php?func=detail&aid=1287&group_id=505&atid=2058

just set.seed to 7 and everything works fine 

-- 
Vladimir Naumov
0079156727733
Skype: snow_wow

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From looongdog at gmail.com  Wed Apr  3 16:54:45 2013
From: looongdog at gmail.com (Vladimir Naumov)
Date: Wed, 3 Apr 2013 18:54:45 +0400
Subject: [GenABEL-dev] patch for bug #2525
Message-ID: <E54DB40280C54723A3A0ACCBA7BEFE57@gmail.com>

http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2525&group_id=505&atid=2058 

It was problem with cycle that didn't renew sex values - so they were periodically written into output file with period of 100 (by default) 

-- 
Vladimir Naumov
0079156727733
Skype: snow_wow

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From yurii.aulchenko at gmail.com  Wed Apr  3 17:11:06 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 3 Apr 2013 17:11:06 +0200
Subject: [GenABEL-dev] patch for bug #1287
In-Reply-To: <75AEC73BD89E4182B0ACC541252048BE@gmail.com>
References: <75AEC73BD89E4182B0ACC541252048BE@gmail.com>
Message-ID: <CAHX9t6L5Th9Yi7T=8j+ExmUsDzhhn2dyH0PD1Y36CEo9=NrjPw@mail.gmail.com>

Thank you, Vladimir!

Indeed with the seed of 7 we get much more clear cluster picture.

I am going to apply the patch, commit, and close the bug.

Yurii

On Wed, Apr 3, 2013 at 3:47 PM, Vladimir Naumov <looongdog at gmail.com> wrote:

>
> http://r-forge.r-project.org/tracker/index.php?func=detail&aid=1287&group_id=505&atid=2058
>
> just set.seed to 7 and everything works fine
>
> --
> Vladimir Naumov
> 0079156727733
> Skype: snow_wow
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From yurii.aulchenko at gmail.com  Thu Apr  4 10:43:08 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 4 Apr 2013 10:43:08 +0200
Subject: [GenABEL-dev] [Genabel-commits] r1180 - pkg/GenABEL/man
In-Reply-To: <20130404084017.9BC9C1846E9@r-forge.r-project.org>
References: <20130404084017.9BC9C1846E9@r-forge.r-project.org>
Message-ID: <CAHX9t6JrHp4NV=MCXssW_yyK3d=TGcWG-yATWr=r1Q-OREn3uQ@mail.gmail.com>

Dear All,

I thought this may be of interest to document: while checking the latest
version of GenABEL-package, I got

* checking Rd files ... WARNING
Error : cocohet.Rd: non-ASCII input and no declared encoding
problem found in 'cocohet.Rd'

Then I could easily track the problem with

bash-3.2$ grep --color='auto' -P -n "[\x80-\xFF]" GenABEL/man/cocohet.Rd
29:Albert Hofman, Andr?? G. Uitterlinden, Yurii S. Aulchenko, and Manfred

(thanks to StackOverflow post
http://stackoverflow.com/questions/3001177/how-do-i-grep-for-non-ascii-characters-in-unix
)

best wishes,
Yurii



On Thu, Apr 4, 2013 at 10:40 AM, <noreply at r-forge.r-project.org> wrote:

> Author: yurii
> Date: 2013-04-04 10:40:16 +0200 (Thu, 04 Apr 2013)
> New Revision: 1180
>
> Modified:
>    pkg/GenABEL/man/cocohet.Rd
> Log:
> removing non-ASCII symbols
>
> Modified: pkg/GenABEL/man/cocohet.Rd
> ===================================================================
> --- pkg/GenABEL/man/cocohet.Rd  2013-04-03 15:05:14 UTC (rev 1179)
> +++ pkg/GenABEL/man/cocohet.Rd  2013-04-04 08:40:16 UTC (rev 1180)
> @@ -1,4 +1,3 @@
> -
>  \name{cocohet}
>  \alias{cocohet}
>  \alias{chi2_CG}
> @@ -26,7 +25,7 @@
>  locus. This method is described in 'Detecting Low Frequent
>  Loss-of-Function Alleles in Genome Wide Association Studies with Red
>  Hair Color as Example'; Fan Liu, Maksim V. Struchalin, Kate van Duijn,
> -Albert Hofman, Andr? G. Uitterlinden, Yurii S. Aulchenko, and Manfred
> +Albert Hofman, Andre G. Uitterlinden, Yurii S. Aulchenko, and Manfred
>  Kayser. PLoS ONE 6(11): e28145. doi:10.1371/journal.pone.0028145
>
>
>
> _______________________________________________
> Genabel-commits mailing list
> Genabel-commits at lists.r-forge.r-project.org
>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
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From yurii.aulchenko at gmail.com  Thu Apr  4 10:55:49 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 4 Apr 2013 10:55:49 +0200
Subject: [GenABEL-dev] Roxygen-generated Rd on SVN
Message-ID: <CAHX9t6LB+2CyMpUhsQ6BmQFrpW6OzM8qk1BhZPoZd5-RePy0Ng@mail.gmail.com>

Dear All,

I am wondering if -- according to the logic of not keeping the generated
files on SVN - we should delete these Rd files, which are generated by
Roxygen from R files?

This seems logical, and I do not see an immediate reason for not doing so.

best wishes,
Yurii
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From lennart at karssen.org  Thu Apr  4 13:14:46 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 04 Apr 2013 13:14:46 +0200
Subject: [GenABEL-dev] [Genabel-commits] r1180 - pkg/GenABEL/man
In-Reply-To: <CAHX9t6JrHp4NV=MCXssW_yyK3d=TGcWG-yATWr=r1Q-OREn3uQ@mail.gmail.com>
References: <20130404084017.9BC9C1846E9@r-forge.r-project.org>
 <CAHX9t6JrHp4NV=MCXssW_yyK3d=TGcWG-yATWr=r1Q-OREn3uQ@mail.gmail.com>
Message-ID: <515D60A6.2030701@karssen.org>

Hi Yurii,

That's an interesting finding! When I entered Andr?'s name (with e +
accent) I assumed that by now most (if not all) applications support
UTF8 character codings. Apparently not :-).

Thanks for pointing this out on the list, it's definitely something to
keep in mind as I guess quite a few of us use extended character sets.


Best regards,

Lennart.

On 04/04/13 10:43, Yurii Aulchenko wrote:
> Dear All,
> 
> I thought this may be of interest to document: while checking the latest
> version of GenABEL-package, I got 
> 
> * checking Rd files ... WARNING
> Error : cocohet.Rd: non-ASCII input and no declared encoding
> problem found in 'cocohet.Rd'
> 
> Then I could easily track the problem with
> 
> bash-3.2$ grep --color='auto' -P -n "[\x80-\xFF]" GenABEL/man/cocohet.Rd 
> 29:Albert Hofman, Andr?? G. Uitterlinden, Yurii S. Aulchenko, and Manfred
> 
> (thanks to StackOverflow post
> http://stackoverflow.com/questions/3001177/how-do-i-grep-for-non-ascii-characters-in-unix)
> 
> best wishes,
> Yurii
> 
> 
> 
> On Thu, Apr 4, 2013 at 10:40 AM, <noreply at r-forge.r-project.org
> <mailto:noreply at r-forge.r-project.org>> wrote:
> 
>     Author: yurii
>     Date: 2013-04-04 10:40:16 +0200 (Thu, 04 Apr 2013)
>     New Revision: 1180
> 
>     Modified:
>        pkg/GenABEL/man/cocohet.Rd
>     Log:
>     removing non-ASCII symbols
> 
>     Modified: pkg/GenABEL/man/cocohet.Rd
>     ===================================================================
>     --- pkg/GenABEL/man/cocohet.Rd  2013-04-03 15:05:14 UTC (rev 1179)
>     +++ pkg/GenABEL/man/cocohet.Rd  2013-04-04 08:40:16 UTC (rev 1180)
>     @@ -1,4 +1,3 @@
>     -
>      \name{cocohet}
>      \alias{cocohet}
>      \alias{chi2_CG}
>     @@ -26,7 +25,7 @@
>      locus. This method is described in 'Detecting Low Frequent
>      Loss-of-Function Alleles in Genome Wide Association Studies with Red
>      Hair Color as Example'; Fan Liu, Maksim V. Struchalin, Kate van Duijn,
>     -Albert Hofman, Andr? G. Uitterlinden, Yurii S. Aulchenko, and Manfred
>     +Albert Hofman, Andre G. Uitterlinden, Yurii S. Aulchenko, and Manfred
>      Kayser. PLoS ONE 6(11): e28145. doi:10.1371/journal.pone.0028145
> 
> 
> 
>     _______________________________________________
>     Genabel-commits mailing list
>     Genabel-commits at lists.r-forge.r-project.org
>     <mailto:Genabel-commits at lists.r-forge.r-project.org>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
> 
> 
> 
> 
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Thu Apr  4 13:44:41 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 4 Apr 2013 13:44:41 +0200
Subject: [GenABEL-dev] patch for bug #2525
In-Reply-To: <E54DB40280C54723A3A0ACCBA7BEFE57@gmail.com>
References: <E54DB40280C54723A3A0ACCBA7BEFE57@gmail.com>
Message-ID: <CAHX9t6+2LY-4PqXb6ocdB3YGWy=+eyEcHBdGk+h=AC74vPcOiQ@mail.gmail.com>

Thank you, Vladimir! - nice fix!

Lennart, I wonder if this fix somehow also address the export.plink bug
#2055 discussed earlier. I also wonder what kind of unit test one can
introduce for such 'memory leak' problem...

Below please find description of testing of the patch and some minor
changes I introduced. I have updated the code on SVN (
http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000575.html)
and closed the bug.

best wishes,
Yurii

I have added a unit test for this bug in r. 1185, see
http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000574.html
)

Then I ran unit tests without applying the patch yet by

cd pkg/GenABEL/inst/unitTests
make

which gave me - as expected -

GenABEL unit testing - 20 test functions, 1 error, 2 failures
FAILURE in test.export.merlin.bug2525: Error in checkIdentical(xN, xO) :
FALSE
FAILURE in test.exports: Error in checkIdentical(xN, xO) : FALSE
ERROR in test.impute2databel: Error in .Call("iterator",

(you can also check report.html for details; the FAILURE's are related to
the bug 2525, and the ERROR is related to other bug, so our aim is to
eliminate these FAILURES)

Next (from ../../../) I have applied the patch by

patch -p0 -i ~/Downloads/patch_2525

and run unit tests again by

cd pkg/GenABEL/inst/unitTests
make

which gave me

GenABEL unit testing - 20 test functions, 1 error, 0 failures
ERROR in test.impute2databel: Error in .Call("iterator",

which I thought was good - basically the test FAILURES were eliminated.

Now, the patch as submitted prints out much debugging (?) related staff to
STDOUT, so next I commented out Rprintf's and ran the tests agin, getting

GenABEL unit testing - 20 test functions, 1 error, 0 failures
ERROR in test.impute2databel: Error in .Call("iterator",

So, I conclude that the bug is fixed!


On Wed, Apr 3, 2013 at 4:54 PM, Vladimir Naumov <looongdog at gmail.com> wrote:

>
> http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2525&group_id=505&atid=2058
>
> It was problem with cycle that didn't renew sex values - so they were
> periodically written into output file with period of 100 (by default)
>
> --
> Vladimir Naumov
> 0079156727733
> Skype: snow_wow
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From kooyman at gmail.com  Thu Apr  4 22:42:07 2013
From: kooyman at gmail.com (Maarten Kooyman)
Date: Thu, 04 Apr 2013 22:42:07 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <267251364989776@web10f.yandex.ru>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru>
Message-ID: <515DE59F.60809@gmail.com>

Dear list,

This sounds like a great improvement. I looked multiple times for this 
link, but I never found it: there is a small usability problem which cam 
be easily fixed.

I have also some irritation about the fact that there is no recognisable 
logo on the page. I looks like a complete default page to me: which 
gives me the impression that there is not any on it. Does someone has 
graphical skills to create a nice logo which we can use on the site, 
posters or presentations? Having a neat logo, is like wearing a suite: 
people think at first sight you are more trustworthy,intelligent etc ect. ;)


Kind regards,

Maarten


On 04/03/2013 01:49 PM, Maria G wrote:
> Another small thing, is it possible to add anywhere on the main page 
> of GenABEL ( http://www.genabel.org ) a direct link to the forum? e.g. 
> within "Primary links"


From lennart at karssen.org  Fri Apr  5 09:37:55 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 05 Apr 2013 09:37:55 +0200
Subject: [GenABEL-dev] Roxygen-generated Rd on SVN
In-Reply-To: <CAHX9t6LB+2CyMpUhsQ6BmQFrpW6OzM8qk1BhZPoZd5-RePy0Ng@mail.gmail.com>
References: <CAHX9t6LB+2CyMpUhsQ6BmQFrpW6OzM8qk1BhZPoZd5-RePy0Ng@mail.gmail.com>
Message-ID: <515E7F53.2070503@karssen.org>

Dear Yurii,

You're right. There is no need to keep them in SVN. Be careful though,
some functions may not have Roxygen-style documentation, IIRC. But I
guess you know those functions better than me.


Lennart.

On 04/04/13 10:55, Yurii Aulchenko wrote:
> Dear All,
> 
> I am wondering if -- according to the logic of not keeping the generated
> files on SVN - we should delete these Rd files, which are generated by
> Roxygen from R files?
> 
> This seems logical, and I do not see an immediate reason for not doing so.
> 
> best wishes,
> Yurii
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Fri Apr  5 11:11:25 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 5 Apr 2013 11:11:25 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <267251364989776@web10f.yandex.ru>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru>
Message-ID: <CAHX9t6JavoRhVT6Rty-F-XS1mZymvkZob1sqZpfzJNZ_gSKHXg@mail.gmail.com>

> Is it possible to duplicate the bugs-info into both:
> http://www.genabel.org  and http://forum.genabel.org ?
>

Not sure that can be done easily, at least I do not see how this can be
done (we do have links to bug tracker from every package page though)


> (Which website is more popular by reading? )
>

I have little idea about this. I know that monthly we have about 5k
visitors on the GenABEL.org, of these about 3k are returning. This is old
statistica though - I did not check the figures in a while.


>
> Another small thing, is it possible to add anywhere on the main page of
> GenABEL ( http://www.genabel.org ) a direct link to the forum? e.g.
> within "Primary links"
>


I think this is not the first request for this. I will try to do this and
let you know. Part of the problem is that I have no idea if it is possible
to have primary link without having a page (so the user is brought directly
to forum). If this is not possible, I will create a minimal page -
basically the link to forum + short description.

Does that sound like a good plan?

Yurii
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From mgmaria at yandex.ru  Fri Apr  5 11:21:42 2013
From: mgmaria at yandex.ru (Maria G)
Date: Fri, 05 Apr 2013 13:21:42 +0400
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <CAHX9t6JavoRhVT6Rty-F-XS1mZymvkZob1sqZpfzJNZ_gSKHXg@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru>
 <CAHX9t6JavoRhVT6Rty-F-XS1mZymvkZob1sqZpfzJNZ_gSKHXg@mail.gmail.com>
Message-ID: <1048381365153702@web15h.yandex.ru>

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From yurii.aulchenko at gmail.com  Fri Apr  5 11:22:05 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 5 Apr 2013 11:22:05 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <515DE59F.60809@gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
Message-ID: <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>

Dear Maarten,

I have also some irritation about the fact that there is no recognisable
> logo on the page. I looks like a complete default page to me: which gives
> me the impression that there is not any on it. Does someone has graphical
> skills to create a nice logo which we can use on the site, posters or
> presentations? Having a neat logo, is like wearing a suite: people think at
> first sight you are more trustworthy,intelligent etc ect. ;)
>
>
Completely agree and fully support the idea! I even tried to design
something myself, but it was SO bad :)

Part of the problem is that obvious meaningful symbols (like chromosomes,
sigmas and Gaussians) are boring and used for long time. Another part is
that we can not just pick say a cute kitty and stop - there should be some
meaning to the symbol (or not?).

Do we have examples of successful, recognizable logos we like?I like
FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.

Yurii
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From yurii.aulchenko at gmail.com  Fri Apr  5 11:33:26 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 5 Apr 2013 11:33:26 +0200
Subject: [GenABEL-dev] Roxygen-generated Rd on SVN
In-Reply-To: <515E7F53.2070503@karssen.org>
References: <CAHX9t6LB+2CyMpUhsQ6BmQFrpW6OzM8qk1BhZPoZd5-RePy0Ng@mail.gmail.com>
 <515E7F53.2070503@karssen.org>
Message-ID: <7234457351217898262@unknownmsgid>

Ok, I am going to test this on GenA-package and if it works well, we
can do the same for other packages as well.

Yurii

----------------------
Yurii Aulchenko
(sent from mobile device)

On 5 Apr 2013, at 09:38, "L.C. Karssen" <lennart at karssen.org> wrote:

> Dear Yurii,
>
> You're right. There is no need to keep them in SVN. Be careful though,
> some functions may not have Roxygen-style documentation, IIRC. But I
> guess you know those functions better than me.
>
>
> Lennart.
>
> On 04/04/13 10:55, Yurii Aulchenko wrote:
>> Dear All,
>>
>> I am wondering if -- according to the logic of not keeping the generated
>> files on SVN - we should delete these Rd files, which are generated by
>> Roxygen from R files?
>>
>> This seems logical, and I do not see an immediate reason for not doing so.
>>
>> best wishes,
>> Yurii
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

From pirastu at burlo.trieste.it  Fri Apr  5 13:21:22 2013
From: pirastu at burlo.trieste.it (pirastu at burlo.trieste.it)
Date: Fri, 5 Apr 2013 13:21:22 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
Message-ID: <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>

Dear all,

I really like the proposal, I just to add a few ideas to the discussion.
I think that there are some important concepts that could be used for a logo:

1) ABEL which is able in the end could be something like a hammer or a
tool of some sort.

2) I think that the great thing about the *ABEL project is that it is not
a single group but it is a network of people and we could rappresent that
also.

3) the * in *ABEL could be made by two crossed Chromosomes or something
else or maybe a DNA strand a tool and something else (Although I do
realize that it could remind of the comunist party this way :) ).

4) I do like animals, but I it should be meanigful somehow (although Linux
does have a penguin for some obscure reason).

Best

Nicola






> Dear Maarten,
>
> I have also some irritation about the fact that there is no recognisable
>> logo on the page. I looks like a complete default page to me: which
>> gives
>> me the impression that there is not any on it. Does someone has
>> graphical
>> skills to create a nice logo which we can use on the site, posters or
>> presentations? Having a neat logo, is like wearing a suite: people think
>> at
>> first sight you are more trustworthy,intelligent etc ect. ;)
>>
>>
> Completely agree and fully support the idea! I even tried to design
> something myself, but it was SO bad :)
>
> Part of the problem is that obvious meaningful symbols (like chromosomes,
> sigmas and Gaussians) are boring and used for long time. Another part is
> that we can not just pick say a cute kitty and stop - there should be some
> meaning to the symbol (or not?).
>
> Do we have examples of successful, recognizable logos we like?I like
> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>
> Yurii
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel



From pirastu at burlo.trieste.it  Fri Apr  5 13:59:58 2013
From: pirastu at burlo.trieste.it (pirastu at burlo.trieste.it)
Date: Fri, 5 Apr 2013 13:59:58 +0200
Subject: [GenABEL-dev]  MixABEL will not copile.
In-Reply-To: <22951_1365160886_515EB3B5_22951_4772_1_1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <22951_1365160886_515EB3B5_22951_4772_1_1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
Message-ID: <6f28be7831c573e4f7a4bea7e74e4ad9.squirrel@webmail-rupar.regione.fvg.it>

Dear all,

as many of you know the last version of MixABEL will not compile properly.

Since we've been receving requests for it especially for the GxE with
kinship (and I actually my self have been asking people whom I collaburate
with to use it).

Could we add a working version to the site even though it's not ready for
CRAN yet?

I do have a working version but shouldn't we share it with the rest of the
world specifying that it is not a stable version?

Best.

Nicola




From kooyman at gmail.com  Sat Apr  6 12:46:36 2013
From: kooyman at gmail.com (Maarten Kooyman)
Date: Sat, 06 Apr 2013 12:46:36 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
Message-ID: <515FFD0C.4060500@gmail.com>

Dear Nicola,

The use of a tool is a nice idea, however I think a screwdriver or a 
wrench is better than a communist party symbol: I do not want to develop 
a PoliticsABEL project ;).  Representing a network of people is hard 
without giving the impression that GenAbel is a browser, chat or other 
program for the internet. Please prove me wrong if you think otherwise. 
Using DNA or chromosome is to my opinion a must.

I think it is also important that the word GenABEL is visible as text in 
the logo. Otherwise people will think "what is this funny looking 
cartoon". It would also be nice to adjust the logo so the name of a 
subproject(Mix, Prob) can be written down into the logo.

cheers,

Maarten


On 04/05/2013 01:21 PM, pirastu at burlo.trieste.it wrote:
> Dear all,
>
> I really like the proposal, I just to add a few ideas to the discussion.
> I think that there are some important concepts that could be used for a logo:
>
> 1) ABEL which is able in the end could be something like a hammer or a
> tool of some sort.
>
> 2) I think that the great thing about the *ABEL project is that it is not
> a single group but it is a network of people and we could rappresent that
> also.
>
> 3) the * in *ABEL could be made by two crossed Chromosomes or something
> else or maybe a DNA strand a tool and something else (Although I do
> realize that it could remind of the comunist party this way :) ).
>
> 4) I do like animals, but I it should be meanigful somehow (although Linux
> does have a penguin for some obscure reason).
>
> Best
>
> Nicola
>
>
>
>
>
>
>> Dear Maarten,
>>
>> I have also some irritation about the fact that there is no recognisable
>>> logo on the page. I looks like a complete default page to me: which
>>> gives
>>> me the impression that there is not any on it. Does someone has
>>> graphical
>>> skills to create a nice logo which we can use on the site, posters or
>>> presentations? Having a neat logo, is like wearing a suite: people think
>>> at
>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>
>>>
>> Completely agree and fully support the idea! I even tried to design
>> something myself, but it was SO bad :)
>>
>> Part of the problem is that obvious meaningful symbols (like chromosomes,
>> sigmas and Gaussians) are boring and used for long time. Another part is
>> that we can not just pick say a cute kitty and stop - there should be some
>> meaning to the symbol (or not?).
>>
>> Do we have examples of successful, recognizable logos we like?I like
>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>
>> Yurii
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>


From yurii.aulchenko at gmail.com  Sat Apr  6 14:44:23 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sat, 6 Apr 2013 14:44:23 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <1048381365153702@web15h.yandex.ru>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru>
 <CAHX9t6JavoRhVT6Rty-F-XS1mZymvkZob1sqZpfzJNZ_gSKHXg@mail.gmail.com>
 <1048381365153702@web15h.yandex.ru>
Message-ID: <CAHX9t6LEOGynxZAyodxbmU39OL7eqhk2xsHQvqyaCPz_kueZrw@mail.gmail.com>

Maarten, thanks for suggestion.

Other question - I have accumulated some presentations for the GenABEL
project, so I thought I should put them on the web site.

- Does "Showcase" (http://genabel.org/showcase) sounds like a proper place
for this?

- I also think of pushing the sources to SVN, though it is a little weird
to have ODP (I used LibreOffice) on SVN.

Yurii


On Fri, Apr 5, 2013 at 11:21 AM, Maria G <mgmaria at yandex.ru> wrote:

>
>
> 05.04.2013, 13:11, "Yurii Aulchenko" <yurii.aulchenko at gmail.com>:
>
>
>
> Is it possible to duplicate the bugs-info into both:
> http://www.genabel.org  and http://forum.genabel.org ?
>
>
> Not sure that can be done easily, at least I do not see how this can be
> done (we do have links to bug tracker from every package page though)
>
>
> (Which website is more popular by reading? )
>
>
> I have little idea about this. I know that monthly we have about 5k
> visitors on the GenABEL.org, of these about 3k are returning. This is old
> statistica though - I did not check the figures in a while.
>
>
>
>
> Another small thing, is it possible to add anywhere on the main page of
> GenABEL ( http://www.genabel.org ) a direct link to the forum? e.g.
> within "Primary links"
>
>
>
> I think this is not the first request for this. I will try to do this and
> let you know. Part of the problem is that I have no idea if it is possible
> to have primary link without having a page (so the user is brought directly
> to forum). If this is not possible, I will create a minimal page -
> basically the link to forum + short description.
>
> Does that sound like a good plan?
>
>
> Yes! Thank you
>
> May be on the same "minimal page", describing the interactions between the
> users and developers, give an idea that bugs-solutions are published in
> each of the package page? (e.g. Me myself didn't pay attantion for that
> untill you say it now ;) )
>
> Mascha
>
>
>
>
> Yurii
>
>
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From darthastu at gmail.com  Sat Apr  6 01:36:57 2013
From: darthastu at gmail.com (Nicola Pirastu)
Date: Sat, 6 Apr 2013 01:36:57 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
Message-ID: <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>

Dear all,


I gave a shot at the logo, it's very simple. Let me know if you like the general idea, if you'd like to add something or change it. 

As colors I've sticked to those of the website but they can be changed. Also the pattern for the formulas have some white spaces, but this is just a quick draft.

If you hate it or think it should go in another direction, I'm not touchy so please do tell me.

Best.

Nicola



Il giorno 05/apr/2013, alle ore 13:21, pirastu at burlo.trieste.it ha scritto:

> Dear all,
> 
> I really like the proposal, I just to add a few ideas to the discussion.
> I think that there are some important concepts that could be used for a logo:
> 
> 1) ABEL which is able in the end could be something like a hammer or a
> tool of some sort.
> 
> 2) I think that the great thing about the *ABEL project is that it is not
> a single group but it is a network of people and we could rappresent that
> also.
> 
> 3) the * in *ABEL could be made by two crossed Chromosomes or something
> else or maybe a DNA strand a tool and something else (Although I do
> realize that it could remind of the comunist party this way :) ).
> 
> 4) I do like animals, but I it should be meanigful somehow (although Linux
> does have a penguin for some obscure reason).
> 
> Best
> 
> Nicola
> 
> 
> 
> 
> 
> 
>> Dear Maarten,
>> 
>> I have also some irritation about the fact that there is no recognisable
>>> logo on the page. I looks like a complete default page to me: which
>>> gives
>>> me the impression that there is not any on it. Does someone has
>>> graphical
>>> skills to create a nice logo which we can use on the site, posters or
>>> presentations? Having a neat logo, is like wearing a suite: people think
>>> at
>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>> 
>>> 
>> Completely agree and fully support the idea! I even tried to design
>> something myself, but it was SO bad :)
>> 
>> Part of the problem is that obvious meaningful symbols (like chromosomes,
>> sigmas and Gaussians) are boring and used for long time. Another part is
>> that we can not just pick say a cute kitty and stop - there should be some
>> meaning to the symbol (or not?).
>> 
>> Do we have examples of successful, recognizable logos we like?I like
>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>> 
>> Yurii
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

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From mgmaria at yandex.ru  Mon Apr  8 10:58:13 2013
From: mgmaria at yandex.ru (Maria G)
Date: Mon, 08 Apr 2013 12:58:13 +0400
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <515446DC.6040602@karssen.org>
References: <515446DC.6040602@karssen.org>
Message-ID: <340771365411493@web24f.yandex.ru>

Dear Lennart,

I've tried both on a small data-set:
export.plink(transpose=FALSE) and export.plink(transpose=TRUE) , 
and the output genotypes look both correct... 
Can it be that the bug is not always "active"?

best
Mascha

28.03.2013, 17:34, "L.C. Karssen" <lennart at karssen.org>:
> Dear list,
>
> We recently got bitten by bug #2055 (ref [1]) in GenABEL's
> export.plink() again. Data was exported to .ped format and everything
> seemed to have gone well, however, we later found out that the exported
> genotypes were wrong. Exporting to .tped (export.plink(...,
> transpose=TRUE)) worked fine.
>
> I think we should change the default for the transpose option to TRUE
> and add a warning in case someone sets it to FALSE. I'm of course
> willing to write the necessary code.
> At least this will safeguard the users from this problem until the
> actual bug is fixed.
>
> What are you're thoughts on this?
>
> Best,
>
> Lennart.
>
> [1]
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
> ,
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

From yurii.aulchenko at gmail.com  Mon Apr  8 12:08:36 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Mon, 8 Apr 2013 12:08:36 +0200
Subject: [GenABEL-dev] export.plink bug: should we change the default?
In-Reply-To: <1048381365153702@web15h.yandex.ru>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru>
 <CAHX9t6JavoRhVT6Rty-F-XS1mZymvkZob1sqZpfzJNZ_gSKHXg@mail.gmail.com>
 <1048381365153702@web15h.yandex.ru>
Message-ID: <CAHX9t6+Sg5psdcdr+m8TyeeN+HKDuTm+Wy1MuaGADMDUoS-1qw@mail.gmail.com>

Dear All,

I have managed to have a direct link to forum introduce to primary menu

I have also changed the order of primary links (also based on access stats).

BTW, latest numbers are that we are getting about 2k visitors per month, of
which about 50% are new visits

YA

On Fri, Apr 5, 2013 at 11:21 AM, Maria G <mgmaria at yandex.ru> wrote:

>
>
> 05.04.2013, 13:11, "Yurii Aulchenko" <yurii.aulchenko at gmail.com>:
>
>
>
> Is it possible to duplicate the bugs-info into both:
> http://www.genabel.org  and http://forum.genabel.org ?
>
>
> Not sure that can be done easily, at least I do not see how this can be
> done (we do have links to bug tracker from every package page though)
>
>
> (Which website is more popular by reading? )
>
>
> I have little idea about this. I know that monthly we have about 5k
> visitors on the GenABEL.org, of these about 3k are returning. This is old
> statistica though - I did not check the figures in a while.
>
>
>
>
> Another small thing, is it possible to add anywhere on the main page of
> GenABEL ( http://www.genabel.org ) a direct link to the forum? e.g.
> within "Primary links"
>
>
>
> I think this is not the first request for this. I will try to do this and
> let you know. Part of the problem is that I have no idea if it is possible
> to have primary link without having a page (so the user is brought directly
> to forum). If this is not possible, I will create a minimal page -
> basically the link to forum + short description.
>
> Does that sound like a good plan?
>
>
> Yes! Thank you
>
> May be on the same "minimal page", describing the interactions between the
> users and developers, give an idea that bugs-solutions are published in
> each of the package page? (e.g. Me myself didn't pay attantion for that
> untill you say it now ;) )
>
> Mascha
>
>
>
>
> Yurii
>
>


-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From yurii.aulchenko at gmail.com  Mon Apr  8 12:25:27 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Mon, 8 Apr 2013 12:25:27 +0200
Subject: [GenABEL-dev] MixABEL will not copile.
In-Reply-To: <6f28be7831c573e4f7a4bea7e74e4ad9.squirrel@webmail-rupar.regione.fvg.it>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <22951_1365160886_515EB3B5_22951_4772_1_1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <6f28be7831c573e4f7a4bea7e74e4ad9.squirrel@webmail-rupar.regione.fvg.it>
Message-ID: <CAHX9t6+a+dJwcNUq1=bRAnus2nTqNWRJuQstFozRSUgiU_zBFA@mail.gmail.com>

Hi Nicola,

I believe the "not compile" problem was solved; see
https://r-forge.r-project.org/tracker/?func=detail&group_id=505&aid=2449&atid=2058

As far as I know William is exploring the opportunities of publishing MixA
on CRAN

YA

On Fri, Apr 5, 2013 at 1:59 PM, <pirastu at burlo.trieste.it> wrote:

> Dear all,
>
> as many of you know the last version of MixABEL will not compile properly.
>
> Since we've been receving requests for it especially for the GxE with
> kinship (and I actually my self have been asking people whom I collaburate
> with to use it).
>
> Could we add a working version to the site even though it's not ready for
> CRAN yet?
>
> I do have a working version but shouldn't we share it with the rest of the
> world specifying that it is not a stable version?
>
> Best.
>
> Nicola
>
>
>
>


-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From yurii.aulchenko at gmail.com  Mon Apr  8 13:53:05 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Mon, 8 Apr 2013 13:53:05 +0200
Subject: [GenABEL-dev] [Genabel-commits] r1171 - tags/DatABEL
In-Reply-To: <20130323153809.D14F2184287@r-forge.r-project.org>
References: <20130323153809.D14F2184287@r-forge.r-project.org>
Message-ID: <CAHX9t6J_94vV9GG8P3SK=ET=CR990vatY2897SgVR7-r9_vvhw@mail.gmail.com>

Lennart, many thanks for tagging the release - I completely forgot to do
that!

YA

On Sat, Mar 23, 2013 at 4:38 PM, <noreply at r-forge.r-project.org> wrote:

> Author: lckarssen
> Date: 2013-03-23 16:38:09 +0100 (Sat, 23 Mar 2013)
> New Revision: 1171
>
> Added:
>    tags/DatABEL/v.0.9-4/
> Log:
> Tagging DatABEL release 0.9-4
>
> _______________________________________________
> Genabel-commits mailing list
> Genabel-commits at lists.r-forge.r-project.org
>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From lennart at karssen.org  Mon Apr  8 16:03:37 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 08 Apr 2013 16:03:37 +0200
Subject: [GenABEL-dev] [Genabel-commits] r1171 - tags/DatABEL
In-Reply-To: <CAHX9t6J_94vV9GG8P3SK=ET=CR990vatY2897SgVR7-r9_vvhw@mail.gmail.com>
References: <20130323153809.D14F2184287@r-forge.r-project.org>
 <CAHX9t6J_94vV9GG8P3SK=ET=CR990vatY2897SgVR7-r9_vvhw@mail.gmail.com>
Message-ID: <5162CE39.6050706@karssen.org>

You're welcome!


Lennart.

On 08/04/13 13:53, Yurii Aulchenko wrote:
> Lennart, many thanks for tagging the release - I completely forgot to do
> that!
> 
> YA
> 
> On Sat, Mar 23, 2013 at 4:38 PM, <noreply at r-forge.r-project.org
> <mailto:noreply at r-forge.r-project.org>> wrote:
> 
>     Author: lckarssen
>     Date: 2013-03-23 16:38:09 +0100 (Sat, 23 Mar 2013)
>     New Revision: 1171
> 
>     Added:
>        tags/DatABEL/v.0.9-4/
>     Log:
>     Tagging DatABEL release 0.9-4
> 
>     _______________________________________________
>     Genabel-commits mailing list
>     Genabel-commits at lists.r-forge.r-project.org
>     <mailto:Genabel-commits at lists.r-forge.r-project.org>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> <http://twitter.com/YuriiAulchenko> ] [ Blog
> <http://yurii-aulchenko.blogspot.nl/> ]

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From pirastu at burlo.trieste.it  Tue Apr  9 11:30:43 2013
From: pirastu at burlo.trieste.it (Nicola Pirastu)
Date: Tue, 9 Apr 2013 11:30:43 +0200
Subject: [GenABEL-dev] MixABEL will not copile.
In-Reply-To: <CAHX9t6+a+dJwcNUq1=bRAnus2nTqNWRJuQstFozRSUgiU_zBFA@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <22951_1365160886_515EB3B5_22951_4772_1_1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <6f28be7831c573e4f7a4bea7e74e4ad9.squirrel@webmail-rupar.regione.fvg.it>
 <CAHX9t6+a+dJwcNUq1=bRAnus2nTqNWRJuQstFozRSUgiU_zBFA@mail.gmail.com>
Message-ID: <74CDCC20-8798-4A96-A300-6D78651CBA99@burlo.trieste.it>

Great,

sorry I didn't notice the notes on the bugs page.

Nicola


Il giorno 08/apr/2013, alle ore 12:25, Yurii Aulchenko <yurii.aulchenko at gmail.com> ha scritto:

> Hi Nicola,
> 
> I believe the "not compile" problem was solved; see https://r-forge.r-project.org/tracker/?func=detail&group_id=505&aid=2449&atid=2058
> 
> As far as I know William is exploring the opportunities of publishing MixA on CRAN
> 
> YA
> 
> On Fri, Apr 5, 2013 at 1:59 PM, <pirastu at burlo.trieste.it> wrote:
> Dear all,
> 
> as many of you know the last version of MixABEL will not compile properly.
> 
> Since we've been receving requests for it especially for the GxE with
> kinship (and I actually my self have been asking people whom I collaburate
> with to use it).
> 
> Could we add a working version to the site even though it's not ready for
> CRAN yet?
> 
> I do have a working version but shouldn't we share it with the rest of the
> world specifying that it is not a stable version?
> 
> Best.
> 
> Nicola
> 
> 
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn ] [ Twitter ] [ Blog ]

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From kooyman at gmail.com  Thu Apr 11 21:39:21 2013
From: kooyman at gmail.com (Maarten Kooyman)
Date: Thu, 11 Apr 2013 21:39:21 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>
Message-ID: <51671169.5090608@gmail.com>

Dear All,

  I made also a small sketch of a logo. It is pretty raw, colours are 
wrong , etcetera, etcetera.

To quote Nicola:
" If you hate it or think it should go in another direction, I'm not 
touchy so please do tell me. "


Cheers,

Maarten


On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
> Dear all,
>
>
> I gave a shot at the logo, it's very simple. Let me know if you like 
> the general idea, if you'd like to add something or change it.
>
> As colors I've sticked to those of the website but they can be 
> changed. Also the pattern for the formulas have some white spaces, but 
> this is just a quick draft.
>
> If you hate it or think it should go in another direction, I'm not 
> touchy so please do tell me.
>
> Best.
>
> Nicola


> Dear all,
>>
>> I really like the proposal, I just to add a few ideas to the discussion.
>> I think that there are some important concepts that could be used for 
>> a logo:
>>
>> 1) ABEL which is able in the end could be something like a hammer or a
>> tool of some sort.
>>
>> 2) I think that the great thing about the *ABEL project is that it is not
>> a single group but it is a network of people and we could rappresent that
>> also.
>>
>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
>> else or maybe a DNA strand a tool and something else (Although I do
>> realize that it could remind of the comunist party this way :) ).
>>
>> 4) I do like animals, but I it should be meanigful somehow (although 
>> Linux
>> does have a penguin for some obscure reason).
>>
>> Best
>>
>> Nicola
>>
>>
>>
>>
>>
>>
>>> Dear Maarten,
>>>
>>> I have also some irritation about the fact that there is no recognisable
>>>> logo on the page. I looks like a complete default page to me: which
>>>> gives
>>>> me the impression that there is not any on it. Does someone has
>>>> graphical
>>>> skills to create a nice logo which we can use on the site, posters or
>>>> presentations? Having a neat logo, is like wearing a suite: people 
>>>> think
>>>> at
>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>>
>>>>
>>> Completely agree and fully support the idea! I even tried to design
>>> something myself, but it was SO bad :)
>>>
>>> Part of the problem is that obvious meaningful symbols (like 
>>> chromosomes,
>>> sigmas and Gaussians) are boring and used for long time. Another part is
>>> that we can not just pick say a cute kitty and stop - there should 
>>> be some
>>> meaning to the symbol (or not?).
>>>
>>> Do we have examples of successful, recognizable logos we like?I like
>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>>
>>> Yurii
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org 
>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org 
>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

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From darthastu at gmail.com  Thu Apr 11 21:58:19 2013
From: darthastu at gmail.com (Nicola Pirastu)
Date: Thu, 11 Apr 2013 21:58:19 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <51671169.5090608@gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
Message-ID: <378870D3-8111-4235-9AEA-5CD25B6B99D9@gmail.com>

As I told Maarten  I think the idea is good although the G should be more ReadABEL and it looks a bit like we are a sequencing company, so maybe we you could try to fit statistics somehow. Maybe part of the writing could be like formulas in Latex? 

Also I really like the subscript in the main page of the website "GenABEL'ing genetic research". 

I also think that my attemps never arrived to anyone but I think his is better anyways :).

Best.

Nicola



Il giorno 11/apr/2013, alle ore 21:39, Maarten Kooyman <kooyman at gmail.com> ha scritto:

> Dear All,
> 
>  I made also a small sketch of a logo. It is pretty raw, colours are wrong , etcetera, etcetera.
> 
> To quote Nicola:
> " If you hate it or think it should go in another direction, I'm not touchy so please do tell me. "
> 
> 
> Cheers,
> 
> Maarten
> 
> 
> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>> Dear all,
>> 
>> 
>> I gave a shot at the logo, it's very simple. Let me know if you like the general idea, if you'd like to add something or change it. 
>> 
>> As colors I've sticked to those of the website but they can be changed. Also the pattern for the formulas have some white spaces, but this is just a quick draft.
>> 
>> If you hate it or think it should go in another direction, I'm not touchy so please do tell me.
>> 
>> Best.
>> 
>> Nicola
> 
> 
>> Dear all,
>>> 
>>> I really like the proposal, I just to add a few ideas to the discussion.
>>> I think that there are some important concepts that could be used for a logo:
>>> 
>>> 1) ABEL which is able in the end could be something like a hammer or a
>>> tool of some sort.
>>> 
>>> 2) I think that the great thing about the *ABEL project is that it is not
>>> a single group but it is a network of people and we could rappresent that
>>> also.
>>> 
>>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
>>> else or maybe a DNA strand a tool and something else (Although I do
>>> realize that it could remind of the comunist party this way :) ).
>>> 
>>> 4) I do like animals, but I it should be meanigful somehow (although Linux
>>> does have a penguin for some obscure reason).
>>> 
>>> Best
>>> 
>>> Nicola
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> Dear Maarten,
>>>> 
>>>> I have also some irritation about the fact that there is no recognisable
>>>>> logo on the page. I looks like a complete default page to me: which
>>>>> gives
>>>>> me the impression that there is not any on it. Does someone has
>>>>> graphical
>>>>> skills to create a nice logo which we can use on the site, posters or
>>>>> presentations? Having a neat logo, is like wearing a suite: people think
>>>>> at
>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>>> 
>>>>> 
>>>> Completely agree and fully support the idea! I even tried to design
>>>> something myself, but it was SO bad :)
>>>> 
>>>> Part of the problem is that obvious meaningful symbols (like chromosomes,
>>>> sigmas and Gaussians) are boring and used for long time. Another part is
>>>> that we can not just pick say a cute kitty and stop - there should be some
>>>> meaning to the symbol (or not?).
>>>> 
>>>> Do we have examples of successful, recognizable logos we like?I like
>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>>> 
>>>> Yurii
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> 
>>> 
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> 
>> 
>> 
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> <logo_genabel_draft.png>_______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

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From lennart at karssen.org  Thu Apr 11 22:14:10 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 11 Apr 2013 22:14:10 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <51671169.5090608@gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
Message-ID: <51671992.9070100@karssen.org>

Not bad! I really like the way you mixed the G and the DNA.
Can't we make a combination with Nicola's creation so that we get some
math in as well? That would nicely integrate two major components of the
project (only programming would be missing).


Lennart

On 11/04/13 21:39, Maarten Kooyman wrote:
> Dear All,
>
>  I made also a small sketch of a logo. It is pretty raw, colours are
> wrong , etcetera, etcetera.
>
> To quote Nicola:
> " If you hate it or think it should go in another direction, I'm not
> touchy so please do tell me. "
>
>
> Cheers,
>
> Maarten
>
>
> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>> Dear all,
>>
>>
>> I gave a shot at the logo, it's very simple. Let me know if you like
>> the general idea, if you'd like to add something or change it.
>>
>> As colors I've sticked to those of the website but they can be
>> changed. Also the pattern for the formulas have some white spaces, but
>> this is just a quick draft.
>>
>> If you hate it or think it should go in another direction, I'm not
>> touchy so please do tell me.
>>
>> Best.
>>
>> Nicola
>
>
>> Dear all,
>>>
>>> I really like the proposal, I just to add a few ideas to the discussion.
>>> I think that there are some important concepts that could be used for
>>> a logo:
>>>
>>> 1) ABEL which is able in the end could be something like a hammer or a
>>> tool of some sort.
>>>
>>> 2) I think that the great thing about the *ABEL project is that it is not
>>> a single group but it is a network of people and we could rappresent that
>>> also.
>>>
>>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
>>> else or maybe a DNA strand a tool and something else (Although I do
>>> realize that it could remind of the comunist party this way :) ).
>>>
>>> 4) I do like animals, but I it should be meanigful somehow (although
>>> Linux
>>> does have a penguin for some obscure reason).
>>>
>>> Best
>>>
>>> Nicola
>>>
>>>
>>>
>>>
>>>
>>>
>>>> Dear Maarten,
>>>>
>>>> I have also some irritation about the fact that there is no recognisable
>>>>> logo on the page. I looks like a complete default page to me: which
>>>>> gives
>>>>> me the impression that there is not any on it. Does someone has
>>>>> graphical
>>>>> skills to create a nice logo which we can use on the site, posters or
>>>>> presentations? Having a neat logo, is like wearing a suite: people
>>>>> think
>>>>> at
>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>>>
>>>>>
>>>> Completely agree and fully support the idea! I even tried to design
>>>> something myself, but it was SO bad :)
>>>>
>>>> Part of the problem is that obvious meaningful symbols (like
>>>> chromosomes,
>>>> sigmas and Gaussians) are boring and used for long time. Another part is
>>>> that we can not just pick say a cute kitty and stop - there should
>>>> be some
>>>> meaning to the symbol (or not?).
>>>>
>>>> Do we have examples of successful, recognizable logos we like?I like
>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>>>
>>>> Yurii
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>
>>>
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>

--
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Thu Apr 11 22:22:15 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 11 Apr 2013 22:22:15 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <51671992.9070100@karssen.org>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>
 <51671169.5090608@gmail.com> <51671992.9070100@karssen.org>
Message-ID: <CAHX9t6KbkTjb_syXUinR6_t2-Mhx0jzLswrwM8c2bX65Ts1_cg@mail.gmail.com>

Hi Guys,

Visually I like Maarten's variant more (cool G!). Nicola's variant seems
too busy (to small to see).

I just had a suggestion from Elena Gusareva to may be have DNA strand
decomposing into sequence of bits (0/1's). I do not know how to do this,
but I like the idea.

Yurii

On Thu, Apr 11, 2013 at 10:14 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Not bad! I really like the way you mixed the G and the DNA.
> Can't we make a combination with Nicola's creation so that we get some
> math in as well? That would nicely integrate two major components of the
> project (only programming would be missing).
>
>
> Lennart
>
> On 11/04/13 21:39, Maarten Kooyman wrote:
> > Dear All,
> >
> >  I made also a small sketch of a logo. It is pretty raw, colours are
> > wrong , etcetera, etcetera.
> >
> > To quote Nicola:
> > " If you hate it or think it should go in another direction, I'm not
> > touchy so please do tell me. "
> >
> >
> > Cheers,
> >
> > Maarten
> >
> >
> > On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
> >> Dear all,
> >>
> >>
> >> I gave a shot at the logo, it's very simple. Let me know if you like
> >> the general idea, if you'd like to add something or change it.
> >>
> >> As colors I've sticked to those of the website but they can be
> >> changed. Also the pattern for the formulas have some white spaces, but
> >> this is just a quick draft.
> >>
> >> If you hate it or think it should go in another direction, I'm not
> >> touchy so please do tell me.
> >>
> >> Best.
> >>
> >> Nicola
> >
> >
> >> Dear all,
> >>>
> >>> I really like the proposal, I just to add a few ideas to the
> discussion.
> >>> I think that there are some important concepts that could be used for
> >>> a logo:
> >>>
> >>> 1) ABEL which is able in the end could be something like a hammer or a
> >>> tool of some sort.
> >>>
> >>> 2) I think that the great thing about the *ABEL project is that it is
> not
> >>> a single group but it is a network of people and we could rappresent
> that
> >>> also.
> >>>
> >>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
> >>> else or maybe a DNA strand a tool and something else (Although I do
> >>> realize that it could remind of the comunist party this way :) ).
> >>>
> >>> 4) I do like animals, but I it should be meanigful somehow (although
> >>> Linux
> >>> does have a penguin for some obscure reason).
> >>>
> >>> Best
> >>>
> >>> Nicola
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>> Dear Maarten,
> >>>>
> >>>> I have also some irritation about the fact that there is no
> recognisable
> >>>>> logo on the page. I looks like a complete default page to me: which
> >>>>> gives
> >>>>> me the impression that there is not any on it. Does someone has
> >>>>> graphical
> >>>>> skills to create a nice logo which we can use on the site, posters or
> >>>>> presentations? Having a neat logo, is like wearing a suite: people
> >>>>> think
> >>>>> at
> >>>>> first sight you are more trustworthy,intelligent etc ect. ;)
> >>>>>
> >>>>>
> >>>> Completely agree and fully support the idea! I even tried to design
> >>>> something myself, but it was SO bad :)
> >>>>
> >>>> Part of the problem is that obvious meaningful symbols (like
> >>>> chromosomes,
> >>>> sigmas and Gaussians) are boring and used for long time. Another part
> is
> >>>> that we can not just pick say a cute kitty and stop - there should
> >>>> be some
> >>>> meaning to the symbol (or not?).
> >>>>
> >>>> Do we have examples of successful, recognizable logos we like?I like
> >>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
> >>>>
> >>>> Yurii
> >>>> _______________________________________________
> >>>> genabel-devel mailing list
> >>>> genabel-devel at lists.r-forge.r-project.org
> >>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
> >>>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>>
> >>>
> >>> _______________________________________________
> >>> genabel-devel mailing list
> >>> genabel-devel at lists.r-forge.r-project.org
> >>> <mailto:genabel-devel at lists.r-forge.r-project.org>
> >>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>
> >>
> >>
> >> _______________________________________________
> >> genabel-devel mailing list
> >> genabel-devel at lists.r-forge.r-project.org
> >>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >
> >
> >
> > _______________________________________________
> > genabel-devel mailing list
> > genabel-devel at lists.r-forge.r-project.org
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From yurii.aulchenko at gmail.com  Thu Apr 11 23:34:55 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 11 Apr 2013 23:34:55 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <51671992.9070100@karssen.org>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org>
Message-ID: <6274237547129198468@unknownmsgid>

What about replacing some letters with Greek ones - this may give some
math flavor?

YA

----------------------
Yurii Aulchenko
(sent from mobile device)

On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org> wrote:

> Not bad! I really like the way you mixed the G and the DNA.
> Can't we make a combination with Nicola's creation so that we get some
> math in as well? That would nicely integrate two major components of the
> project (only programming would be missing).
>
>
> Lennart
>
> On 11/04/13 21:39, Maarten Kooyman wrote:
>> Dear All,
>>
>> I made also a small sketch of a logo. It is pretty raw, colours are
>> wrong , etcetera, etcetera.
>>
>> To quote Nicola:
>> " If you hate it or think it should go in another direction, I'm not
>> touchy so please do tell me. "
>>
>>
>> Cheers,
>>
>> Maarten
>>
>>
>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>>> Dear all,
>>>
>>>
>>> I gave a shot at the logo, it's very simple. Let me know if you like
>>> the general idea, if you'd like to add something or change it.
>>>
>>> As colors I've sticked to those of the website but they can be
>>> changed. Also the pattern for the formulas have some white spaces, but
>>> this is just a quick draft.
>>>
>>> If you hate it or think it should go in another direction, I'm not
>>> touchy so please do tell me.
>>>
>>> Best.
>>>
>>> Nicola
>>
>>
>>> Dear all,
>>>>
>>>> I really like the proposal, I just to add a few ideas to the discussion.
>>>> I think that there are some important concepts that could be used for
>>>> a logo:
>>>>
>>>> 1) ABEL which is able in the end could be something like a hammer or a
>>>> tool of some sort.
>>>>
>>>> 2) I think that the great thing about the *ABEL project is that it is not
>>>> a single group but it is a network of people and we could rappresent that
>>>> also.
>>>>
>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
>>>> else or maybe a DNA strand a tool and something else (Although I do
>>>> realize that it could remind of the comunist party this way :) ).
>>>>
>>>> 4) I do like animals, but I it should be meanigful somehow (although
>>>> Linux
>>>> does have a penguin for some obscure reason).
>>>>
>>>> Best
>>>>
>>>> Nicola
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> Dear Maarten,
>>>>>
>>>>> I have also some irritation about the fact that there is no recognisable
>>>>>> logo on the page. I looks like a complete default page to me: which
>>>>>> gives
>>>>>> me the impression that there is not any on it. Does someone has
>>>>>> graphical
>>>>>> skills to create a nice logo which we can use on the site, posters or
>>>>>> presentations? Having a neat logo, is like wearing a suite: people
>>>>>> think
>>>>>> at
>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>>> Completely agree and fully support the idea! I even tried to design
>>>>> something myself, but it was SO bad :)
>>>>>
>>>>> Part of the problem is that obvious meaningful symbols (like
>>>>> chromosomes,
>>>>> sigmas and Gaussians) are boring and used for long time. Another part is
>>>>> that we can not just pick say a cute kitty and stop - there should
>>>>> be some
>>>>> meaning to the symbol (or not?).
>>>>>
>>>>> Do we have examples of successful, recognizable logos we like?I like
>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>>>>
>>>>> Yurii
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>
>>>>
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>
>>>
>>>
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

From darthastu at gmail.com  Thu Apr 11 23:46:05 2013
From: darthastu at gmail.com (Nicola Pirastu)
Date: Thu, 11 Apr 2013 23:46:05 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <6274237547129198468@unknownmsgid>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
Message-ID: <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com>

I think that the greek letters are a good idea although in GenABEL would look very much the same, maybe in project?

N.

Inviato da iPhone

Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko <yurii.aulchenko at gmail.com> ha scritto:

> What about replacing some letters with Greek ones - this may give some
> math flavor?
> 
> YA
> 
> ----------------------
> Yurii Aulchenko
> (sent from mobile device)
> 
> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org> wrote:
> 
>> Not bad! I really like the way you mixed the G and the DNA.
>> Can't we make a combination with Nicola's creation so that we get some
>> math in as well? That would nicely integrate two major components of the
>> project (only programming would be missing).
>> 
>> 
>> Lennart
>> 
>> On 11/04/13 21:39, Maarten Kooyman wrote:
>>> Dear All,
>>> 
>>> I made also a small sketch of a logo. It is pretty raw, colours are
>>> wrong , etcetera, etcetera.
>>> 
>>> To quote Nicola:
>>> " If you hate it or think it should go in another direction, I'm not
>>> touchy so please do tell me. "
>>> 
>>> 
>>> Cheers,
>>> 
>>> Maarten
>>> 
>>> 
>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>>>> Dear all,
>>>> 
>>>> 
>>>> I gave a shot at the logo, it's very simple. Let me know if you like
>>>> the general idea, if you'd like to add something or change it.
>>>> 
>>>> As colors I've sticked to those of the website but they can be
>>>> changed. Also the pattern for the formulas have some white spaces, but
>>>> this is just a quick draft.
>>>> 
>>>> If you hate it or think it should go in another direction, I'm not
>>>> touchy so please do tell me.
>>>> 
>>>> Best.
>>>> 
>>>> Nicola
>>> 
>>> 
>>>> Dear all,
>>>>> 
>>>>> I really like the proposal, I just to add a few ideas to the discussion.
>>>>> I think that there are some important concepts that could be used for
>>>>> a logo:
>>>>> 
>>>>> 1) ABEL which is able in the end could be something like a hammer or a
>>>>> tool of some sort.
>>>>> 
>>>>> 2) I think that the great thing about the *ABEL project is that it is not
>>>>> a single group but it is a network of people and we could rappresent that
>>>>> also.
>>>>> 
>>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
>>>>> else or maybe a DNA strand a tool and something else (Although I do
>>>>> realize that it could remind of the comunist party this way :) ).
>>>>> 
>>>>> 4) I do like animals, but I it should be meanigful somehow (although
>>>>> Linux
>>>>> does have a penguin for some obscure reason).
>>>>> 
>>>>> Best
>>>>> 
>>>>> Nicola
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> Dear Maarten,
>>>>>> 
>>>>>> I have also some irritation about the fact that there is no recognisable
>>>>>>> logo on the page. I looks like a complete default page to me: which
>>>>>>> gives
>>>>>>> me the impression that there is not any on it. Does someone has
>>>>>>> graphical
>>>>>>> skills to create a nice logo which we can use on the site, posters or
>>>>>>> presentations? Having a neat logo, is like wearing a suite: people
>>>>>>> think
>>>>>>> at
>>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>>>> Completely agree and fully support the idea! I even tried to design
>>>>>> something myself, but it was SO bad :)
>>>>>> 
>>>>>> Part of the problem is that obvious meaningful symbols (like
>>>>>> chromosomes,
>>>>>> sigmas and Gaussians) are boring and used for long time. Another part is
>>>>>> that we can not just pick say a cute kitty and stop - there should
>>>>>> be some
>>>>>> meaning to the symbol (or not?).
>>>>>> 
>>>>>> Do we have examples of successful, recognizable logos we like?I like
>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>>>>> 
>>>>>> Yurii
>>>>>> _______________________________________________
>>>>>> genabel-devel mailing list
>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> 
>> --
>> -----------------------------------------------------------------
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>> 
>> lennart at karssen.org
>> http://blog.karssen.org
>> 
>> Stuur mij aub geen Word of Powerpoint bestanden!
>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>> ------------------------------------------------------------------
>> 
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

From kooyman at gmail.com  Fri Apr 12 09:17:57 2013
From: kooyman at gmail.com (Maarten Kooyman)
Date: Fri, 12 Apr 2013 09:17:57 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com>
Message-ID: <5167B525.6030608@gmail.com>

I think a logo must deliver the message in one go. I think it misses is 
goal if you have to play "where is Waldo?" in a logo: the simpler the 
better. Adding some greek symbols somewhere increase the "where is 
Waldo?"-effect.

Maybe it is a idea to replace "project" with "Statistical toolkit" or 
"statistics project"(or is this plainly rude?)

Maarten

On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
> I think that the greek letters are a good idea although in GenABEL would look very much the same, maybe in project?
>
> N.
>
> Inviato da iPhone
>
> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko <yurii.aulchenko at gmail.com> ha scritto:
>
>> What about replacing some letters with Greek ones - this may give some
>> math flavor?
>>
>> YA
>>
>> ----------------------
>> Yurii Aulchenko
>> (sent from mobile device)
>>
>> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org> wrote:
>>
>>> Not bad! I really like the way you mixed the G and the DNA.
>>> Can't we make a combination with Nicola's creation so that we get some
>>> math in as well? That would nicely integrate two major components of the
>>> project (only programming would be missing).
>>>
>>>
>>> Lennart
>>>
>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>>>> Dear All,
>>>>
>>>> I made also a small sketch of a logo. It is pretty raw, colours are
>>>> wrong , etcetera, etcetera.
>>>>
>>>> To quote Nicola:
>>>> " If you hate it or think it should go in another direction, I'm not
>>>> touchy so please do tell me. "
>>>>
>>>>
>>>> Cheers,
>>>>
>>>> Maarten
>>>>
>>>>
>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>>>>> Dear all,
>>>>>
>>>>>
>>>>> I gave a shot at the logo, it's very simple. Let me know if you like
>>>>> the general idea, if you'd like to add something or change it.
>>>>>
>>>>> As colors I've sticked to those of the website but they can be
>>>>> changed. Also the pattern for the formulas have some white spaces, but
>>>>> this is just a quick draft.
>>>>>
>>>>> If you hate it or think it should go in another direction, I'm not
>>>>> touchy so please do tell me.
>>>>>
>>>>> Best.
>>>>>
>>>>> Nicola
>>>>
>>>>> Dear all,
>>>>>> I really like the proposal, I just to add a few ideas to the discussion.
>>>>>> I think that there are some important concepts that could be used for
>>>>>> a logo:
>>>>>>
>>>>>> 1) ABEL which is able in the end could be something like a hammer or a
>>>>>> tool of some sort.
>>>>>>
>>>>>> 2) I think that the great thing about the *ABEL project is that it is not
>>>>>> a single group but it is a network of people and we could rappresent that
>>>>>> also.
>>>>>>
>>>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
>>>>>> else or maybe a DNA strand a tool and something else (Although I do
>>>>>> realize that it could remind of the comunist party this way :) ).
>>>>>>
>>>>>> 4) I do like animals, but I it should be meanigful somehow (although
>>>>>> Linux
>>>>>> does have a penguin for some obscure reason).
>>>>>>
>>>>>> Best
>>>>>>
>>>>>> Nicola
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Dear Maarten,
>>>>>>>
>>>>>>> I have also some irritation about the fact that there is no recognisable
>>>>>>>> logo on the page. I looks like a complete default page to me: which
>>>>>>>> gives
>>>>>>>> me the impression that there is not any on it. Does someone has
>>>>>>>> graphical
>>>>>>>> skills to create a nice logo which we can use on the site, posters or
>>>>>>>> presentations? Having a neat logo, is like wearing a suite: people
>>>>>>>> think
>>>>>>>> at
>>>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>>>>> Completely agree and fully support the idea! I even tried to design
>>>>>>> something myself, but it was SO bad :)
>>>>>>>
>>>>>>> Part of the problem is that obvious meaningful symbols (like
>>>>>>> chromosomes,
>>>>>>> sigmas and Gaussians) are boring and used for long time. Another part is
>>>>>>> that we can not just pick say a cute kitty and stop - there should
>>>>>>> be some
>>>>>>> meaning to the symbol (or not?).
>>>>>>>
>>>>>>> Do we have examples of successful, recognizable logos we like?I like
>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>>>>>>
>>>>>>> Yurii
>>>>>>> _______________________________________________
>>>>>>> genabel-devel mailing list
>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>
>>>>>> _______________________________________________
>>>>>> genabel-devel mailing list
>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>
>>>>
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> --
>>> -----------------------------------------------------------------
>>> L.C. Karssen
>>> Utrecht
>>> The Netherlands
>>>
>>> lennart at karssen.org
>>> http://blog.karssen.org
>>>
>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>> ------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel


From yurii.aulchenko at gmail.com  Tue Apr 16 09:52:07 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 16 Apr 2013 09:52:07 +0200
Subject: [GenABEL-dev] announcement OmicABEL
Message-ID: <CAHX9t6KBVeKTVuuLqrZpz3cZbNpTtXB1HRoPd_+oh1GzAzSe2Q@mail.gmail.com>

Dear All,

FYI: together with other OmicABEL developers, we have decided to go open
even before publication. We made OmicABEL package page (
http://www.genabel.org/packages/OmicABEL) reachable from the main pages and
announced OmicABEL at the news section of http://genabel.org/ (see
http://genabel.org/news20130416).

Yurii
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From yurii.aulchenko at gmail.com  Tue Apr 16 11:46:26 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 16 Apr 2013 11:46:26 +0200
Subject: [GenABEL-dev] project video tutorial # 2
Message-ID: <CAHX9t6+KoJz56jO57biw04o0uB9VnZzFMYiFYh9fP2RrrwY+gQ@mail.gmail.com>

Dear All,

You may have noticed that I have added a new video tutorial on how you
start using our new open source tutorial (e.g. there is a trick in
uploading the data). The tutorial is available at
http://www.genabel.org/tutorials/video.

I have also tried to compose a quick video introducing the GenABEL project
- some say 1-2-3 minutes video we may want to put on the front page. I must
say I have failed miserably - it is too long, and I made it sound boring
and unprofessional. In case someone would like to improve over existing
video, here is the link to it
http://www.youtube.com[LINKBREAK]u_CkigVtvY8 (replace
[LINKBREAK] with "/watch?v="). You may notice that I put it from my name
and it is 'unlisted' - clearly this is not something for wider
distribution. I can also share the ScreenFlow files upon request.

regards,
Yurii

-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From yurii.aulchenko at gmail.com  Tue Apr 16 23:38:53 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 16 Apr 2013 23:38:53 +0200
Subject: [GenABEL-dev] project video tutorial # 2
In-Reply-To: <CAHX9t6+KoJz56jO57biw04o0uB9VnZzFMYiFYh9fP2RrrwY+gQ@mail.gmail.com>
References: <CAHX9t6+KoJz56jO57biw04o0uB9VnZzFMYiFYh9fP2RrrwY+gQ@mail.gmail.com>
Message-ID: <CAHX9t6LgY_B=Pk6mXrnjG-WyT887qAwkhfaZ4_136vBURPwoYw@mail.gmail.com>

Correction: something went wrong during the upload of this vide to YouTube,
here is updated video:

http://www.youtube.com[LINKBREAK]KNL2nL2VmoI

YA

On Tue, Apr 16, 2013 at 11:46 AM, Yurii Aulchenko <yurii.aulchenko at gmail.com
> wrote:

> Dear All,
>
> You may have noticed that I have added a new video tutorial on how you
> start using our new open source tutorial (e.g. there is a trick in
> uploading the data). The tutorial is available at
> http://www.genabel.org/tutorials/video.
>
> I have also tried to compose a quick video introducing the GenABEL project
> - some say 1-2-3 minutes video we may want to put on the front page. I must
> say I have failed miserably - it is too long, and I made it sound boring
> and unprofessional. In case someone would like to improve over existing
> video, here is the link to it http://www.youtube.com[LINKBREAK]u_CkigVtvY8 (replace
> [LINKBREAK] with "/watch?v="). You may notice that I put it from my name
> and it is 'unlisted' - clearly this is not something for wider
> distribution. I can also share the ScreenFlow files upon request.
>
> regards,
> Yurii
>
>
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From lennart at karssen.org  Wed Apr 17 13:10:31 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 17 Apr 2013 13:10:31 +0200
Subject: [GenABEL-dev] announcement OmicABEL
In-Reply-To: <CAHX9t6KBVeKTVuuLqrZpz3cZbNpTtXB1HRoPd_+oh1GzAzSe2Q@mail.gmail.com>
References: <CAHX9t6KBVeKTVuuLqrZpz3cZbNpTtXB1HRoPd_+oh1GzAzSe2Q@mail.gmail.com>
Message-ID: <516E8327.1040306@karssen.org>

Congratulations!
Let's hope that the beta phase will lead to fruitful discussions and
lots of testing of the code base.


Best,

Lennart.

On 16/04/13 09:52, Yurii Aulchenko wrote:
> Dear All,
> 
> FYI: together with other OmicABEL developers, we have decided to go open
> even before publication. We made OmicABEL package page
> (http://www.genabel.org/packages/OmicABEL) reachable from the main pages
> and announced OmicABEL at the news section of http://genabel.org/ (see
> http://genabel.org/news20130416). 
> 
> Yurii
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Wed Apr 17 13:10:44 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 17 Apr 2013 13:10:44 +0200
Subject: [GenABEL-dev] OmicABEL: GotoBLAS2 issue
Message-ID: <CAHX9t6+z+sCk_LnXB252Ff32PON1CBge4ZB4L=iDoxea1yQZTw@mail.gmail.com>

Dear Diego,

I had another go to try to build GotoBlas2 under Mac OS X and this appears
quite hopeless.

Would that be a big deal to include the OpenBlas (I managed to do that,
http://yurii-aulchenko.blogspot.nl/2013/04/building-openblas-for-mac-os-x-1075-lion.html)
option? - may be you can give me some hints how to do so?

Yurii
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From yurii.aulchenko at gmail.com  Wed Apr 17 15:30:13 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 17 Apr 2013 15:30:13 +0200
Subject: [GenABEL-dev] OmicABEL: GotoBLAS2 issue
In-Reply-To: <CAHX9t6+z+sCk_LnXB252Ff32PON1CBge4ZB4L=iDoxea1yQZTw@mail.gmail.com>
References: <CAHX9t6+z+sCk_LnXB252Ff32PON1CBge4ZB4L=iDoxea1yQZTw@mail.gmail.com>
Message-ID: <CAHX9t6Juh9et+iQJ4xJ8G9CaQdswVbUnqOrxR2agBFGEmxX8WQ@mail.gmail.com>

ok, it looks like if I simply provide openblas instead of gotoblas2
everything compiles, no code changes required

so hope we will be getting Mac binary soon :)

YA

On Wed, Apr 17, 2013 at 1:10 PM, Yurii Aulchenko
<yurii.aulchenko at gmail.com>wrote:

> Dear Diego,
>
> I had another go to try to build GotoBlas2 under Mac OS X and this appears
> quite hopeless.
>
> Would that be a big deal to include the OpenBlas (I managed to do that,
> http://yurii-aulchenko.blogspot.nl/2013/04/building-openblas-for-mac-os-x-1075-lion.html)
> option? - may be you can give me some hints how to do so?
>
> Yurii
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From yurii.aulchenko at gmail.com  Thu Apr 18 17:28:53 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 18 Apr 2013 17:28:53 +0200
Subject: [GenABEL-dev] old html import procedure
Message-ID: <CAHX9t6LUmq8HraiuLte4yB2brGa2v_4jzaix3BA0MufnZaYrpQ@mail.gmail.com>

Hi Tolya,

Can you please remind me what was the 'old' procedure to import static HTML
into Drupal? Somehow HTML_Import is not working in my hands, so I probably
need to stick to the old ways...

YA
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From kianvl at mail.ru  Fri Apr 19 08:14:45 2013
From: kianvl at mail.ru (=?UTF-8?B?QW5hdG9saXkgS2lyaWNoZW5rbw==?=)
Date: Fri, 19 Apr 2013 10:14:45 +0400
Subject: [GenABEL-dev] =?utf-8?q?old_html_import_procedure?=
In-Reply-To: <CAHX9t6LUmq8HraiuLte4yB2brGa2v_4jzaix3BA0MufnZaYrpQ@mail.gmail.com>
References: <CAHX9t6LUmq8HraiuLte4yB2brGa2v_4jzaix3BA0MufnZaYrpQ@mail.gmail.com>
Message-ID: <1366352085.814597202@f277.mail.ru>

 Dear Yurii,

what is a problem?
I just copy/paste html-code, but with some changes.

Anatoly


???????, 18 ?????? 2013, 17:28 +02:00 ?? Yurii Aulchenko <yurii.aulchenko at gmail.com>:
>Hi Tolya,
>
>Can you please remind me what was the 'old' procedure to import static HTML into Drupal? Somehow HTML_Import is not working in my hands, so I probably need to stick to the old ways...
>
>YA
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From yurii.aulchenko at gmail.com  Sat Apr 20 18:22:03 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sat, 20 Apr 2013 18:22:03 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <5167B525.6030608@gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com> <5167B525.6030608@gmail.com>
Message-ID: <7783033322271622686@unknownmsgid>

Dear All,

I now tend to agree with Maarten. I have discussed the logos with a
couple of people who know more about design, and it seems that
introducing Greek letters, 0/1 etc may be bad idea - the logo must be
simple. So if we want to deliver extra message it should probably go
to "subheading". The subheading "project" does not carry much info, I
think. I personally like the "statistical toolkit", but I think it may
miss the point that the idea of the project is a bit broader than the
software.

So, on the top of Maarten's suggestions, what about:

- methodology project
- open methodology
- methodological toolbox
- methodology
- agile methodology

YA
----------------------
Yurii Aulchenko
(sent from mobile device)

On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com> wrote:

> I think a logo must deliver the message in one go. I think it misses is goal if you have to play "where is Waldo?" in a logo: the simpler the better. Adding some greek symbols somewhere increase the "where is Waldo?"-effect.
>
> Maybe it is a idea to replace "project" with "Statistical toolkit" or "statistics project"(or is this plainly rude?)
>
> Maarten
>
> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
>> I think that the greek letters are a good idea although in GenABEL would look very much the same, maybe in project?
>>
>> N.
>>
>> Inviato da iPhone
>>
>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko <yurii.aulchenko at gmail.com> ha scritto:
>>
>>> What about replacing some letters with Greek ones - this may give some
>>> math flavor?
>>>
>>> YA
>>>
>>> ----------------------
>>> Yurii Aulchenko
>>> (sent from mobile device)
>>>
>>> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org> wrote:
>>>
>>>> Not bad! I really like the way you mixed the G and the DNA.
>>>> Can't we make a combination with Nicola's creation so that we get some
>>>> math in as well? That would nicely integrate two major components of the
>>>> project (only programming would be missing).
>>>>
>>>>
>>>> Lennart
>>>>
>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>>>>> Dear All,
>>>>>
>>>>> I made also a small sketch of a logo. It is pretty raw, colours are
>>>>> wrong , etcetera, etcetera.
>>>>>
>>>>> To quote Nicola:
>>>>> " If you hate it or think it should go in another direction, I'm not
>>>>> touchy so please do tell me. "
>>>>>
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Maarten
>>>>>
>>>>>
>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>>>>>> Dear all,
>>>>>>
>>>>>>
>>>>>> I gave a shot at the logo, it's very simple. Let me know if you like
>>>>>> the general idea, if you'd like to add something or change it.
>>>>>>
>>>>>> As colors I've sticked to those of the website but they can be
>>>>>> changed. Also the pattern for the formulas have some white spaces, but
>>>>>> this is just a quick draft.
>>>>>>
>>>>>> If you hate it or think it should go in another direction, I'm not
>>>>>> touchy so please do tell me.
>>>>>>
>>>>>> Best.
>>>>>>
>>>>>> Nicola
>>>>>
>>>>>> Dear all,
>>>>>>> I really like the proposal, I just to add a few ideas to the discussion.
>>>>>>> I think that there are some important concepts that could be used for
>>>>>>> a logo:
>>>>>>>
>>>>>>> 1) ABEL which is able in the end could be something like a hammer or a
>>>>>>> tool of some sort.
>>>>>>>
>>>>>>> 2) I think that the great thing about the *ABEL project is that it is not
>>>>>>> a single group but it is a network of people and we could rappresent that
>>>>>>> also.
>>>>>>>
>>>>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
>>>>>>> else or maybe a DNA strand a tool and something else (Although I do
>>>>>>> realize that it could remind of the comunist party this way :) ).
>>>>>>>
>>>>>>> 4) I do like animals, but I it should be meanigful somehow (although
>>>>>>> Linux
>>>>>>> does have a penguin for some obscure reason).
>>>>>>>
>>>>>>> Best
>>>>>>>
>>>>>>> Nicola
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Dear Maarten,
>>>>>>>>
>>>>>>>> I have also some irritation about the fact that there is no recognisable
>>>>>>>>> logo on the page. I looks like a complete default page to me: which
>>>>>>>>> gives
>>>>>>>>> me the impression that there is not any on it. Does someone has
>>>>>>>>> graphical
>>>>>>>>> skills to create a nice logo which we can use on the site, posters or
>>>>>>>>> presentations? Having a neat logo, is like wearing a suite: people
>>>>>>>>> think
>>>>>>>>> at
>>>>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>>>>>> Completely agree and fully support the idea! I even tried to design
>>>>>>>> something myself, but it was SO bad :)
>>>>>>>>
>>>>>>>> Part of the problem is that obvious meaningful symbols (like
>>>>>>>> chromosomes,
>>>>>>>> sigmas and Gaussians) are boring and used for long time. Another part is
>>>>>>>> that we can not just pick say a cute kitty and stop - there should
>>>>>>>> be some
>>>>>>>> meaning to the symbol (or not?).
>>>>>>>>
>>>>>>>> Do we have examples of successful, recognizable logos we like?I like
>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>>>>>>>
>>>>>>>> Yurii
>>>>>>>> _______________________________________________
>>>>>>>> genabel-devel mailing list
>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> genabel-devel mailing list
>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> genabel-devel mailing list
>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>> --
>>>> -----------------------------------------------------------------
>>>> L.C. Karssen
>>>> Utrecht
>>>> The Netherlands
>>>>
>>>> lennart at karssen.org
>>>> http://blog.karssen.org
>>>>
>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>> ------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

From lennart at karssen.org  Sat Apr 20 23:09:11 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Sat, 20 Apr 2013 23:09:11 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <7783033322271622686@unknownmsgid>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com> <5167B525.6030608@gmail.com>
 <7783033322271622686@unknownmsgid>
Message-ID: <517303F7.9020806@karssen.org>

Short is better in marketing, so in that sense I agree with Maarten and
Yurii. But it should cover what we do in/with the project.
What about:

GenABEL
Statistical Genetics


Methodology is too "open", our project is focused on statistical
genetics (in all its aspects, from methodology development to
implementation and user support, but the core is about analysing genetic
data).


Best,

Lennart.

On 20/04/13 18:22, Yurii Aulchenko wrote:
> Dear All,
> 
> I now tend to agree with Maarten. I have discussed the logos with a
> couple of people who know more about design, and it seems that
> introducing Greek letters, 0/1 etc may be bad idea - the logo must be
> simple. So if we want to deliver extra message it should probably go
> to "subheading". The subheading "project" does not carry much info, I
> think. I personally like the "statistical toolkit", but I think it may
> miss the point that the idea of the project is a bit broader than the
> software.
> 
> So, on the top of Maarten's suggestions, what about:
> 
> - methodology project
> - open methodology
> - methodological toolbox
> - methodology
> - agile methodology
> 
> YA
> ----------------------
> Yurii Aulchenko
> (sent from mobile device)
> 
> On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com> wrote:
> 
>> I think a logo must deliver the message in one go. I think it misses is goal if you have to play "where is Waldo?" in a logo: the simpler the better. Adding some greek symbols somewhere increase the "where is Waldo?"-effect.
>>
>> Maybe it is a idea to replace "project" with "Statistical toolkit" or "statistics project"(or is this plainly rude?)
>>
>> Maarten
>>
>> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
>>> I think that the greek letters are a good idea although in GenABEL would look very much the same, maybe in project?
>>>
>>> N.
>>>
>>> Inviato da iPhone
>>>
>>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko <yurii.aulchenko at gmail.com> ha scritto:
>>>
>>>> What about replacing some letters with Greek ones - this may give some
>>>> math flavor?
>>>>
>>>> YA
>>>>
>>>> ----------------------
>>>> Yurii Aulchenko
>>>> (sent from mobile device)
>>>>
>>>> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org> wrote:
>>>>
>>>>> Not bad! I really like the way you mixed the G and the DNA.
>>>>> Can't we make a combination with Nicola's creation so that we get some
>>>>> math in as well? That would nicely integrate two major components of the
>>>>> project (only programming would be missing).
>>>>>
>>>>>
>>>>> Lennart
>>>>>
>>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>>>>>> Dear All,
>>>>>>
>>>>>> I made also a small sketch of a logo. It is pretty raw, colours are
>>>>>> wrong , etcetera, etcetera.
>>>>>>
>>>>>> To quote Nicola:
>>>>>> " If you hate it or think it should go in another direction, I'm not
>>>>>> touchy so please do tell me. "
>>>>>>
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Maarten
>>>>>>
>>>>>>
>>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>>>>>>> Dear all,
>>>>>>>
>>>>>>>
>>>>>>> I gave a shot at the logo, it's very simple. Let me know if you like
>>>>>>> the general idea, if you'd like to add something or change it.
>>>>>>>
>>>>>>> As colors I've sticked to those of the website but they can be
>>>>>>> changed. Also the pattern for the formulas have some white spaces, but
>>>>>>> this is just a quick draft.
>>>>>>>
>>>>>>> If you hate it or think it should go in another direction, I'm not
>>>>>>> touchy so please do tell me.
>>>>>>>
>>>>>>> Best.
>>>>>>>
>>>>>>> Nicola
>>>>>>
>>>>>>> Dear all,
>>>>>>>> I really like the proposal, I just to add a few ideas to the discussion.
>>>>>>>> I think that there are some important concepts that could be used for
>>>>>>>> a logo:
>>>>>>>>
>>>>>>>> 1) ABEL which is able in the end could be something like a hammer or a
>>>>>>>> tool of some sort.
>>>>>>>>
>>>>>>>> 2) I think that the great thing about the *ABEL project is that it is not
>>>>>>>> a single group but it is a network of people and we could rappresent that
>>>>>>>> also.
>>>>>>>>
>>>>>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or something
>>>>>>>> else or maybe a DNA strand a tool and something else (Although I do
>>>>>>>> realize that it could remind of the comunist party this way :) ).
>>>>>>>>
>>>>>>>> 4) I do like animals, but I it should be meanigful somehow (although
>>>>>>>> Linux
>>>>>>>> does have a penguin for some obscure reason).
>>>>>>>>
>>>>>>>> Best
>>>>>>>>
>>>>>>>> Nicola
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Dear Maarten,
>>>>>>>>>
>>>>>>>>> I have also some irritation about the fact that there is no recognisable
>>>>>>>>>> logo on the page. I looks like a complete default page to me: which
>>>>>>>>>> gives
>>>>>>>>>> me the impression that there is not any on it. Does someone has
>>>>>>>>>> graphical
>>>>>>>>>> skills to create a nice logo which we can use on the site, posters or
>>>>>>>>>> presentations? Having a neat logo, is like wearing a suite: people
>>>>>>>>>> think
>>>>>>>>>> at
>>>>>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>>>>>>>>> Completely agree and fully support the idea! I even tried to design
>>>>>>>>> something myself, but it was SO bad :)
>>>>>>>>>
>>>>>>>>> Part of the problem is that obvious meaningful symbols (like
>>>>>>>>> chromosomes,
>>>>>>>>> sigmas and Gaussians) are boring and used for long time. Another part is
>>>>>>>>> that we can not just pick say a cute kitty and stop - there should
>>>>>>>>> be some
>>>>>>>>> meaning to the symbol (or not?).
>>>>>>>>>
>>>>>>>>> Do we have examples of successful, recognizable logos we like?I like
>>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very distinguished.
>>>>>>>>>
>>>>>>>>> Yurii
>>>>>>>>> _______________________________________________
>>>>>>>>> genabel-devel mailing list
>>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> genabel-devel mailing list
>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> genabel-devel mailing list
>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> genabel-devel mailing list
>>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>> --
>>>>> -----------------------------------------------------------------
>>>>> L.C. Karssen
>>>>> Utrecht
>>>>> The Netherlands
>>>>>
>>>>> lennart at karssen.org
>>>>> http://blog.karssen.org
>>>>>
>>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>>> ------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
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From yurii.aulchenko at gmail.com  Mon Apr 22 21:30:35 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Mon, 22 Apr 2013 21:30:35 +0200
Subject: [GenABEL-dev] old html import procedure
In-Reply-To: <1366352085.814597202@f277.mail.ru>
References: <CAHX9t6LUmq8HraiuLte4yB2brGa2v_4jzaix3BA0MufnZaYrpQ@mail.gmail.com>
 <1366352085.814597202@f277.mail.ru>
Message-ID: <CAHX9t6+7CwSL++ncoHLUFN-4h1oY4Q0TTO+koihw=xdAKeTadg@mail.gmail.com>

Thank you! Sounds simple enough... just need to make sure that all image
files are there and links are corrected. Not something to be done in 5
minutes though...

YA

On Fri, Apr 19, 2013 at 8:14 AM, Anatoliy Kirichenko <kianvl at mail.ru> wrote:

> Dear Yurii,
>
> what is a problem?
> I just copy/paste html-code, but with some changes.
>
> Anatoly
>
>
> ???????, 18 ?????? 2013, 17:28 +02:00 ?? Yurii Aulchenko <
> yurii.aulchenko at gmail.com>:
>
>   Hi Tolya,
>
> Can you please remind me what was the 'old' procedure to import static
> HTML into Drupal? Somehow HTML_Import is not working in my hands, so I
> probably need to stick to the old ways...
>
> YA
>
>
>


-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From lennart at karssen.org  Wed Apr 24 16:37:44 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 24 Apr 2013 16:37:44 +0200
Subject: [GenABEL-dev] OmicABEL: DatABEL double format
Message-ID: <5177EE38.2050008@karssen.org>

Dear list,

I was reading through the OmicABEL tutorial and noted that the DatABEL
files should be in Double format. By default the GenABEL function
mach2databel() creates float files.

This means that all existing DatABEL files should be converted to
double. I guess we should add a "convertType" program to the filevector
utilities to make life easier for people. Or add a similar R function to
DatABEL (and update mach2databel()).

Does anybody have an idea if such a conversion from float to double can
be done quickly? Of course conversion via an intermediate text file is
also possible, but seems a bit awkward.


As an aside, this would probably also fix the problems I ran into while
trying to make ProbABEL compute everything in doubles (see
http://lists.r-forge.r-project.org/pipermail/genabel-devel/2013-February/000505.html).



Lennart.
-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
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From yurii.aulchenko at gmail.com  Fri Apr 26 17:04:46 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 26 Apr 2013 17:04:46 +0200
Subject: [GenABEL-dev] Tablet GWAS
Message-ID: <-3613700242294250055@unknownmsgid>

Hi Lennart,

I think we should make a video of your Pi tablet running a small GWAS
:) Can we do this? - I am serious. Will work great as promotion
material for GenA. Arabidopsis data set is relatively small, and I
have that imported.

Yurii

From lennart at karssen.org  Mon Apr 29 09:07:19 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 29 Apr 2013 09:07:19 +0200
Subject: [GenABEL-dev] Tablet GWAS
In-Reply-To: <-3613700242294250055@unknownmsgid>
References: <-3613700242294250055@unknownmsgid>
Message-ID: <517E1C27.3040408@karssen.org>

Hi Yurii,

That sounds like a fun plan. I'll have a look at it once I've finished
setting up everything in our new study (The Pi is still in a box
somewhere).


Lennart.

On 26/04/13 17:04, Yurii Aulchenko wrote:
> Hi Lennart,
> 
> I think we should make a video of your Pi tablet running a small GWAS
> :) Can we do this? - I am serious. Will work great as promotion
> material for GenA. Arabidopsis data set is relatively small, and I
> have that imported.
> 
> Yurii
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Mon Apr 29 22:15:20 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Mon, 29 Apr 2013 22:15:20 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <517303F7.9020806@karssen.org>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>
 <51671169.5090608@gmail.com> <51671992.9070100@karssen.org>
 <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com>
 <5167B525.6030608@gmail.com> <7783033322271622686@unknownmsgid>
 <517303F7.9020806@karssen.org>
Message-ID: <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>

Agree.

We have discussed this a bit during EMGM-2013 with Lennart and Nicola, and
our suggestion (N, L, please correct me if I am wrong) is to

1) Pick up Maarten's variant

2) Replace "project" with "Statistical Genomics" as suggested below

3) Send this to a professional designer to make it 'nice' (I am willing to
pay it unless it is too expensive)

And of cause the logo can evolve later on if we get better ideas :)

Please let us know what you think.

YA

On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Short is better in marketing, so in that sense I agree with Maarten and
> Yurii. But it should cover what we do in/with the project.
> What about:
>
> GenABEL
> Statistical Genetics
>
>
> Methodology is too "open", our project is focused on statistical
> genetics (in all its aspects, from methodology development to
> implementation and user support, but the core is about analysing genetic
> data).
>
>
> Best,
>
> Lennart.
>
> On 20/04/13 18:22, Yurii Aulchenko wrote:
> > Dear All,
> >
> > I now tend to agree with Maarten. I have discussed the logos with a
> > couple of people who know more about design, and it seems that
> > introducing Greek letters, 0/1 etc may be bad idea - the logo must be
> > simple. So if we want to deliver extra message it should probably go
> > to "subheading". The subheading "project" does not carry much info, I
> > think. I personally like the "statistical toolkit", but I think it may
> > miss the point that the idea of the project is a bit broader than the
> > software.
> >
> > So, on the top of Maarten's suggestions, what about:
> >
> > - methodology project
> > - open methodology
> > - methodological toolbox
> > - methodology
> > - agile methodology
> >
> > YA
> > ----------------------
> > Yurii Aulchenko
> > (sent from mobile device)
> >
> > On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com> wrote:
> >
> >> I think a logo must deliver the message in one go. I think it misses is
> goal if you have to play "where is Waldo?" in a logo: the simpler the
> better. Adding some greek symbols somewhere increase the "where is
> Waldo?"-effect.
> >>
> >> Maybe it is a idea to replace "project" with "Statistical toolkit" or
> "statistics project"(or is this plainly rude?)
> >>
> >> Maarten
> >>
> >> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
> >>> I think that the greek letters are a good idea although in GenABEL
> would look very much the same, maybe in project?
> >>>
> >>> N.
> >>>
> >>> Inviato da iPhone
> >>>
> >>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko <
> yurii.aulchenko at gmail.com> ha scritto:
> >>>
> >>>> What about replacing some letters with Greek ones - this may give some
> >>>> math flavor?
> >>>>
> >>>> YA
> >>>>
> >>>> ----------------------
> >>>> Yurii Aulchenko
> >>>> (sent from mobile device)
> >>>>
> >>>> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org> wrote:
> >>>>
> >>>>> Not bad! I really like the way you mixed the G and the DNA.
> >>>>> Can't we make a combination with Nicola's creation so that we get
> some
> >>>>> math in as well? That would nicely integrate two major components of
> the
> >>>>> project (only programming would be missing).
> >>>>>
> >>>>>
> >>>>> Lennart
> >>>>>
> >>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
> >>>>>> Dear All,
> >>>>>>
> >>>>>> I made also a small sketch of a logo. It is pretty raw, colours are
> >>>>>> wrong , etcetera, etcetera.
> >>>>>>
> >>>>>> To quote Nicola:
> >>>>>> " If you hate it or think it should go in another direction, I'm not
> >>>>>> touchy so please do tell me. "
> >>>>>>
> >>>>>>
> >>>>>> Cheers,
> >>>>>>
> >>>>>> Maarten
> >>>>>>
> >>>>>>
> >>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
> >>>>>>> Dear all,
> >>>>>>>
> >>>>>>>
> >>>>>>> I gave a shot at the logo, it's very simple. Let me know if you
> like
> >>>>>>> the general idea, if you'd like to add something or change it.
> >>>>>>>
> >>>>>>> As colors I've sticked to those of the website but they can be
> >>>>>>> changed. Also the pattern for the formulas have some white spaces,
> but
> >>>>>>> this is just a quick draft.
> >>>>>>>
> >>>>>>> If you hate it or think it should go in another direction, I'm not
> >>>>>>> touchy so please do tell me.
> >>>>>>>
> >>>>>>> Best.
> >>>>>>>
> >>>>>>> Nicola
> >>>>>>
> >>>>>>> Dear all,
> >>>>>>>> I really like the proposal, I just to add a few ideas to the
> discussion.
> >>>>>>>> I think that there are some important concepts that could be used
> for
> >>>>>>>> a logo:
> >>>>>>>>
> >>>>>>>> 1) ABEL which is able in the end could be something like a hammer
> or a
> >>>>>>>> tool of some sort.
> >>>>>>>>
> >>>>>>>> 2) I think that the great thing about the *ABEL project is that
> it is not
> >>>>>>>> a single group but it is a network of people and we could
> rappresent that
> >>>>>>>> also.
> >>>>>>>>
> >>>>>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or
> something
> >>>>>>>> else or maybe a DNA strand a tool and something else (Although I
> do
> >>>>>>>> realize that it could remind of the comunist party this way :) ).
> >>>>>>>>
> >>>>>>>> 4) I do like animals, but I it should be meanigful somehow
> (although
> >>>>>>>> Linux
> >>>>>>>> does have a penguin for some obscure reason).
> >>>>>>>>
> >>>>>>>> Best
> >>>>>>>>
> >>>>>>>> Nicola
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> Dear Maarten,
> >>>>>>>>>
> >>>>>>>>> I have also some irritation about the fact that there is no
> recognisable
> >>>>>>>>>> logo on the page. I looks like a complete default page to me:
> which
> >>>>>>>>>> gives
> >>>>>>>>>> me the impression that there is not any on it. Does someone has
> >>>>>>>>>> graphical
> >>>>>>>>>> skills to create a nice logo which we can use on the site,
> posters or
> >>>>>>>>>> presentations? Having a neat logo, is like wearing a suite:
> people
> >>>>>>>>>> think
> >>>>>>>>>> at
> >>>>>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
> >>>>>>>>> Completely agree and fully support the idea! I even tried to
> design
> >>>>>>>>> something myself, but it was SO bad :)
> >>>>>>>>>
> >>>>>>>>> Part of the problem is that obvious meaningful symbols (like
> >>>>>>>>> chromosomes,
> >>>>>>>>> sigmas and Gaussians) are boring and used for long time. Another
> part is
> >>>>>>>>> that we can not just pick say a cute kitty and stop - there
> should
> >>>>>>>>> be some
> >>>>>>>>> meaning to the symbol (or not?).
> >>>>>>>>>
> >>>>>>>>> Do we have examples of successful, recognizable logos we like?I
> like
> >>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very
> distinguished.
> >>>>>>>>>
> >>>>>>>>> Yurii
> >>>>>>>>> _______________________________________________
> >>>>>>>>> genabel-devel mailing list
> >>>>>>>>> genabel-devel at lists.r-forge.r-project.org
> >>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
> >>>>>>>>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> genabel-devel mailing list
> >>>>>>>> genabel-devel at lists.r-forge.r-project.org
> >>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
> >>>>>>>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> genabel-devel mailing list
> >>>>>>> genabel-devel at lists.r-forge.r-project.org
> >>>>>>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> genabel-devel mailing list
> >>>>>> genabel-devel at lists.r-forge.r-project.org
> >>>>>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>>>> --
> >>>>> -----------------------------------------------------------------
> >>>>> L.C. Karssen
> >>>>> Utrecht
> >>>>> The Netherlands
> >>>>>
> >>>>> lennart at karssen.org
> >>>>> http://blog.karssen.org
> >>>>>
> >>>>> Stuur mij aub geen Word of Powerpoint bestanden!
> >>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> >>>>> ------------------------------------------------------------------
> >>>>>
> >>>>> _______________________________________________
> >>>>> genabel-devel mailing list
> >>>>> genabel-devel at lists.r-forge.r-project.org
> >>>>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>>> _______________________________________________
> >>>> genabel-devel mailing list
> >>>> genabel-devel at lists.r-forge.r-project.org
> >>>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>> _______________________________________________
> >>> genabel-devel mailing list
> >>> genabel-devel at lists.r-forge.r-project.org
> >>>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >>
> >> _______________________________________________
> >> genabel-devel mailing list
> >> genabel-devel at lists.r-forge.r-project.org
> >>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> > _______________________________________________
> > genabel-devel mailing list
> > genabel-devel at lists.r-forge.r-project.org
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >
>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>



-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From mgmaria at yandex.ru  Tue Apr 30 11:51:04 2013
From: mgmaria at yandex.ru (Maria G)
Date: Tue, 30 Apr 2013 13:51:04 +0400
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
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 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>
 <51671169.5090608@gmail.com> <51671992.9070100@karssen.org>
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From fabregat at aices.rwth-aachen.de  Tue Apr 30 12:14:32 2013
From: fabregat at aices.rwth-aachen.de (Diego Fabregat)
Date: Tue, 30 Apr 2013 12:14:32 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
Message-ID: <201304301214.33214.fabregat@aices.rwth-aachen.de>

Hi all,

If I'm allowed some criticism to the logo, even though I like the fusion of 
the G and the DNA, it may compromise its readability. Unfortunately, I don't 
have any better idea.

In any case, great job. And  yes, it sounds like a good plan.

On Monday 29 April 2013 22:15:20 Yurii Aulchenko wrote:
> Agree.
> 
> We have discussed this a bit during EMGM-2013 with Lennart and Nicola, and
> our suggestion (N, L, please correct me if I am wrong) is to
> 
> 1) Pick up Maarten's variant
> 
> 2) Replace "project" with "Statistical Genomics" as suggested below
> 
> 3) Send this to a professional designer to make it 'nice' (I am willing to
> pay it unless it is too expensive)
> 
> And of cause the logo can evolve later on if we get better ideas :)
> 
> Please let us know what you think.
> 
> YA
> 
> On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen <lennart at karssen.org> wrote:
> > Short is better in marketing, so in that sense I agree with Maarten and
> > Yurii. But it should cover what we do in/with the project.
> > What about:
> > 
> > GenABEL
> > Statistical Genetics
> > 
> > 
> > Methodology is too "open", our project is focused on statistical
> > genetics (in all its aspects, from methodology development to
> > implementation and user support, but the core is about analysing genetic
> > data).
> > 
> > 
> > Best,
> > 
> > Lennart.
> > 
> > On 20/04/13 18:22, Yurii Aulchenko wrote:
> > > Dear All,
> > > 
> > > I now tend to agree with Maarten. I have discussed the logos with a
> > > couple of people who know more about design, and it seems that
> > > introducing Greek letters, 0/1 etc may be bad idea - the logo must be
> > > simple. So if we want to deliver extra message it should probably go
> > > to "subheading". The subheading "project" does not carry much info, I
> > > think. I personally like the "statistical toolkit", but I think it may
> > > miss the point that the idea of the project is a bit broader than the
> > > software.
> > > 
> > > So, on the top of Maarten's suggestions, what about:
> > > 
> > > - methodology project
> > > - open methodology
> > > - methodological toolbox
> > > - methodology
> > > - agile methodology
> > > 
> > > YA
> > > ----------------------
> > > Yurii Aulchenko
> > > (sent from mobile device)
> > > 
> > > On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com> wrote:
> > >> I think a logo must deliver the message in one go. I think it misses
> > >> is
> > 
> > goal if you have to play "where is Waldo?" in a logo: the simpler the
> > better. Adding some greek symbols somewhere increase the "where is
> > Waldo?"-effect.
> > 
> > >> Maybe it is a idea to replace "project" with "Statistical toolkit" or
> > 
> > "statistics project"(or is this plainly rude?)
> > 
> > >> Maarten
> > >> 
> > >> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
> > >>> I think that the greek letters are a good idea although in GenABEL
> > 
> > would look very much the same, maybe in project?
> > 
> > >>> N.
> > >>> 
> > >>> Inviato da iPhone
> > >>> 
> > >>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko <
> > 
> > yurii.aulchenko at gmail.com> ha scritto:
> > >>>> What about replacing some letters with Greek ones - this may give
> > >>>> some math flavor?
> > >>>> 
> > >>>> YA
> > >>>> 
> > >>>> ----------------------
> > >>>> Yurii Aulchenko
> > >>>> (sent from mobile device)
> > >>>> 
> > >>>> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org> wrote:
> > >>>>> Not bad! I really like the way you mixed the G and the DNA.
> > >>>>> Can't we make a combination with Nicola's creation so that we get
> > 
> > some
> > 
> > >>>>> math in as well? That would nicely integrate two major components
> > >>>>> of
> > 
> > the
> > 
> > >>>>> project (only programming would be missing).
> > >>>>> 
> > >>>>> 
> > >>>>> Lennart
> > >>>>> 
> > >>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
> > >>>>>> Dear All,
> > >>>>>> 
> > >>>>>> I made also a small sketch of a logo. It is pretty raw, colours
> > >>>>>> are wrong , etcetera, etcetera.
> > >>>>>> 
> > >>>>>> To quote Nicola:
> > >>>>>> " If you hate it or think it should go in another direction, I'm
> > >>>>>> not touchy so please do tell me. "
> > >>>>>> 
> > >>>>>> 
> > >>>>>> Cheers,
> > >>>>>> 
> > >>>>>> Maarten
> > >>>>>> 
> > >>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
> > >>>>>>> Dear all,
> > >>>>>>> 
> > >>>>>>> 
> > >>>>>>> I gave a shot at the logo, it's very simple. Let me know if you
> > 
> > like
> > 
> > >>>>>>> the general idea, if you'd like to add something or change it.
> > >>>>>>> 
> > >>>>>>> As colors I've sticked to those of the website but they can be
> > >>>>>>> changed. Also the pattern for the formulas have some white
> > >>>>>>> spaces,
> > 
> > but
> > 
> > >>>>>>> this is just a quick draft.
> > >>>>>>> 
> > >>>>>>> If you hate it or think it should go in another direction, I'm
> > >>>>>>> not touchy so please do tell me.
> > >>>>>>> 
> > >>>>>>> Best.
> > >>>>>>> 
> > >>>>>>> Nicola
> > >>>>>>> 
> > >>>>>>> Dear all,
> > >>>>>>> 
> > >>>>>>>> I really like the proposal, I just to add a few ideas to the
> > 
> > discussion.
> > 
> > >>>>>>>> I think that there are some important concepts that could be
> > >>>>>>>> used
> > 
> > for
> > 
> > >>>>>>>> a logo:
> > >>>>>>>> 
> > >>>>>>>> 1) ABEL which is able in the end could be something like a
> > >>>>>>>> hammer
> > 
> > or a
> > 
> > >>>>>>>> tool of some sort.
> > >>>>>>>> 
> > >>>>>>>> 2) I think that the great thing about the *ABEL project is that
> > 
> > it is not
> > 
> > >>>>>>>> a single group but it is a network of people and we could
> > 
> > rappresent that
> > 
> > >>>>>>>> also.
> > >>>>>>>> 
> > >>>>>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or
> > 
> > something
> > 
> > >>>>>>>> else or maybe a DNA strand a tool and something else (Although I
> > 
> > do
> > 
> > >>>>>>>> realize that it could remind of the comunist party this way :)
> > >>>>>>>> ).
> > >>>>>>>> 
> > >>>>>>>> 4) I do like animals, but I it should be meanigful somehow
> > 
> > (although
> > 
> > >>>>>>>> Linux
> > >>>>>>>> does have a penguin for some obscure reason).
> > >>>>>>>> 
> > >>>>>>>> Best
> > >>>>>>>> 
> > >>>>>>>> Nicola
> > >>>>>>>> 
> > >>>>>>>>> Dear Maarten,
> > >>>>>>>>> 
> > >>>>>>>>> I have also some irritation about the fact that there is no
> > 
> > recognisable
> > 
> > >>>>>>>>>> logo on the page. I looks like a complete default page to me:
> > which
> > 
> > >>>>>>>>>> gives
> > >>>>>>>>>> me the impression that there is not any on it. Does someone
> > >>>>>>>>>> has graphical
> > >>>>>>>>>> skills to create a nice logo which we can use on the site,
> > 
> > posters or
> > 
> > >>>>>>>>>> presentations? Having a neat logo, is like wearing a suite:
> > people
> > 
> > >>>>>>>>>> think
> > >>>>>>>>>> at
> > >>>>>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
> > >>>>>>>>> 
> > >>>>>>>>> Completely agree and fully support the idea! I even tried to
> > 
> > design
> > 
> > >>>>>>>>> something myself, but it was SO bad :)
> > >>>>>>>>> 
> > >>>>>>>>> Part of the problem is that obvious meaningful symbols (like
> > >>>>>>>>> chromosomes,
> > >>>>>>>>> sigmas and Gaussians) are boring and used for long time.
> > >>>>>>>>> Another
> > 
> > part is
> > 
> > >>>>>>>>> that we can not just pick say a cute kitty and stop - there
> > 
> > should
> > 
> > >>>>>>>>> be some
> > >>>>>>>>> meaning to the symbol (or not?).
> > >>>>>>>>> 
> > >>>>>>>>> Do we have examples of successful, recognizable logos we like?I
> > 
> > like
> > 
> > >>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very
> > 
> > distinguished.
> > 
> > >>>>>>>>> Yurii
> > >>>>>>>>> _______________________________________________
> > >>>>>>>>> genabel-devel mailing list
> > >>>>>>>>> genabel-devel at lists.r-forge.r-project.org
> > >>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l
> > 
> > >>>>>>>> _______________________________________________
> > >>>>>>>> genabel-devel mailing list
> > >>>>>>>> genabel-devel at lists.r-forge.r-project.org
> > >>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l
> > 
> > >>>>>>> _______________________________________________
> > >>>>>>> genabel-devel mailing list
> > >>>>>>> genabel-devel at lists.r-forge.r-project.org
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l
> > 
> > >>>>>> _______________________________________________
> > >>>>>> genabel-devel mailing list
> > >>>>>> genabel-devel at lists.r-forge.r-project.org
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l
> > 
> > >>>>> --
> > >>>>> -----------------------------------------------------------------
> > >>>>> L.C. Karssen
> > >>>>> Utrecht
> > >>>>> The Netherlands
> > >>>>> 
> > >>>>> lennart at karssen.org
> > >>>>> http://blog.karssen.org
> > >>>>> 
> > >>>>> Stuur mij aub geen Word of Powerpoint bestanden!
> > >>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> > >>>>> ------------------------------------------------------------------
> > >>>>> 
> > >>>>> _______________________________________________
> > >>>>> genabel-devel mailing list
> > >>>>> genabel-devel at lists.r-forge.r-project.org
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l
> > 
> > >>>> _______________________________________________
> > >>>> genabel-devel mailing list
> > >>>> genabel-devel at lists.r-forge.r-project.org
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l
> > 
> > >>> _______________________________________________
> > >>> genabel-devel mailing list
> > >>> genabel-devel at lists.r-forge.r-project.org
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l
> > 
> > >> _______________________________________________
> > >> genabel-devel mailing list
> > >> genabel-devel at lists.r-forge.r-project.org
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l
> > 
> > > _______________________________________________
> > > genabel-devel mailing list
> > > genabel-devel at lists.r-forge.r-project.org
> > 
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l
> > 
> > 
> > --
> > -----------------------------------------------------------------
> > L.C. Karssen
> > Utrecht
> > The Netherlands
> > 
> > lennart at karssen.org
> > http://blog.karssen.org
> > 
> > Stuur mij aub geen Word of Powerpoint bestanden!
> > Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> > ------------------------------------------------------------------
> > 
> > 
> > _______________________________________________
> > genabel-devel mailing list
> > genabel-devel at lists.r-forge.r-project.org
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve
> > l