From yurii.aulchenko at gmail.com  Mon Mar  4 13:06:49 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Mon, 4 Mar 2013 13:06:49 +0100
Subject: [GenABEL-dev] introducing Sodbo
Message-ID: <CAHX9t6JJb3YDVnKjsg-ASuqPk4HUfq0wGt_tC6tTe1hXHEE8WQ@mail.gmail.com>

Dear All,

Let me introduce Mr. Sodbo Sharapov to the list.

Sodbo is doing Master's in Biology at the Novosibirsk State University
(Russia) under my supervision. In relation to GenABEL, he works together
with Diego, Paolo and me on the OmicABEL package. Keeping in mind this
specific aim, I have added Sodbo to the list of committers.

Welcome, Sodbo!

with best regards,
Yurii
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From lennart at karssen.org  Mon Mar  4 13:19:21 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 04 Mar 2013 13:19:21 +0100
Subject: [GenABEL-dev] introducing Sodbo
In-Reply-To: <CAHX9t6JJb3YDVnKjsg-ASuqPk4HUfq0wGt_tC6tTe1hXHEE8WQ@mail.gmail.com>
References: <CAHX9t6JJb3YDVnKjsg-ASuqPk4HUfq0wGt_tC6tTe1hXHEE8WQ@mail.gmail.com>
Message-ID: <51349149.9050203@karssen.org>

Welcome Sodbo!
I hope you'll enjoy your stay with us :-).



Best regards,

Lennart.


On 03/04/2013 01:06 PM, Yurii Aulchenko wrote:
> Dear All,
> 
> Let me introduce Mr. Sodbo Sharapov to the list.
> 
> Sodbo is doing Master's in Biology at the Novosibirsk State University
> (Russia) under my supervision. In relation to GenABEL, he works together
> with Diego, Paolo and me on the OmicABEL package. Keeping in mind this
> specific aim, I have added Sodbo to the list of committers.
> 
> Welcome, Sodbo!
> 
> with best regards,
> 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  Tue Mar  5 16:43:10 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 5 Mar 2013 16:43:10 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1114 - in pkg/OmicABEL/src: .
	reshuffle
In-Reply-To: <20130305115244.66FA2184271@r-forge.r-project.org>
References: <20130305115244.66FA2184271@r-forge.r-project.org>
Message-ID: <CAHX9t6+CtAM2hSHFTJ3YwyJkAA9AD7rBhq2AAPq0a9pTiJ8iYQ@mail.gmail.com>

Sodbo,

how do you compile this? - is this going to be an option in general
OmicABEL's Makefile?

Trying to g++ it generates:

YAMacBookPro:reshuffle yuryaulchenko$ g++ reshuffle.cpp
reshuffle.cpp:8:17: error: dir.h: No such file or directory
reshuffle.cpp: In member function 'void Reshuffle::run()':
reshuffle.cpp:286: error: 'mkdir' was not declared in this scope
reshuffle.cpp:291: error: 'mkdir' was not declared in this scope
reshuffle.cpp:297: error: 'mkdir' was not declared in this scope
reshuffle.cpp:329: error: 'mkdir' was not declared in this scope
reshuffle.cpp:334: error: 'mkdir' was not declared in this scope
reshuffle.cpp:340: error: 'mkdir' was not declared in this scope
reshuffle.cpp:346: error: 'mkdir' was not declared in this scope

ok, probably I should just be patient - this is, as indicated, version 0.0
:)

YA

PS I have killed ".exe" from README :)

On Tue, Mar 5, 2013 at 12:52 PM, <noreply at r-forge.r-project.org> wrote:

> Author: sharapovsodbo
> Date: 2013-03-05 12:52:43 +0100 (Tue, 05 Mar 2013)
> New Revision: 1114
>
> Added:
>    pkg/OmicABEL/src/reshuffle/
>    pkg/OmicABEL/src/reshuffle/Parameters.cpp
>    pkg/OmicABEL/src/reshuffle/Parameters.h
>    pkg/OmicABEL/src/reshuffle/README.txt
>    pkg/OmicABEL/src/reshuffle/iout_file.cpp
>    pkg/OmicABEL/src/reshuffle/iout_file.h
>    pkg/OmicABEL/src/reshuffle/main.cpp
>    pkg/OmicABEL/src/reshuffle/reshuffle.cpp
>    pkg/OmicABEL/src/reshuffle/reshuffle.h
> Log:
> ver 0.00
> without tests
>
>
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From lennart at karssen.org  Thu Mar  7 20:12:57 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 07 Mar 2013 20:12:57 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
Message-ID: <5138E6B9.7000802@karssen.org>

Hi Yurii,


On 24/02/13 17:27, Yurii Aulchenko wrote:
> 
> But I think we do not need to choose. We could keep both the "full old
> PDF" together with "incomplete new" on the genabel.org
> <http://genabel.org>'s tutorial section. Next, I am going to try to
> construct a smarter Makefile, which could build both 'private' and
> 'public' version depending on the availability of data files. Then we
> could combine both solutions :) 

I think that's the best solution for now. It also allows other people to
help thinking about or even generate the open data sets.

> 
> I think the next steps are 1) for me to look up how many chapters in the
> GenA tutorial become crap when I remove these datasets 2) try to do
> smart Makefile - hopefully with your help

Sure! I have some experience writing Makefiles for LaTeX (the biggest
one being for my PhD thesis, which also took care of image conversion to
PDF and the like). I've also played around with rubber
(https://launchpad.net/rubber/) a bit and it seems to be a nice tool.
However, for most smaller project usually do stuff by hand (or actually
Emacs' AucTeX keybindings). But I'm digressing...
Building a Makefile (-like?) solution for this sounds like a fun challenge.


Lennart.

> 
> Let me know what you think, and I will keep you updated
> 
> best wishes,
> Yurii
> 
> On Wed, Feb 20, 2013 at 10:40 PM, Maarten Kooyman <kooyman at gmail.com
> <mailto:kooyman at gmail.com>> wrote:
> 
>     Dear All,
> 
>     I think on the long run replacing the data is the best thing to do.
>     (although it will take quite some effort).
> 
>     As an temporary solution we could use a build server with jenkins
>     (http://jenkins-ci.org/), that recreates the document after each
>     alteration on svn and publish this on a public place(by coping it to
>     a webserver). On this build server the datasets are secure in a
>     trusted environment and the results are visible to the outer world.
>     I use  Jenkins also  for monitoring Probabel, but the goal is the
>     same: keep the quality of the code in check.
> 
>     This solution prevent coping binary files to svn and this can be
>     done in a completely automated way.
> 
>     Kind regards,
> 
>     Maarten
> 
> 
> 
>     On 02/20/2013 06:54 PM, L.C. Karssen wrote:
> 
>         Dear Yurii,
> 
>         Great idea. I'm all for putting the tutorials in SVN. They are
>         already
>         of high quality and together with our community we can make them
>         even
>         better.
>         I do see the problem with the data sets, of course.
> 
>         You are using Sweave, right? I'm wondering how much not having
>         the data
>         will impact the possibility to tweak the document. Fixing small
>         typos
>         will be alright, but before you know it a typo can mess up the
>         LaTeX or
>         R code and since you can't compile the document to check it this may
>         lead to a lot of bug hunting for you, once you recompile it again.
>         That's the only potential problem I see.
> 
>         How about also including the latest PDF version of the tutorial
>         (I know,
>         this is against SVN's principles) each time you compile a
>         version? This
>         way people who don't have the data know what it is supposed to
>         look like
>         and could even help creating replacement data sets.
> 
> 
>         Best,
> 
>         Lennart.
> 
>         On 02/20/2013 04:35 PM, Yurii Aulchenko wrote:
> 
>             Dear All,
> 
>             For long time I was thinking that GenABEL tutorial(s) should
>             be a part of
>             the project - the same logic as with the code, with the same
>             idea that in
>             such case people can easily contribute by submitting patches
>             and new
>             pieces.
> 
>             The problem was (and still is) that the tutorial uses some
>             data sets, which
>             are not public domain, and it is quite awkward if we as the
>             project start
>             re-distributing them. Little by little I am trying to switch
>             the whole
>             thing to the use of only public and simulated data, but this
>             is a lengthy
>             process.
> 
>             So I thought that may be a good solution is to put the code
>             of tutorials on
>             our SVN; and put the data only if these are either public or
>             simulated. Of
>             cause in this way the tutorials will not be really
>             "functional" (e.g. they
>             would not compile right away), but this may become a
>             starting point for
>             others to build up something new and really
>             free-for-all-to-use-and-__contribute.
> 
>             Let me know what you think,
>             best regards,
>             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
>     <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  Fri Mar  8 09:30:52 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 8 Mar 2013 09:30:52 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <5138E6B9.7000802@karssen.org>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
 <5138E6B9.7000802@karssen.org>
Message-ID: <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>

Ok, great, I think this is the way to go.

Will make an account of private/public files, will push things to SVN
(hopefully some time next week), and see what we can do :)

best wishes,
Yurii

On Thu, Mar 7, 2013 at 8:12 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Hi Yurii,
>
>
> On 24/02/13 17:27, Yurii Aulchenko wrote:
> >
> > But I think we do not need to choose. We could keep both the "full old
> > PDF" together with "incomplete new" on the genabel.org
> > <http://genabel.org>'s tutorial section. Next, I am going to try to
> > construct a smarter Makefile, which could build both 'private' and
> > 'public' version depending on the availability of data files. Then we
> > could combine both solutions :)
>
> I think that's the best solution for now. It also allows other people to
> help thinking about or even generate the open data sets.
>
> >
> > I think the next steps are 1) for me to look up how many chapters in the
> > GenA tutorial become crap when I remove these datasets 2) try to do
> > smart Makefile - hopefully with your help
>
> Sure! I have some experience writing Makefiles for LaTeX (the biggest
> one being for my PhD thesis, which also took care of image conversion to
> PDF and the like). I've also played around with rubber
> (https://launchpad.net/rubber/) a bit and it seems to be a nice tool.
> However, for most smaller project usually do stuff by hand (or actually
> Emacs' AucTeX keybindings). But I'm digressing...
> Building a Makefile (-like?) solution for this sounds like a fun challenge.
>
>
> Lennart.
>
> >
> > Let me know what you think, and I will keep you updated
> >
> > best wishes,
> > Yurii
> >
> > On Wed, Feb 20, 2013 at 10:40 PM, Maarten Kooyman <kooyman at gmail.com
> > <mailto:kooyman at gmail.com>> wrote:
> >
> >     Dear All,
> >
> >     I think on the long run replacing the data is the best thing to do.
> >     (although it will take quite some effort).
> >
> >     As an temporary solution we could use a build server with jenkins
> >     (http://jenkins-ci.org/), that recreates the document after each
> >     alteration on svn and publish this on a public place(by coping it to
> >     a webserver). On this build server the datasets are secure in a
> >     trusted environment and the results are visible to the outer world.
> >     I use  Jenkins also  for monitoring Probabel, but the goal is the
> >     same: keep the quality of the code in check.
> >
> >     This solution prevent coping binary files to svn and this can be
> >     done in a completely automated way.
> >
> >     Kind regards,
> >
> >     Maarten
> >
> >
> >
> >     On 02/20/2013 06:54 PM, L.C. Karssen wrote:
> >
> >         Dear Yurii,
> >
> >         Great idea. I'm all for putting the tutorials in SVN. They are
> >         already
> >         of high quality and together with our community we can make them
> >         even
> >         better.
> >         I do see the problem with the data sets, of course.
> >
> >         You are using Sweave, right? I'm wondering how much not having
> >         the data
> >         will impact the possibility to tweak the document. Fixing small
> >         typos
> >         will be alright, but before you know it a typo can mess up the
> >         LaTeX or
> >         R code and since you can't compile the document to check it this
> may
> >         lead to a lot of bug hunting for you, once you recompile it
> again.
> >         That's the only potential problem I see.
> >
> >         How about also including the latest PDF version of the tutorial
> >         (I know,
> >         this is against SVN's principles) each time you compile a
> >         version? This
> >         way people who don't have the data know what it is supposed to
> >         look like
> >         and could even help creating replacement data sets.
> >
> >
> >         Best,
> >
> >         Lennart.
> >
> >         On 02/20/2013 04:35 PM, Yurii Aulchenko wrote:
> >
> >             Dear All,
> >
> >             For long time I was thinking that GenABEL tutorial(s) should
> >             be a part of
> >             the project - the same logic as with the code, with the same
> >             idea that in
> >             such case people can easily contribute by submitting patches
> >             and new
> >             pieces.
> >
> >             The problem was (and still is) that the tutorial uses some
> >             data sets, which
> >             are not public domain, and it is quite awkward if we as the
> >             project start
> >             re-distributing them. Little by little I am trying to switch
> >             the whole
> >             thing to the use of only public and simulated data, but this
> >             is a lengthy
> >             process.
> >
> >             So I thought that may be a good solution is to put the code
> >             of tutorials on
> >             our SVN; and put the data only if these are either public or
> >             simulated. Of
> >             cause in this way the tutorials will not be really
> >             "functional" (e.g. they
> >             would not compile right away), but this may become a
> >             starting point for
> >             others to build up something new and really
> >             free-for-all-to-use-and-__contribute.
> >
> >             Let me know what you think,
> >             best regards,
> >             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
> >     <
> 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  Fri Mar  8 09:37:14 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 8 Mar 2013 09:37:14 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
 <5138E6B9.7000802@karssen.org>
 <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>
Message-ID: <CAHX9t6KKLCqncnmHK0CZPzLwZZUZhmsShDczj1BUX=v57jf36Q@mail.gmail.com>

Here is another question: for the tutorials we need relative large data
sets (as text files or in RData or other binary format).

On one hand, it is handy to have "all in"; on the other hand - why putting
files which are either binary and/or not likely to change to SVN? - this is
not logical.

The only thing I can think of is to put data files to some server and then
as the first part of the tutorial to "pull" it e.g. using wget. Does affect
cross-platform compatibility though... Also, where we put the files? -
Drupal? - if we have say 100 Megs in data, would it generate too much
traffic so the bill becomes somewhat sensible?

I am really not sure what to do in this respect.

Yurii

On Fri, Mar 8, 2013 at 9:30 AM, Yurii Aulchenko
<yurii.aulchenko at gmail.com>wrote:

> Ok, great, I think this is the way to go.
>
> Will make an account of private/public files, will push things to SVN
> (hopefully some time next week), and see what we can do :)
>
> best wishes,
> Yurii
>
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From yurii.aulchenko at gmail.com  Fri Mar  8 10:14:11 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 8 Mar 2013 10:14:11 +0100
Subject: [GenABEL-dev] CRAN package DatABEL 0.9-2
In-Reply-To: <5139AB62.1060901@R-project.org>
References: <5139AB62.1060901@R-project.org>
Message-ID: <CAHX9t6+tGwjotsbwBwyEqq3W8369GanT8EoyPBLUwenrx-mUyA@mail.gmail.com>

Dear Uwe,

many thanks - we will fix these problems before 22nd of March

Yurii

On Fri, Mar 8, 2013 at 10:12 AM, Uwe Ligges wrote:

> Dear package maintainer,
>
> 1. please note that the maintainer address given in your DatABEL package,
> i.e.
>
>         Yurii Aulchenko <i.aoultchenko at erasmusmc.nl>
>
> bounces.
>
> Please fix.
>
> 2. We tried to send the folowing message to the other address:
>
>
> Your package DatABEL_0.9-2.tar.gz did pass 'R CMD check' only with
> WARNING(s).
> (CRAN/bin/windows/contrib/3.0/**).
>
> Please note that we are talking about R-3.0.0 prerelease
> (not the current release R-2.15.3).
> R-3.0.0 will be released on April 3.
>
> Please submit a fixed version without any ERROR or WARNING
> until March 22, otherwise your package will be archived.
> For details (and for results on other platforms) see
> http://cran.r-project.org/web/**checks/check_summary.html<http://cran.r-project.org/web/checks/check_summary.html>
>
> Please read and follow the CRAN policies
> (http://cran.r-project.org/**web/packages/policies.html<http://cran.r-project.org/web/packages/policies.html>
> ).
>
> R version 3.0.0 alpha (2013-03-06 r62150)
>
> All the best,
> Uwe Ligges
> (Maintainer of binary packages for Windows)
>
>
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From lennart at karssen.org  Fri Mar  8 16:50:28 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 08 Mar 2013 16:50:28 +0100
Subject: [GenABEL-dev] CRAN package DatABEL 0.9-2
In-Reply-To: <CAHX9t6+tGwjotsbwBwyEqq3W8369GanT8EoyPBLUwenrx-mUyA@mail.gmail.com>
References: <5139AB62.1060901@R-project.org>
 <CAHX9t6+tGwjotsbwBwyEqq3W8369GanT8EoyPBLUwenrx-mUyA@mail.gmail.com>
Message-ID: <513A08C4.8050404@karssen.org>

Dear Yurii,

Your e-mail address was already changed in SVN (r936, Bug #2173).
Apparently we never released v.0-9.3 to CRAN (understandably, since it
had only a very small change).


Lennart.


On 08-03-13 10:14, Yurii Aulchenko wrote:
> Dear Uwe,
> 
> many thanks - we will fix these problems before 22nd of March
> 
> Yurii
> 
> On Fri, Mar 8, 2013 at 10:12 AM, Uwe Ligges wrote:
> 
>     Dear package maintainer,
> 
>     1. please note that the maintainer address given in your DatABEL
>     package, i.e.
> 
>             Yurii Aulchenko <i.aoultchenko at erasmusmc.nl
>     <http://erasmusmc.nl>>
> 
>     bounces.
> 
>     Please fix.
> 
>     2. We tried to send the folowing message to the other address:
> 
> 
>     Your package DatABEL_0.9-2.tar.gz did pass 'R CMD check' only with
>     WARNING(s).
>     (CRAN/bin/windows/contrib/3.0/__).
> 
>     Please note that we are talking about R-3.0.0 prerelease
>     (not the current release R-2.15.3).
>     R-3.0.0 will be released on April 3.
> 
>     Please submit a fixed version without any ERROR or WARNING
>     until March 22, otherwise your package will be archived.
>     For details (and for results on other platforms) see
>     http://cran.r-project.org/web/__checks/check_summary.html
>     <http://cran.r-project.org/web/checks/check_summary.html>
> 
>     Please read and follow the CRAN policies
>     (http://cran.r-project.org/__web/packages/policies.html
>     <http://cran.r-project.org/web/packages/policies.html>).
> 
>     R version 3.0.0 alpha (2013-03-06 r62150)
> 
>     All the best,
>     Uwe Ligges
>     (Maintainer of binary packages for Windows)
> 
> 
> 
> 
> 
> _______________________________________________
> 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 lennart at karssen.org  Sun Mar 10 23:24:23 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Sun, 10 Mar 2013 23:24:23 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <CAHX9t6KKLCqncnmHK0CZPzLwZZUZhmsShDczj1BUX=v57jf36Q@mail.gmail.com>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
 <5138E6B9.7000802@karssen.org>
 <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>
 <CAHX9t6KKLCqncnmHK0CZPzLwZZUZhmsShDczj1BUX=v57jf36Q@mail.gmail.com>
Message-ID: <513D0817.7070904@karssen.org>

Dear all,

On 08-03-13 09:37, Yurii Aulchenko wrote:
> Here is another question: for the tutorials we need relative large data
> sets (as text files or in RData or other binary format).

Good question, I hadn't thought of that yet.

> 
> On one hand, it is handy to have "all in"; on the other hand - why
> putting files which are either binary and/or not likely to change to
> SVN? - this is not logical.

True. Having binary data in SVN is not ideal. On the other hand, a
definition of what goes into a revision control system is: all the files
that cannot be created by other files. From that point of view having
the data sets in SVN isn't a problem and it does give us the benefit of
the "all in" system.

> 
> The only thing I can think of is to put data files to some server and
> then as the first part of the tutorial to "pull" it e.g. using wget.
> Does affect cross-platform compatibility though... Also, where we put
> the files? - Drupal? - if we have say 100 Megs in data, would it
> generate too much traffic so the bill becomes somewhat sensible?

We could try that. We still have quite some room on our server account:
space and network bandwith are > 90% unused.

> 
> I am really not sure what to do in this respect. 


All in all, I think we should have the data in SVN. We don't want to
make building the documentation too hard. Working around the non-free
data will be hard enough work.
I tried to find out if there is a maximum of storage on the R-forge SVN
server, but I couldn't find an answer.


Lennart.

> 
> Yurii
> 
> On Fri, Mar 8, 2013 at 9:30 AM, Yurii Aulchenko
> <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> 
>     Ok, great, I think this is the way to go.
> 
>     Will make an account of private/public files, will push things to
>     SVN (hopefully some time next week), and see what we can do :)
> 
>     best wishes,
>     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 lennart at karssen.org  Tue Mar 12 00:43:33 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Tue, 12 Mar 2013 00:43:33 +0100
Subject: [GenABEL-dev] CRAN package DatABEL 0.9-2
In-Reply-To: <CAHX9t6+tGwjotsbwBwyEqq3W8369GanT8EoyPBLUwenrx-mUyA@mail.gmail.com>
References: <5139AB62.1060901@R-project.org>
 <CAHX9t6+tGwjotsbwBwyEqq3W8369GanT8EoyPBLUwenrx-mUyA@mail.gmail.com>
Message-ID: <513E6C25.3040903@karssen.org>

Dear Yurii,

I think I've fixed all the DatABEL warnings. Can you check? If all is
well feel free to upload to CRAN.


Best,

Lennart.

On 08-03-13 10:14, Yurii Aulchenko wrote:
> Dear Uwe,
> 
> many thanks - we will fix these problems before 22nd of March
> 
> Yurii
> 
> On Fri, Mar 8, 2013 at 10:12 AM, Uwe Ligges wrote:
> 
>     Dear package maintainer,
> 
>     1. please note that the maintainer address given in your DatABEL
>     package, i.e.
> 
>             Yurii Aulchenko <i.aoultchenko at erasmusmc.nl
>     <http://erasmusmc.nl>>
> 
>     bounces.
> 
>     Please fix.
> 
>     2. We tried to send the folowing message to the other address:
> 
> 
>     Your package DatABEL_0.9-2.tar.gz did pass 'R CMD check' only with
>     WARNING(s).
>     (CRAN/bin/windows/contrib/3.0/__).
> 
>     Please note that we are talking about R-3.0.0 prerelease
>     (not the current release R-2.15.3).
>     R-3.0.0 will be released on April 3.
> 
>     Please submit a fixed version without any ERROR or WARNING
>     until March 22, otherwise your package will be archived.
>     For details (and for results on other platforms) see
>     http://cran.r-project.org/web/__checks/check_summary.html
>     <http://cran.r-project.org/web/checks/check_summary.html>
> 
>     Please read and follow the CRAN policies
>     (http://cran.r-project.org/__web/packages/policies.html
>     <http://cran.r-project.org/web/packages/policies.html>).
> 
>     R version 3.0.0 alpha (2013-03-06 r62150)
> 
>     All the best,
>     Uwe Ligges
>     (Maintainer of binary packages for Windows)
> 
> 
> 
> 
> 
> _______________________________________________
> 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  Tue Mar 12 17:24:12 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 12 Mar 2013 17:24:12 +0100
Subject: [GenABEL-dev] CRAN package DatABEL 0.9-2
In-Reply-To: <513E6C25.3040903@karssen.org>
References: <5139AB62.1060901@R-project.org>
 <CAHX9t6+tGwjotsbwBwyEqq3W8369GanT8EoyPBLUwenrx-mUyA@mail.gmail.com>
 <513E6C25.3040903@karssen.org>
Message-ID: <CAHX9t6+ZrurBgF-fJj+aoq7nK_DJGgucSh2wNz5E+=WY0yi5zA@mail.gmail.com>

Thank you very much, Lennart!

I made few more fixes (documentation, version #) and submitted to CRAN

YA

On Tue, Mar 12, 2013 at 12:43 AM, L.C. Karssen <lennart at karssen.org> wrote:

> Dear Yurii,
>
> I think I've fixed all the DatABEL warnings. Can you check? If all is
> well feel free to upload to CRAN.
>
>
> Best,
>
> Lennart.
>
> On 08-03-13 10:14, Yurii Aulchenko wrote:
> > Dear Uwe,
> >
> > many thanks - we will fix these problems before 22nd of March
> >
> > Yurii
> >
> > On Fri, Mar 8, 2013 at 10:12 AM, Uwe Ligges wrote:
> >
> >     Dear package maintainer,
> >
> >     1. please note that the maintainer address given in your DatABEL
> >     package, i.e.
> >
> >             Yurii Aulchenko <i.aoultchenko at erasmusmc.nl
> >     <http://erasmusmc.nl>>
> >
> >     bounces.
> >
> >     Please fix.
> >
> >     2. We tried to send the folowing message to the other address:
> >
> >
> >     Your package DatABEL_0.9-2.tar.gz did pass 'R CMD check' only with
> >     WARNING(s).
> >     (CRAN/bin/windows/contrib/3.0/__).
> >
> >     Please note that we are talking about R-3.0.0 prerelease
> >     (not the current release R-2.15.3).
> >     R-3.0.0 will be released on April 3.
> >
> >     Please submit a fixed version without any ERROR or WARNING
> >     until March 22, otherwise your package will be archived.
> >     For details (and for results on other platforms) see
> >     http://cran.r-project.org/web/__checks/check_summary.html
> >     <http://cran.r-project.org/web/checks/check_summary.html>
> >
> >     Please read and follow the CRAN policies
> >     (http://cran.r-project.org/__web/packages/policies.html
> >     <http://cran.r-project.org/web/packages/policies.html>).
> >
> >     R version 3.0.0 alpha (2013-03-06 r62150)
> >
> >     All the best,
> >     Uwe Ligges
> >     (Maintainer of binary packages for Windows)
> >
> >
> >
> >
> >
> > _______________________________________________
> > 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 yurii.aulchenko at gmail.com  Tue Mar 12 17:36:20 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 12 Mar 2013 17:36:20 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1130 - in pkg/DatABEL: .
	inst/doc vignettes
In-Reply-To: <20130311233507.EE7981810A3@r-forge.r-project.org>
References: <20130311233507.EE7981810A3@r-forge.r-project.org>
Message-ID: <CAHX9t6KPsp+K0ETfN+R6nuaQOE0FeXdgeLT5E6oM9VkuyggETA@mail.gmail.com>

This is quite useful info: vignettes used to be in doc/inst, and
Lennart's commit suggests they should be in 'vignettes'

Lennart, is this correct?

On Tue, Mar 12, 2013 at 12:35 AM, <noreply at r-forge.r-project.org> wrote:

> Author: lckarssen
> Date: 2013-03-12 00:35:07 +0100 (Tue, 12 Mar 2013)
> New Revision: 1130
>
> Added:
>    pkg/DatABEL/vignettes/
>    pkg/DatABEL/vignettes/intro_DatABEL.Rnw
> Removed:
>    pkg/DatABEL/inst/doc/intro_DatABEL.Rnw
> Log:
> Fixed the last warnings in DatABEL when building for CRAN.
>
>
>
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From yurii.aulchenko at gmail.com  Tue Mar 12 21:47:04 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 12 Mar 2013 21:47:04 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <513D0817.7070904@karssen.org>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
 <5138E6B9.7000802@karssen.org>
 <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>
 <CAHX9t6KKLCqncnmHK0CZPzLwZZUZhmsShDczj1BUX=v57jf36Q@mail.gmail.com>
 <513D0817.7070904@karssen.org>
Message-ID: <CAHX9t6LZ2FCbyx0R_KQ12vjc9z3aKwn=-apwTu2Xqm7j7e7mXg@mail.gmail.com>

Dear All,

Many thanks for your valuable input!

This is how it looks now: I have cleaned up the data/code (actually, only
one chapter - on stratified analyses - really suffered and does not make
much sense anymore; most of the others were rather ok). I put the data on
the GenABEL.org site; and made a small chapter fetching the data following
Lennart's suggestion (using 'download.file').

I am ready to submit the resulting code.

I think I should make a new directory - say, 'tutorials' - at the same
level, as 'pkg', 'tags', 'www' and then will have a sub-directory called
'GenABEL_general' to keep this general tutorial. What do you think?

best wishes,
Yurii

On Sun, Mar 10, 2013 at 11:24 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Dear all,
>
> On 08-03-13 09:37, Yurii Aulchenko wrote:
> > Here is another question: for the tutorials we need relative large data
> > sets (as text files or in RData or other binary format).
>
> Good question, I hadn't thought of that yet.
>
> >
> > On one hand, it is handy to have "all in"; on the other hand - why
> > putting files which are either binary and/or not likely to change to
> > SVN? - this is not logical.
>
> True. Having binary data in SVN is not ideal. On the other hand, a
> definition of what goes into a revision control system is: all the files
> that cannot be created by other files. From that point of view having
> the data sets in SVN isn't a problem and it does give us the benefit of
> the "all in" system.
>
> >
> > The only thing I can think of is to put data files to some server and
> > then as the first part of the tutorial to "pull" it e.g. using wget.
> > Does affect cross-platform compatibility though... Also, where we put
> > the files? - Drupal? - if we have say 100 Megs in data, would it
> > generate too much traffic so the bill becomes somewhat sensible?
>
> We could try that. We still have quite some room on our server account:
> space and network bandwith are > 90% unused.
>
> >
> > I am really not sure what to do in this respect.
>
>
> All in all, I think we should have the data in SVN. We don't want to
> make building the documentation too hard. Working around the non-free
> data will be hard enough work.
> I tried to find out if there is a maximum of storage on the R-forge SVN
> server, but I couldn't find an answer.
>
>
> Lennart.
>
> >
> > Yurii
> >
> > On Fri, Mar 8, 2013 at 9:30 AM, Yurii Aulchenko
> > <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> >
> >     Ok, great, I think this is the way to go.
> >
> >     Will make an account of private/public files, will push things to
> >     SVN (hopefully some time next week), and see what we can do :)
> >
> >     best wishes,
> >     Yurii
> >
> >
>
>
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From lennart at karssen.org  Wed Mar 13 08:34:25 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 13 Mar 2013 08:34:25 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1130 - in pkg/DatABEL: .
 inst/doc vignettes
In-Reply-To: <CAHX9t6KPsp+K0ETfN+R6nuaQOE0FeXdgeLT5E6oM9VkuyggETA@mail.gmail.com>
References: <20130311233507.EE7981810A3@r-forge.r-project.org>
 <CAHX9t6KPsp+K0ETfN+R6nuaQOE0FeXdgeLT5E6oM9VkuyggETA@mail.gmail.com>
Message-ID: <51402C01.6090008@karssen.org>

Yes, that's correct. From the documentation [1]:
"A special case are PDF documents with sources in Sweave format, which
we call package vignettes. The preferred location for the Sweave sources
is the subdirectory vignettes of the source packages, but for
compatibility with earlier versions of R, vignette sources will be
looked for in inst/doc if vignettes does not exist."

R CMD check gave a warning on this, that's why I decided to re-read a
part of "Writing R Extensions" :-).


Lennart.


[1]
http://cran.r-project.org/doc/manuals/R-exts.html#Writing-package-vignettes

On 12/03/13 17:36, Yurii Aulchenko wrote:
> This is quite useful info: vignettes used to be in doc/inst, and
> Lennart's commit suggests they should be in 'vignettes'
> 
> Lennart, is this correct?
> 
> On Tue, Mar 12, 2013 at 12:35 AM, <noreply at r-forge.r-project.org
> <mailto:noreply at r-forge.r-project.org>> wrote:
> 
>     Author: lckarssen
>     Date: 2013-03-12 00:35:07 +0100 (Tue, 12 Mar 2013)
>     New Revision: 1130
> 
>     Added:
>        pkg/DatABEL/vignettes/
>        pkg/DatABEL/vignettes/intro_DatABEL.Rnw
>     Removed:
>        pkg/DatABEL/inst/doc/intro_DatABEL.Rnw
>     Log:
>     Fixed the last warnings in DatABEL when building for CRAN.
> 
> 
> 
> 
> 
> _______________________________________________
> 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 lennart at karssen.org  Wed Mar 13 08:39:39 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 13 Mar 2013 08:39:39 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <CAHX9t6LZ2FCbyx0R_KQ12vjc9z3aKwn=-apwTu2Xqm7j7e7mXg@mail.gmail.com>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
 <5138E6B9.7000802@karssen.org>
 <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>
 <CAHX9t6KKLCqncnmHK0CZPzLwZZUZhmsShDczj1BUX=v57jf36Q@mail.gmail.com>
 <513D0817.7070904@karssen.org>
 <CAHX9t6LZ2FCbyx0R_KQ12vjc9z3aKwn=-apwTu2Xqm7j7e7mXg@mail.gmail.com>
Message-ID: <51402D3B.20107@karssen.org>

Dear Yurii,

On 12/03/13 21:47, Yurii Aulchenko wrote:
> Dear All,
> 
> Many thanks for your valuable input!
> 
> This is how it looks now: I have cleaned up the data/code (actually,
> only one chapter - on stratified analyses - really suffered and does not
> make much sense anymore; most of the others were rather ok). 

That's good news. Glad that most of the tutorial is still in
good/reasonable shape.

> I put the
> data on the GenABEL.org site; 

With that you mean the free/non-problematic data, I assume.

> and made a small chapter fetching the data
> following Lennart's suggestion (using 'download.file').
> 
> I am ready to submit the resulting code.
> 
> I think I should make a new directory - say, 'tutorials' - at the same
> level, as 'pkg', 'tags', 'www' and then will have a sub-directory called
> 'GenABEL_general' to keep this general tutorial. What do you think?

I agree. That seems the most logical way. Alternatively we can put
tutorials in the same directory as the respective package (e.g.
pkg/GenABEL), but that will probably mess up r-forge's automatic package
building even more (than it is now because of the way we need the
filevector files).


Best,

Lennart.

> 
> best wishes,
> Yurii
> 
> On Sun, Mar 10, 2013 at 11:24 PM, L.C. Karssen <lennart at karssen.org
> <mailto:lennart at karssen.org>> wrote:
> 
>     Dear all,
> 
>     On 08-03-13 09:37, Yurii Aulchenko wrote:
>     > Here is another question: for the tutorials we need relative large
>     data
>     > sets (as text files or in RData or other binary format).
> 
>     Good question, I hadn't thought of that yet.
> 
>     >
>     > On one hand, it is handy to have "all in"; on the other hand - why
>     > putting files which are either binary and/or not likely to change to
>     > SVN? - this is not logical.
> 
>     True. Having binary data in SVN is not ideal. On the other hand, a
>     definition of what goes into a revision control system is: all the files
>     that cannot be created by other files. From that point of view having
>     the data sets in SVN isn't a problem and it does give us the benefit of
>     the "all in" system.
> 
>     >
>     > The only thing I can think of is to put data files to some server and
>     > then as the first part of the tutorial to "pull" it e.g. using wget.
>     > Does affect cross-platform compatibility though... Also, where we put
>     > the files? - Drupal? - if we have say 100 Megs in data, would it
>     > generate too much traffic so the bill becomes somewhat sensible?
> 
>     We could try that. We still have quite some room on our server account:
>     space and network bandwith are > 90% unused.
> 
>     >
>     > I am really not sure what to do in this respect.
> 
> 
>     All in all, I think we should have the data in SVN. We don't want to
>     make building the documentation too hard. Working around the non-free
>     data will be hard enough work.
>     I tried to find out if there is a maximum of storage on the R-forge SVN
>     server, but I couldn't find an answer.
> 
> 
>     Lennart.
> 
>     >
>     > Yurii
>     >
>     > On Fri, Mar 8, 2013 at 9:30 AM, Yurii Aulchenko
>     > <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>
>     <mailto:yurii.aulchenko at gmail.com
>     <mailto:yurii.aulchenko at gmail.com>>> wrote:
>     >
>     >     Ok, great, I think this is the way to go.
>     >
>     >     Will make an account of private/public files, will push things to
>     >     SVN (hopefully some time next week), and see what we can do :)
>     >
>     >     best wishes,
>     >     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  Wed Mar 13 09:12:02 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 13 Mar 2013 09:12:02 +0100
Subject: [GenABEL-dev] Fwd: Package DatABEL_0.9-4.tar.gz has been built for
	Windows
References: <01ce1f92$Blat.v2.2.2$419231fd@mail.statistik.tu-dortmund.de>
Message-ID: <-153091502019421748@unknownmsgid>

FYI

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

Begin forwarded message:

*From:* Uwe.Ligges
*Date:* 13 March 2013 03:27:06 CET
*To:* yurii
*Cc:* Uwe.Ligges
*Subject:* *Package DatABEL_0.9-4.tar.gz has been built for Windows*

Dear package maintainer,

this notification has been generated automatically.
Your package DatABEL_0.9-4.tar.gz has been built for Windows and
will be published within 24 hours in the corresponding CRAN directory
(CRAN/bin/windows/contrib/2.15/).
R version 2.15.3 (2013-03-01)

All the best,
Uwe Ligges
(Maintainer of binary packages for Windows)
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From yurii.aulchenko at gmail.com  Wed Mar 13 09:32:13 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 13 Mar 2013 09:32:13 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <51402D3B.20107@karssen.org>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
 <5138E6B9.7000802@karssen.org>
 <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>
 <CAHX9t6KKLCqncnmHK0CZPzLwZZUZhmsShDczj1BUX=v57jf36Q@mail.gmail.com>
 <513D0817.7070904@karssen.org>
 <CAHX9t6LZ2FCbyx0R_KQ12vjc9z3aKwn=-apwTu2Xqm7j7e7mXg@mail.gmail.com>
 <51402D3B.20107@karssen.org>
Message-ID: <CAHX9t6JmUKA_xA=cMEvRQJrKOXy=4KGHhfiTtmyJGR9zPsqQtw@mail.gmail.com>

> > I put the
> > data on the GenABEL.org site;
>
> With that you mean the free/non-problematic data, I assume.
>
>
Yes, sure


> >
> > I think I should make a new directory - say, 'tutorials' - at the same
> > level, as 'pkg', 'tags', 'www' and then will have a sub-directory called
> > 'GenABEL_general' to keep this general tutorial. What do you think?
>
> I agree. That seems the most logical way. Alternatively we can put
> tutorials in the same directory as the respective package (e.g.
> pkg/GenABEL), but that will probably mess up r-forge's automatic package
> building even more (than it is now because of the way we need the
> filevector files).
>
>
Ok. Will do that and comment on what is in.

Yurii
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From pirastu at burlo.trieste.it  Wed Mar 13 09:44:41 2013
From: pirastu at burlo.trieste.it (Nicola Pirastu)
Date: Wed, 13 Mar 2013 09:44:41 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <CAHX9t6JmUKA_xA=cMEvRQJrKOXy=4KGHhfiTtmyJGR9zPsqQtw@mail.gmail.com>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
 <5138E6B9.7000802@karssen.org>
 <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>
 <CAHX9t6KKLCqncnmHK0CZPzLwZZUZhmsShDczj1BUX=v57jf36Q@mail.gmail.com>
 <513D0817.7070904@karssen.org>
 <CAHX9t6LZ2FCbyx0R_KQ12vjc9z3aKwn=-apwTu2Xqm7j7e7mXg@mail.gmail.com>
 <51402D3B.20107@karssen.org>
 <CAHX9t6JmUKA_xA=cMEvRQJrKOXy=4KGHhfiTtmyJGR9zPsqQtw@mail.gmail.com>
Message-ID: <B40FF198-9F30-4BB5-82B1-F230BA255E75@burlo.trieste.it>

Dear all,

just to add a small suggestion to the whole discussion. Why don't we use public animal data, say on pigs or dogs, for the tutorials? 

This should solve the whole privacy issue and they should look to all uses the same as humans. 
In the end we don't need to have data which produces results but that only shows how to do things.

Best

Nicola


Il giorno 13/mar/2013, alle ore 09:32, Yurii Aulchenko <yurii.aulchenko at gmail.com> ha scritto:

> 
> > I put the
> > data on the GenABEL.org site;
> 
> With that you mean the free/non-problematic data, I assume.
> 
> 
> Yes, sure
>  
> >
> > I think I should make a new directory - say, 'tutorials' - at the same
> > level, as 'pkg', 'tags', 'www' and then will have a sub-directory called
> > 'GenABEL_general' to keep this general tutorial. What do you think?
> 
> I agree. That seems the most logical way. Alternatively we can put
> tutorials in the same directory as the respective package (e.g.
> pkg/GenABEL), but that will probably mess up r-forge's automatic package
> building even more (than it is now because of the way we need the
> filevector files).
> 
> 
> Ok. Will do that and comment on what is in. 
> 
> 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

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From yurii.aulchenko at gmail.com  Wed Mar 13 09:45:25 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 13 Mar 2013 09:45:25 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <CAHX9t6JmUKA_xA=cMEvRQJrKOXy=4KGHhfiTtmyJGR9zPsqQtw@mail.gmail.com>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
 <5138E6B9.7000802@karssen.org>
 <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>
 <CAHX9t6KKLCqncnmHK0CZPzLwZZUZhmsShDczj1BUX=v57jf36Q@mail.gmail.com>
 <513D0817.7070904@karssen.org>
 <CAHX9t6LZ2FCbyx0R_KQ12vjc9z3aKwn=-apwTu2Xqm7j7e7mXg@mail.gmail.com>
 <51402D3B.20107@karssen.org>
 <CAHX9t6JmUKA_xA=cMEvRQJrKOXy=4KGHhfiTtmyJGR9zPsqQtw@mail.gmail.com>
Message-ID: <CAHX9t6LYnL3nY-77m2OPHyin0xu-=JD=FCLq8XNqOOuWiDZrKg@mail.gmail.com>

I just realized there is yet another question.

What we do about figures? There are two problems with these:

1) they are binary files

2) some (two?) of them are coming from journals/books, and we do not have
explicit copyright holder's permission - in that I would definitely be
unwilling to put these in a place where we can not delete it forever (such
as RForge SVN)

With 2, I probably need to contact the copyright holders - this may be or
may be not a big deal; for now I can replace these parts with "void"

With 1 - what should we do? Put it on the server as data files?

YA

On Wed, Mar 13, 2013 at 9:32 AM, Yurii Aulchenko
<yurii.aulchenko at gmail.com>wrote:

>
> > I put the
>> > data on the GenABEL.org site;
>>
>> With that you mean the free/non-problematic data, I assume.
>>
>>
> Yes, sure
>
>
>> >
>> > I think I should make a new directory - say, 'tutorials' - at the same
>> > level, as 'pkg', 'tags', 'www' and then will have a sub-directory called
>> > 'GenABEL_general' to keep this general tutorial. What do you think?
>>
>> I agree. That seems the most logical way. Alternatively we can put
>> tutorials in the same directory as the respective package (e.g.
>> pkg/GenABEL), but that will probably mess up r-forge's automatic package
>> building even more (than it is now because of the way we need the
>> filevector files).
>>
>>
> Ok. Will do that and comment on what is in.
>
> 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  Wed Mar 13 09:50:59 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 13 Mar 2013 09:50:59 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN
In-Reply-To: <B40FF198-9F30-4BB5-82B1-F230BA255E75@burlo.trieste.it>
References: <CAHX9t6LXvd4qO7wg2GtiiVd0CSEuUmCjq7jB=hx3oE2vFyV3Jw@mail.gmail.com>
 <51250DC1.5040505@karssen.org> <512542DA.5090700@gmail.com>
 <CAHX9t6LeKOMQyFGBZ_cyRdfyzH0zDVF9-cMbODPTwq7QJfPuew@mail.gmail.com>
 <5138E6B9.7000802@karssen.org>
 <CAHX9t6JJf0xkTn8MUKbeSxEi3OgWU+5jGUYjPW8y4tOFEkfk=Q@mail.gmail.com>
 <CAHX9t6KKLCqncnmHK0CZPzLwZZUZhmsShDczj1BUX=v57jf36Q@mail.gmail.com>
 <513D0817.7070904@karssen.org>
 <CAHX9t6LZ2FCbyx0R_KQ12vjc9z3aKwn=-apwTu2Xqm7j7e7mXg@mail.gmail.com>
 <51402D3B.20107@karssen.org>
 <CAHX9t6JmUKA_xA=cMEvRQJrKOXy=4KGHhfiTtmyJGR9zPsqQtw@mail.gmail.com>
 <B40FF198-9F30-4BB5-82B1-F230BA255E75@burlo.trieste.it>
Message-ID: <CAHX9t6JQKBe8C6b2_ujtyUpmh2z4rZue7JmLRo4oBN2prQTsAA@mail.gmail.com>

> just to add a small suggestion to the whole discussion. Why don't we use
> public animal data, say on pigs or dogs, for the tutorials?
>
>
Great idea, and I totally agree!

The data from plants (Arabidopsis) GWAS is freely around, also with some
nice phenotypes (compliments to Susanna Atwell, Magnus Nordborg, et al.,
for making this public, see
http://www.nature.com/nature/journal/v465/n7298/full/nature08800.html).
I actually have a tutorial using them (will push to SVN next).

However, I am not aware of any public animal data which would be really
available right away without signing a personal binding agreement.

Marcin and Xia work on a tutorial using dog data, as far as I know, - may
be they could comment?

best wishes,
Yurii
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From yurii.aulchenko at gmail.com  Wed Mar 13 10:12:32 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 13 Mar 2013 10:12:32 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN - figures
Message-ID: <CAHX9t6+9GZip3QgU-FVo_Zza2k8mJm8fash8yfmKzDD0uH23ug@mail.gmail.com>

Dear All,

changing the subject a bit so it is easier to track things.

I think for one figure (figure 2 from
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005472)
we are fine - see below the extract from PLoS ONE site. It looks like we do
not even need to request permission.

I will investigate the issue with chapter "GWA analysis in presence of
stratification: theory" of the tutorial further (it overlaps - both in
figures and text - with a a chapter of a published book,
http://www.sciencedirect.com/science/article/pii/B9780123751423100094). For
the moment it may be more safe to just skip it in the SVN.

YA

Extract from http://www.plosone.org/static/editorial

5. Copyright and Licensing

Open Access Agreement

Upon submitting an article, authors are asked to indicate their agreement
to abide by an open access Creative Commons license (CC-BY). Under the
terms of this license, authors retain ownership of the copyright of their
articles. However, the license permits any user to download, print out,
extract, reuse, archive, and distribute the article, so long as appropriate
credit is given to the authors and the source of the work. The license
ensures that the article will be available as widely as possible and that
the article can be included in any scientific archive.


On Wed, Mar 13, 2013 at 9:45 AM, Yurii Aulchenko
<yurii.aulchenko at gmail.com>wrote:

> I just realized there is yet another question.
>
> What we do about figures? There are two problems with these:
>
> 1) they are binary files
>
> 2) some (two?) of them are coming from journals/books, and we do not have
> explicit copyright holder's permission - in that I would definitely be
> unwilling to put these in a place where we can not delete it forever (such
> as RForge SVN)
>
> With 2, I probably need to contact the copyright holders - this may be or
> may be not a big deal; for now I can replace these parts with "void"
>
> With 1 - what should we do? Put it on the server as data files?
>
> YA
>
>
> On Wed, Mar 13, 2013 at 9:32 AM, Yurii Aulchenko <
> yurii.aulchenko at gmail.com> wrote:
>
>>
>>  > I put the
>>> > data on the GenABEL.org site;
>>>
>>> With that you mean the free/non-problematic data, I assume.
>>>
>>>
>> Yes, sure
>>
>>
>>> >
>>> > I think I should make a new directory - say, 'tutorials' - at the same
>>> > level, as 'pkg', 'tags', 'www' and then will have a sub-directory
>>> called
>>> > 'GenABEL_general' to keep this general tutorial. What do you think?
>>>
>>> I agree. That seems the most logical way. Alternatively we can put
>>> tutorials in the same directory as the respective package (e.g.
>>> pkg/GenABEL), but that will probably mess up r-forge's automatic package
>>> building even more (than it is now because of the way we need the
>>> filevector files).
>>>
>>>
>> Ok. Will do that and comment on what is in.
>>
>> Yurii
>>
>
>
>
> --
> -----------------------------------------------------
> Yurii S. Aulchenko
>
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter<http://twitter.com/YuriiAulchenko>] [
> Blog <http://yurii-aulchenko.blogspot.nl/> ]
>



-- 
-----------------------------------------------------
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  Wed Mar 13 18:48:16 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 13 Mar 2013 18:48:16 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1137 -
	tutorials/GenABEL_general
In-Reply-To: <20130313173520.A5BDA183F97@r-forge.r-project.org>
References: <20130313173520.A5BDA183F97@r-forge.r-project.org>
Message-ID: <CAHX9t6+aMq-V_=xeBwGD63+etH3g2jn0Woh-FM+gJZG6Q3fhpw@mail.gmail.com>

These of you who are subscribed to genabel-commits have probably noticed
that I have published the GenABEL tutorial on our SVN

For me, it works fine, e.g.

svn export svn://svn.r-forge.r-project.org/svnroot/genabel/tutorials
cd tutorials/GenABEL_general
make

The latter takes some minutes, but then I can open GenABEL-tutorial.pdf :)

These willing to contribute: please check my comments in the text and in
the Makefile - all this can be improved a lot :)

best wishes,
YA

On Wed, Mar 13, 2013 at 6:35 PM, <noreply at r-forge.r-project.org> wrote:

> Author: yurii
> Date: 2013-03-13 18:35:20 +0100 (Wed, 13 Mar 2013)
> New Revision: 1137
>
> Added:
>    tutorials/GenABEL_general/GWA.Rnw
>    tutorials/GenABEL_general/GWAprotocol.Rnw
>    tutorials/GenABEL_general/GWAsimple.Rnw
>    tutorials/GenABEL_general/GenABEL-tutorial.Rnw
>    tutorials/GenABEL_general/ImputedDataAnalysis.Rnw
>    tutorials/GenABEL_general/Makefile
>    tutorials/GenABEL_general/QC.Rnw
>    tutorials/GenABEL_general/Sweave.sty
>    tutorials/GenABEL_general/answers.Rnw
>    tutorials/GenABEL_general/answers2.Rnw
>    tutorials/GenABEL_general/assoc.Rnw
>    tutorials/GenABEL_general/bibliography.bib
>    tutorials/GenABEL_general/dataimport.Rnw
>    tutorials/GenABEL_general/dbasing.Rnw
>    tutorials/GenABEL_general/fetchData.Rnw
>    tutorials/GenABEL_general/genetics.bst
>    tutorials/GenABEL_general/impute.Rnw
>    tutorials/GenABEL_general/internals.Rnw
>    tutorials/GenABEL_general/intro.Rnw
>    tutorials/GenABEL_general/introR.Rnw
>    tutorials/GenABEL_general/meta.Rnw
>    tutorials/GenABEL_general/myxhtml.cfg
>    tutorials/GenABEL_general/preface.Rnw
>    tutorials/GenABEL_general/probabel.Rnw
>    tutorials/GenABEL_general/reg.Rnw
>    tutorials/GenABEL_general/siman.Rnw
>    tutorials/GenABEL_general/strat.Rnw
>    tutorials/GenABEL_general/strat0.Rnw
>    tutorials/GenABEL_general/workgwaaclass.Rnw
> Log:
> first version of GenABEL-general tutorial
>
>
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From lennart at karssen.org  Wed Mar 13 20:54:52 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 13 Mar 2013 20:54:52 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1137 -
	tutorials/GenABEL_general
In-Reply-To: <CAHX9t6+aMq-V_=xeBwGD63+etH3g2jn0Woh-FM+gJZG6Q3fhpw@mail.gmail.com>
References: <20130313173520.A5BDA183F97@r-forge.r-project.org>
 <CAHX9t6+aMq-V_=xeBwGD63+etH3g2jn0Woh-FM+gJZG6Q3fhpw@mail.gmail.com>
Message-ID: <5140D98C.6000304@karssen.org>

Dear Yurii,

Great news! And congratulations with this milestone. The tutorial has
always gotten a lot of positive comments. I'm sure that having it out in
the open will make it even better.

On 13-03-13 18:48, Yurii Aulchenko wrote:
> These of you who are subscribed to genabel-commits have probably noticed
> that I have published the GenABEL tutorial on our SVN
> 
> For me, it works fine, e.g. 
> 
> svn export svn://svn.r-forge.r-project.org/svnroot/genabel/tutorials
> <http://svn.r-forge.r-project.org/svnroot/genabel/tutorials>
> cd tutorials/GenABEL_general
> make
> 
> The latter takes some minutes, but then I can open GenABEL-tutorial.pdf :)

I ran into the following:
- I didn't have MetABEL or MixABEL installed, so at some point the make
run aborted. Would it make sense to let each chapter install the
packages it needs? You could argue that something like that isn't needed
because make is only to be run by developers who know how to do it. Or
that you don't want to mess with the user's installed packages. On the
other hand it would make the system more robust: only R, LaTeX, svn,
ProbABEL and make would be the dependencies as far as I can see now. Oh
and MixABEL, which doesn't seem to be on CRAN yet.

- ImputedDataAnalysis.Rnw runs ProbABEL but suffers from the "weird
filename bug" (#2575) that has been fixed in SVN, but not released yet.
For now I've added the -o option to the command.

So my experience is a bit buggier than yours, but it looks like these
can be solved easily. Something for the weekend maybe.

> 
> These willing to contribute: please check my comments in the text and in
> the Makefile - all this can be improved a lot :)

I'd say the Makefile looks good. Especially for someone who claims not
to be good in Makefiles :-). I like the idea of generating the HTML
version through make. I've played around with mk4ht in the past. It
would be fun to pick that up again.

Another question popped up while looking at the files: what is your/our
policy on the style of R that is in the tutorial. I see you abbreviate a
lot of options (e.g. head=T instead of header=TRUE when using
read.table()). Personally I always write these out in full because it
reduces possible errors and it is enforced by CRAN I think (and Emacs
makes the TRUEs and FALSEs light up nicely ;-)).


Keep up the good work,

Lennart.

> 
> best wishes,
> YA
> 
> On Wed, Mar 13, 2013 at 6:35 PM, <noreply at r-forge.r-project.org
> <mailto:noreply at r-forge.r-project.org>> wrote:
> 
>     Author: yurii
>     Date: 2013-03-13 18:35:20 +0100 (Wed, 13 Mar 2013)
>     New Revision: 1137
> 
>     Added:
>        tutorials/GenABEL_general/GWA.Rnw
>        tutorials/GenABEL_general/GWAprotocol.Rnw
>        tutorials/GenABEL_general/GWAsimple.Rnw
>        tutorials/GenABEL_general/GenABEL-tutorial.Rnw
>        tutorials/GenABEL_general/ImputedDataAnalysis.Rnw
>        tutorials/GenABEL_general/Makefile
>        tutorials/GenABEL_general/QC.Rnw
>        tutorials/GenABEL_general/Sweave.sty
>        tutorials/GenABEL_general/answers.Rnw
>        tutorials/GenABEL_general/answers2.Rnw
>        tutorials/GenABEL_general/assoc.Rnw
>        tutorials/GenABEL_general/bibliography.bib
>        tutorials/GenABEL_general/dataimport.Rnw
>        tutorials/GenABEL_general/dbasing.Rnw
>        tutorials/GenABEL_general/fetchData.Rnw
>        tutorials/GenABEL_general/genetics.bst
>        tutorials/GenABEL_general/impute.Rnw
>        tutorials/GenABEL_general/internals.Rnw
>        tutorials/GenABEL_general/intro.Rnw
>        tutorials/GenABEL_general/introR.Rnw
>        tutorials/GenABEL_general/meta.Rnw
>        tutorials/GenABEL_general/myxhtml.cfg
>        tutorials/GenABEL_general/preface.Rnw
>        tutorials/GenABEL_general/probabel.Rnw
>        tutorials/GenABEL_general/reg.Rnw
>        tutorials/GenABEL_general/siman.Rnw
>        tutorials/GenABEL_general/strat.Rnw
>        tutorials/GenABEL_general/strat0.Rnw
>        tutorials/GenABEL_general/workgwaaclass.Rnw
>     Log:
>     first version of GenABEL-general tutorial
> 
> 
> 
> _______________________________________________
> 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!
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From lennart at karssen.org  Wed Mar 13 21:02:03 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 13 Mar 2013 21:02:03 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN - figures
In-Reply-To: <CAHX9t6+9GZip3QgU-FVo_Zza2k8mJm8fash8yfmKzDD0uH23ug@mail.gmail.com>
References: <CAHX9t6+9GZip3QgU-FVo_Zza2k8mJm8fash8yfmKzDD0uH23ug@mail.gmail.com>
Message-ID: <5140DB3B.5000603@karssen.org>

Dear all,

On 13-03-13 10:12, Yurii Aulchenko wrote:
> Dear All,
> 
> changing the subject a bit so it is easier to track things.
> 
> I think for one figure (figure 2 from
> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005472)
> we are fine - see below the extract from PLoS ONE site. It looks like we
> do not even need to request permission.

Good. +1 for Creative Commons and open access publishing!


> 
> I will investigate the issue with chapter "GWA analysis in presence of
> stratification: theory" of the tutorial further (it overlaps - both in
> figures and text - with a a chapter of a published book,
> http://www.sciencedirect.com/science/article/pii/B9780123751423100094).
> For the moment it may be more safe to just skip it in the SVN.

That's an interesting question since you are the author of that text. I
guess you'll need to dig a bit deeper into Elsevier's legal texts...


Lennart.

> 
> YA
> 
> Extract from http://www.plosone.org/static/editorial
> 
> 5. Copyright and Licensing
> 
> Open Access Agreement
> 
> Upon submitting an article, authors are asked to indicate their
> agreement to abide by an open access Creative Commons license (CC-BY).
> Under the terms of this license, authors retain ownership of the
> copyright of their articles. However, the license permits any user to
> download, print out, extract, reuse, archive, and distribute the
> article, so long as appropriate credit is given to the authors and the
> source of the work. The license ensures that the article will be
> available as widely as possible and that the article can be included in
> any scientific archive.
> 
> 
> On Wed, Mar 13, 2013 at 9:45 AM, Yurii Aulchenko
> <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> 
>     I just realized there is yet another question.
> 
>     What we do about figures? There are two problems with these:
> 
>     1) they are binary files
> 
>     2) some (two?) of them are coming from journals/books, and we do not
>     have explicit copyright holder's permission - in that I would
>     definitely be unwilling to put these in a place where we can not
>     delete it forever (such as RForge SVN)
> 
>     With 2, I probably need to contact the copyright holders - this may
>     be or may be not a big deal; for now I can replace these parts with
>     "void"
> 
>     With 1 - what should we do? Put it on the server as data files?
> 
>     YA
> 
> 
>     On Wed, Mar 13, 2013 at 9:32 AM, Yurii Aulchenko
>     <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> 
> 
>             > I put the
>             > data on the GenABEL.org site;
> 
>             With that you mean the free/non-problematic data, I assume.
> 
> 
>         Yes, sure
>          
> 
>             >
>             > I think I should make a new directory - say, 'tutorials' -
>             at the same
>             > level, as 'pkg', 'tags', 'www' and then will have a
>             sub-directory called
>             > 'GenABEL_general' to keep this general tutorial. What do
>             you think?
> 
>             I agree. That seems the most logical way. Alternatively we
>             can put
>             tutorials in the same directory as the respective package (e.g.
>             pkg/GenABEL), but that will probably mess up r-forge's
>             automatic package
>             building even more (than it is now because of the way we
>             need the
>             filevector files).
> 
> 
>         Ok. Will do that and comment on what is in. 
> 
>         Yurii
> 
> 
> 
> 
>     -- 
>     -----------------------------------------------------
>     Yurii S. Aulchenko
> 
>     [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
>     <http://twitter.com/YuriiAulchenko> ] [ Blog
>     <http://yurii-aulchenko.blogspot.nl/> ]
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> 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 lennart at karssen.org  Thu Mar 14 01:10:19 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 14 Mar 2013 01:10:19 +0100
Subject: [GenABEL-dev] Fwd: Package DatABEL_0.9-4.tar.gz has been built
 for Windows
In-Reply-To: <-153091502019421748@unknownmsgid>
References: <01ce1f92$Blat.v2.2.2$419231fd@mail.statistik.tu-dortmund.de>
 <-153091502019421748@unknownmsgid>
Message-ID: <5141156B.7050003@karssen.org>

Great! Thanks for submitting to CRAN, Yurii.

All test builds that have finished are OK now:
http://cran.r-project.org/web/checks/check_results_DatABEL.html



Lennart.

On 13-03-13 09:12, Yurii Aulchenko wrote:
> FYI
> 
> ----------------------
> Yurii Aulchenko 
> (sent from mobile device)
> 
> Begin forwarded message:
> 
>> *From:* Uwe.Ligges
>> *Date:* 13 March 2013 03:27:06 CET
>> *To:* yurii
>> *Cc:* Uwe.Ligges
>> *Subject:* *Package DatABEL_0.9-4.tar.gz has been built for Windows*
>>
>> Dear package maintainer,
>>
>> this notification has been generated automatically.
>> Your package DatABEL_0.9-4.tar.gz has been built for Windows and
>> will be published within 24 hours in the corresponding CRAN directory
>> (CRAN/bin/windows/contrib/2.15/).
>> R version 2.15.3 (2013-03-01)
>>
>> All the best,
>> Uwe Ligges
>> (Maintainer of binary packages for Windows)
>>
> 
> 
> _______________________________________________
> 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 Mar 14 09:22:29 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 14 Mar 2013 09:22:29 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1139 - pkg/ProbABEL/src
In-Reply-To: <20130313220718.49041184FA1@r-forge.r-project.org>
References: <20130313220718.49041184FA1@r-forge.r-project.org>
Message-ID: <CAHX9t6L_sAoud-LENEyT4ao4H8gkfazcsA5P5yOsBxEUVEu8dg@mail.gmail.com>

Hi Maarten,

Wow - not a trivial amount of code commented out. Great job on cleaning the
ProbABEL!

best,
Yurii

On Wed, Mar 13, 2013 at 11:07 PM, <noreply at r-forge.r-project.org> wrote:

> Author: maartenk
> Date: 2013-03-13 23:07:17 +0100 (Wed, 13 Mar 2013)
> New Revision: 1139
>
> Modified:
>    pkg/ProbABEL/src/main.cpp
> Log:
> commented out unneeded code (+-230 lines) and removed some duplicated code
> by a function
>
>
>
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From yurii.aulchenko at gmail.com  Thu Mar 14 09:38:19 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 14 Mar 2013 09:38:19 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1137 -
	tutorials/GenABEL_general
In-Reply-To: <5140D98C.6000304@karssen.org>
References: <20130313173520.A5BDA183F97@r-forge.r-project.org>
 <CAHX9t6+aMq-V_=xeBwGD63+etH3g2jn0Woh-FM+gJZG6Q3fhpw@mail.gmail.com>
 <5140D98C.6000304@karssen.org>
Message-ID: <CAHX9t6+0PdnRo49N6N34+YJBmQcttQDj+W-QbP2H0afyO_kX-A@mail.gmail.com>

> Great news! And congratulations with this milestone. The tutorial has
> always gotten a lot of positive comments. I'm sure that having it out in
> the open will make it even better.
>
>
This is the hope :) - and given there are already a couple of fixes (by you
:) ) things look good to me

>
> > For me, it works fine, e.g.
> >
> > svn export svn://svn.r-forge.r-project.org/svnroot/genabel/tutorials
> > <http://svn.r-forge.r-project.org/svnroot/genabel/tutorials>
> > cd tutorials/GenABEL_general
> > make
> >
> > The latter takes some minutes, but then I can open GenABEL-tutorial.pdf
> :)
>
> I ran into the following:
> - I didn't have MetABEL or MixABEL installed, so at some point the make
> run aborted. Would it make sense to let each chapter install the
> packages it needs? You could argue that something like that isn't needed
> because make is only to be run by developers who know how to do it. Or
> that you don't want to mess with the user's installed packages. On the
> other hand it would make the system more robust: only R, LaTeX, svn,
> ProbABEL and make would be the dependencies as far as I can see now.


I totally missed this problem. I think we should not mess up with the
user's set up, I would actually think whether we can make a kind of
'checks' (as they are in autoconf) so that if some package is not
installed, instead of the part tied to this package a page is generated
saying that the package is required...

I actually think this is among the smaller of the troubles :)



> Oh
> and MixABEL, which doesn't seem to be on CRAN yet.
>
>
This is true. I actually have no problem to (try to) publish it on CRAN,
but I am not the only person to have a say - we should definitely check
with William (William, please comment if you are reading this :) )

Next thing is that MixA requires GSL, so I am not sure how useful the CRAN
version - if they ever accept it - will be for a general user, I always had
a feeling that this is kind of 'advanced' skill to get MixA working.



>
> I'd say the Makefile looks good. Especially for someone who claims not
> to be good in Makefiles :-).


This is flattering :) I have copied it from someone else (the power of
community support!), and I do not quite understand how it works :)


>
> Another question popped up while looking at the files: what is your/our
> policy on the style of R that is in the tutorial. I see you abbreviate a
> lot of options (e.g. head=T instead of header=TRUE when using
> read.table()). Personally I always write these out in full because it
> reduces possible errors and it is enforced by CRAN I think (and Emacs
> makes the TRUEs and FALSEs light up nicely ;-)).
>
>
I agree that full argument names should be preferred. I was just being
lazy; I am trying to improve. If other people come up with things which are
"not in good style" we should probably think of a "good style rules"
document and then ask people to please to follow them.

best wishes,
Yurii
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From yurii.aulchenko at gmail.com  Thu Mar 14 09:41:52 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 14 Mar 2013 09:41:52 +0100
Subject: [GenABEL-dev] GenABEL tutorials to SVN - figures
In-Reply-To: <5140DB3B.5000603@karssen.org>
References: <CAHX9t6+9GZip3QgU-FVo_Zza2k8mJm8fash8yfmKzDD0uH23ug@mail.gmail.com>
 <5140DB3B.5000603@karssen.org>
Message-ID: <CAHX9t6+ZhdYF2gf9dSvzKfruhCPEqPyQRGEjqs2071YbOyk5ZA@mail.gmail.com>

> I think for one figure (figure 2 from

> >
> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005472
> )
> > we are fine - see below the extract from PLoS ONE site. It looks like we
> > do not even need to request permission.
>
> Good. +1 for Creative Commons and open access publishing!
>
>
Agree. The problem is that it is in this chapter which overlaps quite a bit
with  Elsevier's text. So I just killed all for the moment.

>
> > I will investigate the issue with chapter "GWA analysis in presence of
> > stratification: theory" of the tutorial further (it overlaps - both in
> > figures and text - with a a chapter of a published book,
> > http://www.sciencedirect.com/science/article/pii/B9780123751423100094).
> > For the moment it may be more safe to just skip it in the SVN.
>
> That's an interesting question since you are the author of that text. I
> guess you'll need to dig a bit deeper into Elsevier's legal texts...
>
>
They say that "you can re-use up to 10%" with no problem.

I have sent a request to them if we can use figures; will need to figure
out about the text... Or just update it so much that it can not count as
old text. Still may be some problem. Well, hope to find some help and clear
guidance from Elsevier's :)

best wishes,
Yurii
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From asa.johansson at igp.uu.se  Thu Mar 14 11:27:30 2013
From: asa.johansson at igp.uu.se (=?iso-8859-1?Q?=C5sa_Johansson?=)
Date: Thu, 14 Mar 2013 11:27:30 +0100
Subject: [GenABEL-dev] configuration erroe
Message-ID: <1A01EEB6-F02E-478D-8458-0F257F144250@igp.uu.se>

Hi,

I got a lot of warnings when configuring probable.0.3.0 on linux.

Best Regards,
?sa


configure: WARNING: float.h: present but cannot be compiled
configure: WARNING: float.h:     check for missing prerequisite headers?
configure: WARNING: float.h: see the Autoconf documentation
configure: WARNING: float.h:     section "Present But Cannot Be Compiled"
configure: WARNING: float.h: proceeding with the compiler's result
configure: WARNING:     ## -------------------------------------------------- ##
configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
configure: WARNING:     ## -------------------------------------------------- ##
checking for float.h... no
checking for inttypes.h... (cached) no
checking libintl.h usability... no
checking libintl.h presence... yes
configure: WARNING: libintl.h: present but cannot be compiled
configure: WARNING: libintl.h:     check for missing prerequisite headers?
configure: WARNING: libintl.h: see the Autoconf documentation
configure: WARNING: libintl.h:     section "Present But Cannot Be Compiled"
configure: WARNING: libintl.h: proceeding with the compiler's result
configure: WARNING:     ## -------------------------------------------------- ##
configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
configure: WARNING:     ## -------------------------------------------------- ##
checking for libintl.h... no
checking limits.h usability... no
checking limits.h presence... yes
configure: WARNING: limits.h: present but cannot be compiled
configure: WARNING: limits.h:     check for missing prerequisite headers?
configure: WARNING: limits.h: see the Autoconf documentation
configure: WARNING: limits.h:     section "Present But Cannot Be Compiled"
configure: WARNING: limits.h: proceeding with the compiler's result
configure: WARNING:     ## -------------------------------------------------- ##
configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
configure: WARNING:     ## -------------------------------------------------- ##
checking for limits.h... no
checking stddef.h usability... no
checking stddef.h presence... yes
configure: WARNING: stddef.h: present but cannot be compiled
configure: WARNING: stddef.h:     check for missing prerequisite headers?
configure: WARNING: stddef.h: see the Autoconf documentation
configure: WARNING: stddef.h:     section "Present But Cannot Be Compiled"
configure: WARNING: stddef.h: proceeding with the compiler's result
configure: WARNING:     ## -------------------------------------------------- ##
configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
configure: WARNING:     ## -------------------------------------------------- ##
checking for stddef.h... no
checking for stdint.h... (cached) no
checking for stdlib.h... (cached) no
checking for string.h... (cached) no
checking sys/param.h usability... no
checking sys/param.h presence... yes
configure: WARNING: sys/param.h: present but cannot be compiled
configure: WARNING: sys/param.h:     check for missing prerequisite headers?
configure: WARNING: sys/param.h: see the Autoconf documentation
configure: WARNING: sys/param.h:     section "Present But Cannot Be Compiled"
configure: WARNING: sys/param.h: proceeding with the compiler's result
configure: WARNING:     ## -------------------------------------------------- ##
configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
configure: WARNING:     ## -------------------------------------------------- ##
checking for sys/param.h... no
checking wchar.h usability... no
checking wchar.h presence... yes
configure: WARNING: wchar.h: present but cannot be compiled
configure: WARNING: wchar.h:     check for missing prerequisite headers?
configure: WARNING: wchar.h: see the Autoconf documentation
configure: WARNING: wchar.h:     section "Present But Cannot Be Compiled"
configure: WARNING: wchar.h: proceeding with the compiler's result
configure: WARNING:     ## -------------------------------------------------- ##
configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
configure: WARNING:     ## -------------------------------------------------- ##
checking for wchar.h... no
checking wctype.h usability... no
checking wctype.h presence... yes
configure: WARNING: wctype.h: present but cannot be compiled
configure: WARNING: wctype.h:     check for missing prerequisite headers?
configure: WARNING: wctype.h: see the Autoconf documentation
configure: WARNING: wctype.h:     section "Present But Cannot Be Compiled"
configure: WARNING: wctype.h: proceeding with the compiler's result
configure: WARNING:     ## -------------------------------------------------- ##
configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
configure: WARNING:     ## -------------------------------------------------- ##


From lennart at karssen.org  Thu Mar 14 12:39:13 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 14 Mar 2013 12:39:13 +0100
Subject: [GenABEL-dev] configuration erroe
In-Reply-To: <1A01EEB6-F02E-478D-8458-0F257F144250@igp.uu.se>
References: <1A01EEB6-F02E-478D-8458-0F257F144250@igp.uu.se>
Message-ID: <5141B6E1.1020703@karssen.org>

Dear ?sa,

Thanks for reporting this error. I'm going to have a look at it. In the
mean time, can you tell me which Linux distribution are you running
(name and version)?
Can you also mail the result of the following command:
 autoconf --version


Best,

Lennart.

On 03/14/2013 11:27 AM, ?sa Johansson wrote:
> Hi,
> 
> I got a lot of warnings when configuring probable.0.3.0 on linux.
> 
> Best Regards,
> ?sa
> 
> 
> configure: WARNING: float.h: present but cannot be compiled
> configure: WARNING: float.h:     check for missing prerequisite headers?
> configure: WARNING: float.h: see the Autoconf documentation
> configure: WARNING: float.h:     section "Present But Cannot Be Compiled"
> configure: WARNING: float.h: proceeding with the compiler's result
> configure: WARNING:     ## -------------------------------------------------- ##
> configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
> configure: WARNING:     ## -------------------------------------------------- ##
> checking for float.h... no
> checking for inttypes.h... (cached) no
> checking libintl.h usability... no
> checking libintl.h presence... yes
> configure: WARNING: libintl.h: present but cannot be compiled
> configure: WARNING: libintl.h:     check for missing prerequisite headers?
> configure: WARNING: libintl.h: see the Autoconf documentation
> configure: WARNING: libintl.h:     section "Present But Cannot Be Compiled"
> configure: WARNING: libintl.h: proceeding with the compiler's result
> configure: WARNING:     ## -------------------------------------------------- ##
> configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
> configure: WARNING:     ## -------------------------------------------------- ##
> checking for libintl.h... no
> checking limits.h usability... no
> checking limits.h presence... yes
> configure: WARNING: limits.h: present but cannot be compiled
> configure: WARNING: limits.h:     check for missing prerequisite headers?
> configure: WARNING: limits.h: see the Autoconf documentation
> configure: WARNING: limits.h:     section "Present But Cannot Be Compiled"
> configure: WARNING: limits.h: proceeding with the compiler's result
> configure: WARNING:     ## -------------------------------------------------- ##
> configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
> configure: WARNING:     ## -------------------------------------------------- ##
> checking for limits.h... no
> checking stddef.h usability... no
> checking stddef.h presence... yes
> configure: WARNING: stddef.h: present but cannot be compiled
> configure: WARNING: stddef.h:     check for missing prerequisite headers?
> configure: WARNING: stddef.h: see the Autoconf documentation
> configure: WARNING: stddef.h:     section "Present But Cannot Be Compiled"
> configure: WARNING: stddef.h: proceeding with the compiler's result
> configure: WARNING:     ## -------------------------------------------------- ##
> configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
> configure: WARNING:     ## -------------------------------------------------- ##
> checking for stddef.h... no
> checking for stdint.h... (cached) no
> checking for stdlib.h... (cached) no
> checking for string.h... (cached) no
> checking sys/param.h usability... no
> checking sys/param.h presence... yes
> configure: WARNING: sys/param.h: present but cannot be compiled
> configure: WARNING: sys/param.h:     check for missing prerequisite headers?
> configure: WARNING: sys/param.h: see the Autoconf documentation
> configure: WARNING: sys/param.h:     section "Present But Cannot Be Compiled"
> configure: WARNING: sys/param.h: proceeding with the compiler's result
> configure: WARNING:     ## -------------------------------------------------- ##
> configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
> configure: WARNING:     ## -------------------------------------------------- ##
> checking for sys/param.h... no
> checking wchar.h usability... no
> checking wchar.h presence... yes
> configure: WARNING: wchar.h: present but cannot be compiled
> configure: WARNING: wchar.h:     check for missing prerequisite headers?
> configure: WARNING: wchar.h: see the Autoconf documentation
> configure: WARNING: wchar.h:     section "Present But Cannot Be Compiled"
> configure: WARNING: wchar.h: proceeding with the compiler's result
> configure: WARNING:     ## -------------------------------------------------- ##
> configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
> configure: WARNING:     ## -------------------------------------------------- ##
> checking for wchar.h... no
> checking wctype.h usability... no
> checking wctype.h presence... yes
> configure: WARNING: wctype.h: present but cannot be compiled
> configure: WARNING: wctype.h:     check for missing prerequisite headers?
> configure: WARNING: wctype.h: see the Autoconf documentation
> configure: WARNING: wctype.h:     section "Present But Cannot Be Compiled"
> configure: WARNING: wctype.h: proceeding with the compiler's result
> configure: WARNING:     ## -------------------------------------------------- ##
> configure: WARNING:     ## Report this to genabel-devel at r-forge.wu-wien.ac.at ##
> configure: WARNING:     ## -------------------------------------------------- ##
> 
> _______________________________________________
> 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 Mar 14 14:23:07 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 14 Mar 2013 14:23:07 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1134 -
	pkg/OmicABEL/src/reshuffle
In-Reply-To: <20130313060922.947B8184ED2@r-forge.r-project.org>
References: <20130313060922.947B8184ED2@r-forge.r-project.org>
Message-ID: <CAHX9t6LST0ORBHB+=_UF9+qn6TPeEN_JxJ_3n5ctb2jrkgmGzQ@mail.gmail.com>

Hi Sodbo,

compiled with make -f makereshuffle, just wanted to let you know of
warnings I got:

g++ main.cpp iout_file.cpp Parameters.cpp reshuffle.cpp test.cpp -Wall -o
reshuffle
iout_file.cpp: In function ?std::ostream& operator<<(std::ostream&,
labels_data)?:
iout_file.cpp:79: warning: control reaches end of non-void function
Parameters.cpp: In constructor ?Parameter::Parameter(std::string,
std::string)?:
Parameters.cpp:86: warning: comparison between signed and unsigned integer
expressions
Parameters.cpp:92: warning: comparison between signed and unsigned integer
expressions
Parameters.cpp: In member function ?void
Parameter::setbynames(std::vector<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> > > >)?:
Parameters.cpp:172: warning: comparison between signed and unsigned integer
expressions
Parameters.cpp:197: warning: comparison between signed and unsigned integer
expressions
Parameters.cpp:207: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp: In member function ?void
Reshuffle::write_snpnames(std::ofstream&)?:
reshuffle.cpp:47: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp: In member function ?void
Reshuffle::write_traitnames(std::ofstream&)?:
reshuffle.cpp:59: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp: In member function ?void
Reshuffle::write_data(std::ifstream&)?:
reshuffle.cpp:78: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp:80: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp:82: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp: In member function ?void
Reshuffle::write_data_chi(std::ifstream&)?:
reshuffle.cpp:123: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp:125: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp:127: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp: In member function ?void
Reshuffle::write_slim_data(std::ifstream&)?:
reshuffle.cpp:173: warning: unused variable ?s?
reshuffle.cpp:198: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp:200: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp:202: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp: In member function ?void
Reshuffle::write_herest(std::ifstream&)?:
reshuffle.cpp:246: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp:273: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp:275: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp: In member function ?void Reshuffle::run()?:
reshuffle.cpp:324: warning: comparison between signed and unsigned integer
expressions
reshuffle.cpp:330: warning: comparison between signed and unsigned integer
expressions

On Wed, Mar 13, 2013 at 7:09 AM, <noreply at r-forge.r-project.org> wrote:

> Author: sharapovsodbo
> Date: 2013-03-13 07:09:22 +0100 (Wed, 13 Mar 2013)
> New Revision: 1134
>
> Added:
>    pkg/OmicABEL/src/reshuffle/makereshuffle
> Modified:
>    pkg/OmicABEL/src/reshuffle/Parameters.cpp
>    pkg/OmicABEL/src/reshuffle/main.cpp
>    pkg/OmicABEL/src/reshuffle/reshuffle.h
>    pkg/OmicABEL/src/reshuffle/test.cpp
>    pkg/OmicABEL/src/reshuffle/test.h
> Log:
> ver 0.004 makefile+resolved problem of compiling in *unix systems
>
>
>
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From yurii.aulchenko at gmail.com  Fri Mar 15 09:46:45 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 15 Mar 2013 09:46:45 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1148 -
	tutorials/GenABEL_general
In-Reply-To: <20130315081210.4892D1810A3@r-forge.r-project.org>
References: <20130315081210.4892D1810A3@r-forge.r-project.org>
Message-ID: <5380354259529835566@unknownmsgid>

Oops, did not notice that! Thank you, Lennart!

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

On 15 Mar 2013, at 09:12, "noreply at r-forge.r-project.org"
<noreply at r-forge.r-project.org> wrote:

> Author: lckarssen
> Date: 2013-03-15 09:12:09 +0100 (Fri, 15 Mar 2013)
> New Revision: 1148
>
> Modified:
>   tutorials/GenABEL_general/GWA.Rnw
>   tutorials/GenABEL_general/GWAprotocol.Rnw
>   tutorials/GenABEL_general/GWAsimple.Rnw
>   tutorials/GenABEL_general/GenABEL-tutorial.Rnw
>   tutorials/GenABEL_general/QC.Rnw
>   tutorials/GenABEL_general/answers.Rnw
>   tutorials/GenABEL_general/answers2.Rnw
>   tutorials/GenABEL_general/assoc.Rnw
>   tutorials/GenABEL_general/dataimport.Rnw
>   tutorials/GenABEL_general/dbasing.Rnw
>   tutorials/GenABEL_general/impute.Rnw
>   tutorials/GenABEL_general/intro.Rnw
>   tutorials/GenABEL_general/introR.Rnw
>   tutorials/GenABEL_general/meta.Rnw
>   tutorials/GenABEL_general/preface.Rnw
>   tutorials/GenABEL_general/probabel.Rnw
>   tutorials/GenABEL_general/reg.Rnw
>   tutorials/GenABEL_general/siman.Rnw
>   tutorials/GenABEL_general/strat.Rnw
>   tutorials/GenABEL_general/workgwaaclass.Rnw
> Log:
> Tutorial: removed executable property from .Rnw files
>
>
> Property changes on: tutorials/GenABEL_general/GWA.Rnw
>

From kooyman at gmail.com  Fri Mar 15 11:00:53 2013
From: kooyman at gmail.com (Maarten Kooyman)
Date: Fri, 15 Mar 2013 11:00:53 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1139 - pkg/ProbABEL/src
In-Reply-To: <CAHX9t6L_sAoud-LENEyT4ao4H8gkfazcsA5P5yOsBxEUVEu8dg@mail.gmail.com>
References: <20130313220718.49041184FA1@r-forge.r-project.org>
 <CAHX9t6L_sAoud-LENEyT4ao4H8gkfazcsA5P5yOsBxEUVEu8dg@mail.gmail.com>
Message-ID: <CABDEZoTdZb62GMCyqff7xYMj4rPjKZukiWgZP-CcGt=QCd5PVQ@mail.gmail.com>

Hi Yurii et al,

As you might known there are quite some users who like to have the
P-value in there Probabel output. The part where the output is handled
is quite complex and I did not had at first sight  a clue where to
start without being afraid that the whole thing would fall like house
of cards. This was the main functions (which should not do output, but
that is a topic of another discussion) It had a McCabe index
(cyclomatic complexity)  of over 80. To keep a long story short:
everything with a cyclomatic complexity over 30 is might be sketchy in
terms of code quality and in terms of code maintainability just
plainly bad.  You can find more about this at
http://en.wikipedia.org/wiki/Cyclomatic_complexity.

I was able to simplify the code because the part were each snp  is
"calculated" was duplicated for two cases: one for probability files
and one dose files.  I merged the 2 parts of code which removed lots
of duplicated code and some of the cyclomatic complexity: this dropped
by almost 20 percent to 67. This is still far from perfect but it is a
start.


Kind regards,

Maarten Kooyman

p.s. 2 tools to calculate this kind of statistics:
CCCC - C and C++ Code Counter (Command line tool which outputs in html)
metriculator- a plugin for Eclipse CDT (I like this one! )

On Thu, Mar 14, 2013 at 9:22 AM, Yurii Aulchenko
<yurii.aulchenko at gmail.com> wrote:
> Hi Maarten,
>
> Wow - not a trivial amount of code commented out. Great job on cleaning the
> ProbABEL!
>
> best,
> Yurii
>
>
> On Wed, Mar 13, 2013 at 11:07 PM, <noreply at r-forge.r-project.org> wrote:
>>
>> Author: maartenk
>> Date: 2013-03-13 23:07:17 +0100 (Wed, 13 Mar 2013)
>> New Revision: 1139
>>
>> Modified:
>>    pkg/ProbABEL/src/main.cpp
>> Log:
>> commented out unneeded code (+-230 lines) and removed some duplicated code
>> by a function
>>
>>
>
> _______________________________________________
> 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  Fri Mar 15 11:31:47 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 15 Mar 2013 11:31:47 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1139 - pkg/ProbABEL/src
In-Reply-To: <CABDEZoTdZb62GMCyqff7xYMj4rPjKZukiWgZP-CcGt=QCd5PVQ@mail.gmail.com>
References: <20130313220718.49041184FA1@r-forge.r-project.org>
 <CAHX9t6L_sAoud-LENEyT4ao4H8gkfazcsA5P5yOsBxEUVEu8dg@mail.gmail.com>
 <CABDEZoTdZb62GMCyqff7xYMj4rPjKZukiWgZP-CcGt=QCd5PVQ@mail.gmail.com>
Message-ID: <CAHX9t6Jz+niOr6FwHYeYGfYbGceMTGiYJV3Xpvp1K3H22gaHGw@mail.gmail.com>

Dear Maarten,

Many thanks for this post - it was very interesting to read
about cyclomatic complexity. Something new for me!

Also many thanks for mentioning the tools - definitely something to run my
code through next time.

best wishes,
Yurii

On Fri, Mar 15, 2013 at 11:00 AM, Maarten Kooyman <kooyman at gmail.com> wrote:

> Hi Yurii et al,
>
> As you might known there are quite some users who like to have the
> P-value in there Probabel output. The part where the output is handled
> is quite complex and I did not had at first sight  a clue where to
> start without being afraid that the whole thing would fall like house
> of cards. This was the main functions (which should not do output, but
> that is a topic of another discussion) It had a McCabe index
> (cyclomatic complexity)  of over 80. To keep a long story short:
> everything with a cyclomatic complexity over 30 is might be sketchy in
> terms of code quality and in terms of code maintainability just
> plainly bad.  You can find more about this at
> http://en.wikipedia.org/wiki/Cyclomatic_complexity.
>
> I was able to simplify the code because the part were each snp  is
> "calculated" was duplicated for two cases: one for probability files
> and one dose files.  I merged the 2 parts of code which removed lots
> of duplicated code and some of the cyclomatic complexity: this dropped
> by almost 20 percent to 67. This is still far from perfect but it is a
> start.
>
>
> Kind regards,
>
> Maarten Kooyman
>
> p.s. 2 tools to calculate this kind of statistics:
> CCCC - C and C++ Code Counter (Command line tool which outputs in html)
> metriculator- a plugin for Eclipse CDT (I like this one! )
>
> On Thu, Mar 14, 2013 at 9:22 AM, Yurii Aulchenko
> <yurii.aulchenko at gmail.com> wrote:
> > Hi Maarten,
> >
> > Wow - not a trivial amount of code commented out. Great job on cleaning
> the
> > ProbABEL!
> >
> > best,
> > Yurii
> >
> >
> > On Wed, Mar 13, 2013 at 11:07 PM, <noreply at r-forge.r-project.org> wrote:
> >>
> >> Author: maartenk
> >> Date: 2013-03-13 23:07:17 +0100 (Wed, 13 Mar 2013)
> >> New Revision: 1139
> >>
> >> Modified:
> >>    pkg/ProbABEL/src/main.cpp
> >> Log:
> >> commented out unneeded code (+-230 lines) and removed some duplicated
> code
> >> by a function
> >>
> >>
> >
> > _______________________________________________
> > 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 william.astle at mail.mcgill.ca  Fri Mar 15 14:47:52 2013
From: william.astle at mail.mcgill.ca (William Astle)
Date: Fri, 15 Mar 2013 13:47:52 +0000
Subject: [GenABEL-dev] [Genabel-commits] r1137 -
 tutorials/GenABEL_general
In-Reply-To: <CAHX9t6+0pHLhvJ26rqmY8hjadJLW-qCdf9Le3ygKG_hGnM9E8A@mail.gmail.com>
References: <20130313173520.A5BDA183F97@r-forge.r-project.org>
 <CAHX9t6+aMq-V_=xeBwGD63+etH3g2jn0Woh-FM+gJZG6Q3fhpw@mail.gmail.com>
 <5140D98C.6000304@karssen.org>
 <CAHX9t6+0PdnRo49N6N34+YJBmQcttQDj+W-QbP2H0afyO_kX-A@mail.gmail.com>
 <CAHX9t6+0pHLhvJ26rqmY8hjadJLW-qCdf9Le3ygKG_hGnM9E8A@mail.gmail.com>
Message-ID: <8137DCC37877D6428FCE92A4C8E7ADCAF44096@EXMBX2010-1.campus.MCGILL.CA>


On 15 Mar 2013, at 05:02, Yurii Aulchenko <yurii.aulchenko at gmail.com<mailto:yurii.aulchenko at gmail.com>> wrote:


Oh
and MixABEL, which doesn't seem to be on CRAN yet.


This is true. I actually have no problem to (try to) publish it on CRAN, but I am not the only person to have a say - we should definitely check with William (William, please comment if you are reading this :) )


This would be fine by me in principle, but I guess it will require some work to get it up to scratch. I need to write some manual pages etc?

Next thing is that MixA requires GSL, so I am not sure how useful the CRAN version - if they ever accept it - will be for a general user, I always had a feeling that this is kind of 'advanced' skill to get MixA working.


Is this a matter of writing an autoconf script? I guess there must be CRAN packages that use gsl? (the gsl package for one :)) I can look into it.

Will
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From p.s.devries at erasmusmc.nl  Fri Mar 15 15:03:11 2013
From: p.s.devries at erasmusmc.nl (P.S. de Vries)
Date: Fri, 15 Mar 2013 14:03:11 +0000
Subject: [GenABEL-dev] ld-based pruning
Message-ID: <E6EBBA81BC4F6F4988D93E600F485C2E09677B@EXCH-RX02.erasmusmc.nl>

Dear all,

In my research I constantly work with genetic risk scores based on a large amount of SNPs. Sometimes it is appropriate to prune the SNPs by LD before constructing the genetic risk score to obtain a set of independent SNPs. The most widely used function for this (plink --indep-pairwise) uses a sliding window to find pairs of SNPs in high LD with each other according to their R^2 and then removes one. However, it removes the SNP with the lowest minor allele frequency. In practice we may instead want to keep the SNP with the lowest p-value: i.e. the most important to us. This should lead to higher quality genetic risk scores.

I have written a function that reads in a list of SNPs and then prunes it for LD by choosing which SNP to remove from a pair in high LD according to its position in the snp list. So the SNP that comes first in the SNP list will never be pruned out, and the second one only if it is in LD with the first one. The LD structure is based on your own data: it relies on the probabel configuration file for filepaths, and on databel for accessing the dosages.

I initially did this just to apply it to my own data, but Lennart suggested it might be a nice addition to genabel. I am interested in developing this further if there is indeed interest in such a function. If so I will share the code and we can go from there.

Let me know what you think,

Paul

P.S. de Vries
PhD Scientist
Cardiovascular group
Department of Epidemiology

Erasmus MC, University Medical Center Rotterdam
Office Ee 21-33
PO Box 2040, 3000 CA Rotterdam,
The Netherlands

Email: p.s.devries at erasmusmc.nl<mailto:p.s.devries at erasmusmc.nl>
http://www.erasmus-epidemiology.nl/

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From yurii.aulchenko at gmail.com  Sat Mar 16 14:06:23 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sat, 16 Mar 2013 14:06:23 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1137 -
	tutorials/GenABEL_general
In-Reply-To: <8137DCC37877D6428FCE92A4C8E7ADCAF44096@EXMBX2010-1.campus.MCGILL.CA>
References: <20130313173520.A5BDA183F97@r-forge.r-project.org>
 <CAHX9t6+aMq-V_=xeBwGD63+etH3g2jn0Woh-FM+gJZG6Q3fhpw@mail.gmail.com>
 <5140D98C.6000304@karssen.org>
 <CAHX9t6+0PdnRo49N6N34+YJBmQcttQDj+W-QbP2H0afyO_kX-A@mail.gmail.com>
 <CAHX9t6+0pHLhvJ26rqmY8hjadJLW-qCdf9Le3ygKG_hGnM9E8A@mail.gmail.com>
 <8137DCC37877D6428FCE92A4C8E7ADCAF44096@EXMBX2010-1.campus.MCGILL.CA>
Message-ID: <CAHX9t6LnHt3O=55empebLXTpzYjCHwPWqcNYzt=r7mAS8T6wyA@mail.gmail.com>

Dear William,


>  This is true. I actually have no problem to (try to) publish it on CRAN,
> but I am not the only person to have a say - we should definitely check
> with William (William, please comment if you are reading this :) )
>
>
>  This would be fine by me in principle, but I guess it will require some
> work to get it up to scratch. I need to write some manual pages etc?
>
>
The man pages are - in principle - there, though they probably need to be
updated in terms of citation at least.

If this is on your agenda - would still be great to split the FMM into:
eigen-part, heritability-part and the GWAS-itself-part -- I think this will
really increase the flexibility and usability. Do count on my help with
that. But af cause this can be done at later stage in updating the package.



>   Next thing is that MixA requires GSL, so I am not sure how useful the
> CRAN version - if they ever accept it - will be for a general user, I
> always had a feeling that this is kind of 'advanced' skill to get MixA
> working.
>
>
>
>  Is this a matter of writing an autoconf script? I guess there must be
> CRAN packages that use gsl? (the gsl package for one :)) I can look into it.
>
>
Please do - I am really curious how this can be arranged.

Yurii
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From yurii.aulchenko at gmail.com  Sat Mar 16 14:20:47 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sat, 16 Mar 2013 14:20:47 +0100
Subject: [GenABEL-dev] ld-based pruning
In-Reply-To: <E6EBBA81BC4F6F4988D93E600F485C2E09677B@EXCH-RX02.erasmusmc.nl>
References: <E6EBBA81BC4F6F4988D93E600F485C2E09677B@EXCH-RX02.erasmusmc.nl>
Message-ID: <CAHX9t6JP+ea_N3Y8ndTs9BKH1wABDVkL_5EwJGhabUoQaUGkUg@mail.gmail.com>

Paul, I think this indeed may be interesting for other people as well; at
least I ran across similar problem a couple of times.

Could you please let us know more details about the implementation and your
thoughts about 'architecture' (is it / should it become a part of GenA,
ProbA, or something else, e.g. we have something called "GanABEL-suite
general" - smaller things not tied specifically to any package).

I also refer you to our set of devel-tutorials (
http://genabel.r-forge.r-project.org/) and some documents about our
policies (at http://www.genabel.org/developers) for general information

best wishes,
YA

On Fri, Mar 15, 2013 at 3:03 PM, P.S. de Vries <p.s.devries at erasmusmc.nl>wrote:

>  Dear all,****
>
> ** **
>
> In my research I constantly work with genetic risk scores based on a large
> amount of SNPs. Sometimes it is appropriate to prune the SNPs by LD before
> constructing the genetic risk score to obtain a set of independent SNPs.
> The most widely used function for this (plink --indep-pairwise) uses a
> sliding window to find pairs of SNPs in high LD with each other according
> to their R^2 and then removes one. However, it removes the SNP with the
> lowest minor allele frequency. In practice we may instead want to keep the
> SNP with the lowest p-value: i.e. the most important to us. This should
> lead to higher quality genetic risk scores.****
>
> ** **
>
> I have written a function that reads in a list of SNPs and then prunes it
> for LD by choosing which SNP to remove from a pair in high LD according to
> its position in the snp list. So the SNP that comes first in the SNP list
> will never be pruned out, and the second one only if it is in LD with the
> first one. The LD structure is based on your own data: it relies on the
> probabel configuration file for filepaths, and on databel for accessing the
> dosages.****
>
> ** **
>
> I initially did this just to apply it to my own data, but Lennart
> suggested it might be a nice addition to genabel. I am interested in
> developing this further if there is indeed interest in such a function. If
> so I will share the code and we can go from there.****
>
> ** **
>
> Let me know what you think,****
>
> ** **
>
> Paul****
>
> **
>
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From yurii.aulchenko at gmail.com  Sat Mar 16 14:35:28 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sat, 16 Mar 2013 14:35:28 +0100
Subject: [GenABEL-dev] svn tutorial to www.genabel.org
Message-ID: <CAHX9t6KeeBkax6HT+Zg-32-BeoBvtCXjcQ3RbbYZRRt3kNmppg@mail.gmail.com>

Dear All,

Some of you may have noticed that I have 'suspended' the "GenABEL tutorial"
on http://www.genabel.org/tutorials with message

General extensive tutorial on GenABEL suite [ TEMPORARILY UNAVAILABLE,
EXPECTED TO BE BACK ON MARCH 18, 2013]

- the idea being that by that time we already switch to the new public
version.

Should I compile what we have as current version and then we publish?

A bit of problem is that I never did that (import large HTML documentation
files) before - if I send the bundled HTML/PNG could someone help me with
importing that in a proper way?

best wishes,
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 lennart at karssen.org  Mon Mar 18 09:32:17 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 18 Mar 2013 09:32:17 +0100
Subject: [GenABEL-dev] GenABEL project style guide
Message-ID: <5146D111.7050604@karssen.org>

Dear all,

I'd like to follow up on something Yurii wrote in the discussion on the
GenABEL tutorial:

On 03/14/2013 09:38 AM, Yurii Aulchenko wrote:
> I agree that full argument names should be preferred. I was just being
> lazy; I am trying to improve. If other people come up with things
> which are "not in good style" we should probably think of a "good
> style rules" document and then ask people to please to follow them.
>

I completely agree with Yurii. In fact, I think we should not only set
guidelines for the style of the code in the tutorial, but more generally
for all R and C/C++ code in the GenABEL project.

What about setting up a shared editing environment (e.g. on
piratepad.net) to work on an initial draft of these quidelines? Once
they are more or less fixed we can move the document to SVN as part of
the developer documentation.

From my experience over the last few years I think the following points
are the most commonly occurring ones (for any language) that need
harmonisation:
- comma's should be followed by a space
- operators (= + - * etc.) should be surrounded by a space (and in R the
<- operator too)
- a file should always have a newline at the end
- don't use tabs (as everyone seems to have a different setting for the
tab stop): use spaces. How many spaces is up for debate. Of course
Makefiles are exempt from this rule as tabs are mandatory
- style of brackets: is the opening bracket on the same line as the name
of the loop/function or on a new line on its own? (e.g. K&R, Allman or
bsd style)
- always use {} in if clauses/for loops (even if there is only one
statement in the clause/loop
- lines should not be longer than 80 characters (you may call me old
fashioned ;-))

I think most of these can be set as options in modern development
environment. I'm not an Eclipse user, like many of you, but in Emacs
these can easily be set in your .emacs file. We should also provide info
on how to implement these settings in various DEs in our guidelines
document so that new developers can easily use them.


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 lennart at karssen.org  Mon Mar 18 09:41:37 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 18 Mar 2013 09:41:37 +0100
Subject: [GenABEL-dev] ld-based pruning
In-Reply-To: <CAHX9t6JP+ea_N3Y8ndTs9BKH1wABDVkL_5EwJGhabUoQaUGkUg@mail.gmail.com>
References: <E6EBBA81BC4F6F4988D93E600F485C2E09677B@EXCH-RX02.erasmusmc.nl>
 <CAHX9t6JP+ea_N3Y8ndTs9BKH1wABDVkL_5EwJGhabUoQaUGkUg@mail.gmail.com>
Message-ID: <5146D341.303@karssen.org>

Dear all,

On 16/03/13 14:20, Yurii Aulchenko wrote:
> Paul, I think this indeed may be interesting for other people as well;
> at least I ran across similar problem a couple of times.
> 
> Could you please let us know more details about the implementation and
> your thoughts about 'architecture' (is it / should it become a part of
> GenA, ProbA, or something else, e.g. we have something called
> "GanABEL-suite general" - smaller things not tied specifically to any
> package).

This is a point Paul and I discussed and I think it's quite open. It
seems to me that this function is at the intersection of GenABEL,
ProbABEL (and maybe DatABEL).

Technically, if we make it part of GenABEL would that mean that GenABEL
depends on DatABEL (now it is only a suggested dependency) since Paul's
function 'require()'s DatABEL? Are there any other R packages that have
functionality that only works if a given package is installed (that is
not in the dependency list but only in the suggested list)?

We could distribute it as part of ProbABEL as well. ProbABEL has a
"soft" dependency on DatABEL and we already provide some accompanying R
scripts.
I'm not sure if making it a part of the general scripts will work out
well as we don't have a way to distribute these (yet).


Having taken a quick look at Paul's code the only major thing that needs
to be implemented, as Paul pointed out, is how to deal with chunked
DatABEL files (when the data of a single chromosome is split into
smaller chunks). The present implementation assumes LD is broken at
chromosome (= file) borders.
My guess is that that is quite easy to implement by simply asking the
file system to list all files with a given chomosome number. It does
requires a bit of pattern matching though (you don't want it to return
chr 10, 11, 12 etc, when looking for chr 1 only).

> 
> I also refer you to our set of devel-tutorials
> (http://genabel.r-forge.r-project.org/) and some documents about our
> policies (at http://www.genabel.org/developers) for general information
> 

Good point!



Lennart.

> best wishes,
> YA
> 
> On Fri, Mar 15, 2013 at 3:03 PM, P.S. de Vries <p.s.devries at erasmusmc.nl
> <mailto:p.s.devries at erasmusmc.nl>> wrote:
> 
>     Dear all,____
> 
>     __ __
> 
>     In my research I constantly work with genetic risk scores based on a
>     large amount of SNPs. Sometimes it is appropriate to prune the SNPs
>     by LD before constructing the genetic risk score to obtain a set of
>     independent SNPs. The most widely used function for this (plink
>     --indep-pairwise) uses a sliding window to find pairs of SNPs in
>     high LD with each other according to their R^2 and then removes one.
>     However, it removes the SNP with the lowest minor allele frequency.
>     In practice we may instead want to keep the SNP with the lowest
>     p-value: i.e. the most important to us. This should lead to higher
>     quality genetic risk scores.____
> 
>     __ __
> 
>     I have written a function that reads in a list of SNPs and then
>     prunes it for LD by choosing which SNP to remove from a pair in high
>     LD according to its position in the snp list. So the SNP that comes
>     first in the SNP list will never be pruned out, and the second one
>     only if it is in LD with the first one. The LD structure is based on
>     your own data: it relies on the probabel configuration file for
>     filepaths, and on databel for accessing the dosages.____
> 
>     __ __
> 
>     I initially did this just to apply it to my own data, but Lennart
>     suggested it might be a nice addition to genabel. I am interested in
>     developing this further if there is indeed interest in such a
>     function. If so I will share the code and we can go from there.____
> 
>     __ __
> 
>     Let me know what you think,____
> 
>     __ __
> 
>     Paul____
> 
>     __ 
> 
> 
> 
> _______________________________________________
> 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 lennart at karssen.org  Mon Mar 18 09:45:17 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 18 Mar 2013 09:45:17 +0100
Subject: [GenABEL-dev] svn tutorial to www.genabel.org
In-Reply-To: <CAHX9t6KeeBkax6HT+Zg-32-BeoBvtCXjcQ3RbbYZRRt3kNmppg@mail.gmail.com>
References: <CAHX9t6KeeBkax6HT+Zg-32-BeoBvtCXjcQ3RbbYZRRt3kNmppg@mail.gmail.com>
Message-ID: <5146D41D.9010700@karssen.org>

Hi Yurii,

The quick and easy thing to do is to at least upload the PDF version, of
course. I think we should do that asap (based on the version in SVN).

As the the HTML, I may have done that once when we just set up Drupal,
but I'm not sure. It would take me some time to figure it out again. If
Anatolij could help us out that would be great!


Lennart.

On 16/03/13 14:35, Yurii Aulchenko wrote:
> Dear All,
> 
> Some of you may have noticed that I have 'suspended' the "GenABEL
> tutorial" on http://www.genabel.org/tutorials with message 
> 
> General extensive tutorial on GenABEL suite [ TEMPORARILY UNAVAILABLE,
> EXPECTED TO BE BACK ON MARCH 18, 2013]
> 
> - the idea being that by that time we already switch to the new public
> version. 
> 
> Should I compile what we have as current version and then we publish?
> 
> A bit of problem is that I never did that (import large
> HTML documentation files) before - if I send the bundled HTML/PNG could
> someone help me with importing that in a proper way?
> 
> best wishes,
> Yurii
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> <http://twitter.com/YuriiAulchenko> ] [ Blog
> <http://yurii-aulchenko.blogspot.nl/> ]
> 
> 
> _______________________________________________
> 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 p.s.devries at erasmusmc.nl  Mon Mar 18 14:56:06 2013
From: p.s.devries at erasmusmc.nl (P.S. de Vries)
Date: Mon, 18 Mar 2013 13:56:06 +0000
Subject: [GenABEL-dev] ld-based pruning
In-Reply-To: <5146D341.303@karssen.org>
References: <E6EBBA81BC4F6F4988D93E600F485C2E09677B@EXCH-RX02.erasmusmc.nl>
 <CAHX9t6JP+ea_N3Y8ndTs9BKH1wABDVkL_5EwJGhabUoQaUGkUg@mail.gmail.com>
 <5146D341.303@karssen.org>
Message-ID: <E6EBBA81BC4F6F4988D93E600F485C2E0968AF@EXCH-RX02.erasmusmc.nl>

Dear all,

Although I like the idea of it being available as a regular R function (so GenABEL), I think it would also fit very well with probabel: after all, it completely relies on the existence of a probabel configuration file. I have attached the code: it is by no means fully annotated yet. 

Something else that I have worked on in the past is a script to extract dosages of specific SNPs using databel objects. Again this was needed for me to make genetic risk scores. I think this may be faster than perl scripts when we want to extract many (hundreds of thousands) SNPs. In any case it may also be a nice feature for the GenABEL suite. It would rely on databel objects and the probabel configuration file in the same way as the LD pruning function. This extraction syntax was my first real R project and therefore it very messy at the moment, but maybe it is also something interesting to develop further?

Kind regards,

Paul 

-----Original Message-----
From: genabel-devel-bounces at lists.r-forge.r-project.org [mailto:genabel-devel-bounces at lists.r-forge.r-project.org] On Behalf Of L.C. Karssen
Sent: maandag 18 maart 2013 09:42
To: genabel-devel at lists.r-forge.r-project.org
Subject: Re: [GenABEL-dev] ld-based pruning

Dear all,

On 16/03/13 14:20, Yurii Aulchenko wrote:
> Paul, I think this indeed may be interesting for other people as well; 
> at least I ran across similar problem a couple of times.
> 
> Could you please let us know more details about the implementation and 
> your thoughts about 'architecture' (is it / should it become a part of 
> GenA, ProbA, or something else, e.g. we have something called 
> "GanABEL-suite general" - smaller things not tied specifically to any 
> package).

This is a point Paul and I discussed and I think it's quite open. It seems to me that this function is at the intersection of GenABEL, ProbABEL (and maybe DatABEL).

Technically, if we make it part of GenABEL would that mean that GenABEL depends on DatABEL (now it is only a suggested dependency) since Paul's function 'require()'s DatABEL? Are there any other R packages that have functionality that only works if a given package is installed (that is not in the dependency list but only in the suggested list)?

We could distribute it as part of ProbABEL as well. ProbABEL has a "soft" dependency on DatABEL and we already provide some accompanying R scripts.
I'm not sure if making it a part of the general scripts will work out well as we don't have a way to distribute these (yet).


Having taken a quick look at Paul's code the only major thing that needs to be implemented, as Paul pointed out, is how to deal with chunked DatABEL files (when the data of a single chromosome is split into smaller chunks). The present implementation assumes LD is broken at chromosome (= file) borders.
My guess is that that is quite easy to implement by simply asking the file system to list all files with a given chomosome number. It does requires a bit of pattern matching though (you don't want it to return chr 10, 11, 12 etc, when looking for chr 1 only).

> 
> I also refer you to our set of devel-tutorials
> (http://genabel.r-forge.r-project.org/) and some documents about our 
> policies (at http://www.genabel.org/developers) for general 
> information
> 

Good point!



Lennart.

> best wishes,
> YA
> 
> On Fri, Mar 15, 2013 at 3:03 PM, P.S. de Vries 
> <p.s.devries at erasmusmc.nl <mailto:p.s.devries at erasmusmc.nl>> wrote:
> 
>     Dear all,____
> 
>     __ __
> 
>     In my research I constantly work with genetic risk scores based on a
>     large amount of SNPs. Sometimes it is appropriate to prune the SNPs
>     by LD before constructing the genetic risk score to obtain a set of
>     independent SNPs. The most widely used function for this (plink
>     --indep-pairwise) uses a sliding window to find pairs of SNPs in
>     high LD with each other according to their R^2 and then removes one.
>     However, it removes the SNP with the lowest minor allele frequency.
>     In practice we may instead want to keep the SNP with the lowest
>     p-value: i.e. the most important to us. This should lead to higher
>     quality genetic risk scores.____
> 
>     __ __
> 
>     I have written a function that reads in a list of SNPs and then
>     prunes it for LD by choosing which SNP to remove from a pair in high
>     LD according to its position in the snp list. So the SNP that comes
>     first in the SNP list will never be pruned out, and the second one
>     only if it is in LD with the first one. The LD structure is based on
>     your own data: it relies on the probabel configuration file for
>     filepaths, and on databel for accessing the dosages.____
> 
>     __ __
> 
>     I initially did this just to apply it to my own data, but Lennart
>     suggested it might be a nice addition to genabel. I am interested in
>     developing this further if there is indeed interest in such a
>     function. If so I will share the code and we can go from 
> there.____
> 
>     __ __
> 
>     Let me know what you think,____
> 
>     __ __
> 
>     Paul____
> 
>     __
> 
> 
> 
> _______________________________________________
> 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-d
> evel
> 

--
-----------------------------------------------------------------
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 lennart at karssen.org  Mon Mar 18 21:07:20 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 18 Mar 2013 21:07:20 +0100
Subject: [GenABEL-dev] ld-based pruning
In-Reply-To: <E6EBBA81BC4F6F4988D93E600F485C2E0968AF@EXCH-RX02.erasmusmc.nl>
References: <E6EBBA81BC4F6F4988D93E600F485C2E09677B@EXCH-RX02.erasmusmc.nl>
 <CAHX9t6JP+ea_N3Y8ndTs9BKH1wABDVkL_5EwJGhabUoQaUGkUg@mail.gmail.com>
 <5146D341.303@karssen.org>
 <E6EBBA81BC4F6F4988D93E600F485C2E0968AF@EXCH-RX02.erasmusmc.nl>
Message-ID: <514773F8.8090801@karssen.org>

Dear Paul,

On 18/03/13 14:56, P.S. de Vries wrote:
> Dear all,
>
> Although I like the idea of it being available as a regular R
> function (so GenABEL), I think it would also fit very well with
> probabel: after all, it completely relies on the existence of a
> probabel configuration file. I have attached the code: it is by no
> means fully annotated yet.

I'm fine with incorporating it into the ProbABEL package. Your
argument about the PA config file is a good one.

In order to inform people of the function's existence we should add a
section to the ProbABEL manual.

>
> Something else that I have worked on in the past is a script to
> extract dosages of specific SNPs using databel objects. Again this
> was needed for me to make genetic risk scores. I think this may be
> faster than perl scripts when we want to extract many (hundreds of
> thousands) SNPs. In any case it may also be a nice feature for the
> GenABEL suite.

I totally agree. I've worked on a C/C++ version of such a script, but
never got to finish it.

> It would rely on databel objects and the probabel
> configuration file in the same way as the LD pruning function. This
> extraction syntax was my first real R project and therefore it very
> messy at the moment, but maybe it is also something interesting to
> develop further?

I think that will earn you lots of kudos from our users.

Maybe we should combine these companion functions into an R package
"ProbABEL-tools" (or something similar) that PA users can simply
install. What does the list think about that?

The current R scripts distributed as part of ProbABEL are quite simple
and merely serve as examples, so I don't think they need to be part of
such a package.


Lennart.

>
> Kind regards,
>
> Paul
>
> -----Original Message----- From:
> genabel-devel-bounces at lists.r-forge.r-project.org
> [mailto:genabel-devel-bounces at lists.r-forge.r-project.org] On Behalf
> Of L.C. Karssen Sent: maandag 18 maart 2013 09:42 To:
> genabel-devel at lists.r-forge.r-project.org Subject: Re: [GenABEL-dev]
> ld-based pruning
>
> Dear all,
>
> On 16/03/13 14:20, Yurii Aulchenko wrote:
>> Paul, I think this indeed may be interesting for other people as
>> well; at least I ran across similar problem a couple of times.
>>
>> Could you please let us know more details about the implementation
>> and your thoughts about 'architecture' (is it / should it become a
>> part of GenA, ProbA, or something else, e.g. we have something
>> called "GanABEL-suite general" - smaller things not tied
>> specifically to any package).
>
> This is a point Paul and I discussed and I think it's quite open. It
> seems to me that this function is at the intersection of GenABEL,
> ProbABEL (and maybe DatABEL).
>
> Technically, if we make it part of GenABEL would that mean that
> GenABEL depends on DatABEL (now it is only a suggested dependency)
> since Paul's function 'require()'s DatABEL? Are there any other R
> packages that have functionality that only works if a given package
> is installed (that is not in the dependency list but only in the
> suggested list)?
>
> We could distribute it as part of ProbABEL as well. ProbABEL has a
> "soft" dependency on DatABEL and we already provide some accompanying
> R scripts. I'm not sure if making it a part of the general scripts
> will work out well as we don't have a way to distribute these (yet).
>
>
> Having taken a quick look at Paul's code the only major thing that
> needs to be implemented, as Paul pointed out, is how to deal with
> chunked DatABEL files (when the data of a single chromosome is split
> into smaller chunks). The present implementation assumes LD is broken
> at chromosome (= file) borders. My guess is that that is quite easy
> to implement by simply asking the file system to list all files with
> a given chomosome number. It does requires a bit of pattern matching
> though (you don't want it to return chr 10, 11, 12 etc, when looking
> for chr 1 only).
>
>>
>> I also refer you to our set of devel-tutorials
>> (http://genabel.r-forge.r-project.org/) and some documents about
>> our policies (at http://www.genabel.org/developers) for general
>> information
>>
>
> Good point!
>
>
>
> Lennart.
>
>> best wishes, YA
>>
>> On Fri, Mar 15, 2013 at 3:03 PM, P.S. de Vries
>> <p.s.devries at erasmusmc.nl <mailto:p.s.devries at erasmusmc.nl>>
>> wrote:
>>
>> Dear all,____
>>
>> __ __
>>
>> In my research I constantly work with genetic risk scores based on
>> a large amount of SNPs. Sometimes it is appropriate to prune the
>> SNPs by LD before constructing the genetic risk score to obtain a
>> set of independent SNPs. The most widely used function for this
>> (plink --indep-pairwise) uses a sliding window to find pairs of
>> SNPs in high LD with each other according to their R^2 and then
>> removes one. However, it removes the SNP with the lowest minor
>> allele frequency. In practice we may instead want to keep the SNP
>> with the lowest p-value: i.e. the most important to us. This should
>> lead to higher quality genetic risk scores.____
>>
>> __ __
>>
>> I have written a function that reads in a list of SNPs and then
>> prunes it for LD by choosing which SNP to remove from a pair in
>> high LD according to its position in the snp list. So the SNP that
>> comes first in the SNP list will never be pruned out, and the
>> second one only if it is in LD with the first one. The LD structure
>> is based on your own data: it relies on the probabel configuration
>> file for filepaths, and on databel for accessing the dosages.____
>>
>> __ __
>>
>> I initially did this just to apply it to my own data, but Lennart
>> suggested it might be a nice addition to genabel. I am interested
>> in developing this further if there is indeed interest in such a
>> function. If so I will share the code and we can go from
>> there.____
>>
>> __ __
>>
>> Let me know what you think,____
>>
>> __ __
>>
>> Paul____
>>
>> __
>>
>>
>>
>> _______________________________________________ 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-d
>>
>>
evel
>>
>
> -- -----------------------------------------------------------------
> 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  Tue Mar 19 12:52:43 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 19 Mar 2013 12:52:43 +0100
Subject: [GenABEL-dev] svn tutorial to www.genabel.org
In-Reply-To: <5146D41D.9010700@karssen.org>
References: <CAHX9t6KeeBkax6HT+Zg-32-BeoBvtCXjcQ3RbbYZRRt3kNmppg@mail.gmail.com>
 <5146D41D.9010700@karssen.org>
Message-ID: <CAHX9t6K+yEZnH88S2CWy-VTzkZvWua_bYR29KBGnQ-obJBgDzg@mail.gmail.com>

I did so at http://www.genabel.org/tutorials

But I see something very weird, and hope you could help:

I put PDF in

ftp> pwd
Remote directory: /domains/
genabel.org/htdocs/genabel/sites/default/files/pdfs

and make link to

<a href="/sites/default/files/pdfs/GenABEL-tutorial.pdf">PDF</a>

which translates to

http://www.genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf

but very funny thing I see is that old version of PDF pops up, dated Aug 29
and having 257 pages (new one is dated today and is shorter).

I am a bit lost with what is going on - need to update cache? or what?... -
disabling the link for the moment ("href" -> "hhref").

Yurii

On Mon, Mar 18, 2013 at 9:45 AM, L.C. Karssen <lennart at karssen.org> wrote:

> Hi Yurii,
>
> The quick and easy thing to do is to at least upload the PDF version, of
> course. I think we should do that asap (based on the version in SVN).
>
> As the the HTML, I may have done that once when we just set up Drupal,
> but I'm not sure. It would take me some time to figure it out again. If
> Anatolij could help us out that would be great!
>
>
> Lennart.
>
> On 16/03/13 14:35, Yurii Aulchenko wrote:
> > Dear All,
> >
> > Some of you may have noticed that I have 'suspended' the "GenABEL
> > tutorial" on http://www.genabel.org/tutorials with message
> >
> > General extensive tutorial on GenABEL suite [ TEMPORARILY UNAVAILABLE,
> > EXPECTED TO BE BACK ON MARCH 18, 2013]
> >
> > - the idea being that by that time we already switch to the new public
> > version.
> >
> > Should I compile what we have as current version and then we publish?
> >
> > A bit of problem is that I never did that (import large
> > HTML documentation files) before - if I send the bundled HTML/PNG could
> > someone help me with importing that in a proper way?
> >
> > best wishes,
> > Yurii
> >
> > --
> > -----------------------------------------------------
> > Yurii S. Aulchenko
> >
> > [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> > <http://twitter.com/YuriiAulchenko> ] [ Blog
> > <http://yurii-aulchenko.blogspot.nl/> ]
> >
> >
> > _______________________________________________
> > 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  Tue Mar 19 15:45:45 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 19 Mar 2013 15:45:45 +0100
Subject: [GenABEL-dev] svn tutorial to www.genabel.org
In-Reply-To: <w2c6ebmol2g9xw24jbwwr01o.1363694991706@email.android.com>
References: <CAHX9t6KeeBkax6HT+Zg-32-BeoBvtCXjcQ3RbbYZRRt3kNmppg@mail.gmail.com>
 <5146D41D.9010700@karssen.org>
 <CAHX9t6K+yEZnH88S2CWy-VTzkZvWua_bYR29KBGnQ-obJBgDzg@mail.gmail.com>
 <w2c6ebmol2g9xw24jbwwr01o.1363694991706@email.android.com>
Message-ID: <CAHX9t6K6FOkV3oKW_j1_tPQGRpMyEmMidNr2Xa4=2Y3QwT12iw@mail.gmail.com>

You are right, Maarten, it is the browser (and not Drupal) cache.

Very stupid of me!

The funny thing was that I did test from my phone - and it also gave me old
version. So I must have had it in my phone cache as well.

I am going to add "GenABEL developers" as copyright holders from 2013,
compile new version, and then fix the link - will be there in 10-20 minutes
from now.

We still need to address the problem with html, but that comes next :) And
next we can proudly announce "self-contained tutorial" :)

YA

On Tue, Mar 19, 2013 at 1:51 PM, M. Kooijman <m.kooijman at erasmusmc.nl>wrote:

>  It works for me on my phone
> . Please try to empty your cache on your machine.
>
> Cheers ,
> Maarten
>
> Yurii Aulchenko <yurii.aulchenko at gmail.com> wrote:
>
>
> I did so at http://www.genabel.org/tutorials
>
>  But I see something very weird, and hope you could help:
>
>  I put PDF in
>
>  ftp> pwd
> Remote directory: /domains/
> genabel.org/htdocs/genabel/sites/default/files/pdfs
>
>  and make link to
>
>  <a href="/sites/default/files/pdfs/GenABEL-tutorial.pdf">PDF</a>
>
>  which translates to
>
>  http://www.genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf
>
>  but very funny thing I see is that old version of PDF pops up, dated Aug
> 29 and having 257 pages (new one is dated today and is shorter).
>
>  I am a bit lost with what is going on - need to update cache? or
> what?... - disabling the link for the moment ("href" -> "hhref").
>
>  Yurii
>
> On Mon, Mar 18, 2013 at 9:45 AM, L.C. Karssen <lennart at karssen.org> wrote:
>
>> Hi Yurii,
>>
>> The quick and easy thing to do is to at least upload the PDF version, of
>> course. I think we should do that asap (based on the version in SVN).
>>
>> As the the HTML, I may have done that once when we just set up Drupal,
>> but I'm not sure. It would take me some time to figure it out again. If
>> Anatolij could help us out that would be great!
>>
>>
>> Lennart.
>>
>> On 16/03/13 14:35, Yurii Aulchenko wrote:
>> > Dear All,
>> >
>> > Some of you may have noticed that I have 'suspended' the "GenABEL
>> > tutorial" on http://www.genabel.org/tutorials with message
>> >
>> > General extensive tutorial on GenABEL suite [ TEMPORARILY UNAVAILABLE,
>> > EXPECTED TO BE BACK ON MARCH 18, 2013]
>> >
>> > - the idea being that by that time we already switch to the new public
>> > version.
>> >
>> > Should I compile what we have as current version and then we publish?
>> >
>> > A bit of problem is that I never did that (import large
>> > HTML documentation files) before - if I send the bundled HTML/PNG could
>> > someone help me with importing that in a proper way?
>> >
>> > best wishes,
>> > Yurii
>> >
>> > --
>> > -----------------------------------------------------
>> > Yurii S. Aulchenko
>> >
>>  > [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
>> > <http://twitter.com/YuriiAulchenko> ] [ Blog
>> > <http://yurii-aulchenko.blogspot.nl/> ]
>> >
>> >
>> > _______________________________________________
>> > 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
>>
>
>
>
>
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From yurii.aulchenko at gmail.com  Tue Mar 19 15:57:49 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 19 Mar 2013 15:57:49 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1154 -
	tutorials/GenABEL_general
In-Reply-To: <20130316124833.60A4318449B@r-forge.r-project.org>
References: <20130316124833.60A4318449B@r-forge.r-project.org>
Message-ID: <CAHX9t6+WhdwCjPL+oT9e5snCa==WLhQMmLOQPxnONr-TP=i_8w@mail.gmail.com>

Just had a look at newly compiled PDF

xcolors look nice, thank you, Lennart!

YA



On Sat, Mar 16, 2013 at 1:48 PM, <noreply at r-forge.r-project.org> wrote:

> Author: lckarssen
> Date: 2013-03-16 13:48:32 +0100 (Sat, 16 Mar 2013)
> New Revision: 1154
>
> Modified:
>    tutorials/GenABEL_general/GenABEL-tutorial.Rnw
>    tutorials/GenABEL_general/introR.Rnw
> Log:
> - IntroR.Rnw: fix \ref to figure
> - GenABEL-tutorial.Rnw: coloured hyperlinks instead of boxes, finetuned
> the PDF experience (e.g. added metadata). Changed from the color package to
> the xcolor package.
>
>
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From lennart at karssen.org  Tue Mar 19 17:04:12 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Tue, 19 Mar 2013 17:04:12 +0100
Subject: [GenABEL-dev] svn tutorial to www.genabel.org
In-Reply-To: <CAHX9t6K6FOkV3oKW_j1_tPQGRpMyEmMidNr2Xa4=2Y3QwT12iw@mail.gmail.com>
References: <CAHX9t6KeeBkax6HT+Zg-32-BeoBvtCXjcQ3RbbYZRRt3kNmppg@mail.gmail.com>
 <5146D41D.9010700@karssen.org>
 <CAHX9t6K+yEZnH88S2CWy-VTzkZvWua_bYR29KBGnQ-obJBgDzg@mail.gmail.com>
 <w2c6ebmol2g9xw24jbwwr01o.1363694991706@email.android.com>
 <CAHX9t6K6FOkV3oKW_j1_tPQGRpMyEmMidNr2Xa4=2Y3QwT12iw@mail.gmail.com>
Message-ID: <51488C7C.9060503@karssen.org>

Nice! Good to see the benefits of the opening up of the tutorial on such
short notice.


Lennart.

On 19-03-13 15:45, Yurii Aulchenko wrote:
> You are right, Maarten, it is the browser (and not Drupal) cache. 
> 
> Very stupid of me!
> 
> The funny thing was that I did test from my phone - and it also gave me
> old version. So I must have had it in my phone cache as well.
> 
> I am going to add "GenABEL developers" as copyright holders from 2013,
> compile new version, and then fix the link - will be there in 10-20
> minutes from now. 
> 
> We still need to address the problem with html, but that comes next :)
> And next we can proudly announce "self-contained tutorial" :)
> 
> YA
> 
> On Tue, Mar 19, 2013 at 1:51 PM, M. Kooijman <m.kooijman at erasmusmc.nl
> <mailto:m.kooijman at erasmusmc.nl>> wrote:
> 
>     It works for me on my phone
>     . Please try to empty your cache on your machine.
> 
>     Cheers ,
>     Maarten
> 
>     Yurii Aulchenko <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> 
>     I did so at http://www.genabel.org/tutorials
> 
>     But I see something very weird, and hope you could help:
> 
>     I put PDF in 
> 
>     ftp> pwd
>     Remote directory:
>     /domains/genabel.org/htdocs/genabel/sites/default/files/pdfs
>     <http://genabel.org/htdocs/genabel/sites/default/files/pdfs>
> 
>     and make link to 
> 
>     <a href="/sites/default/files/pdfs/GenABEL-tutorial.pdf">PDF</a>
> 
>     which translates to
> 
>     http://www.genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf
> 
>     but very funny thing I see is that old version of PDF pops up, dated
>     Aug 29 and having 257 pages (new one is dated today and is shorter).
> 
>     I am a bit lost with what is going on - need to update cache? or
>     what?... - disabling the link for the moment ("href" -> "hhref").
> 
>     Yurii
> 
>     On Mon, Mar 18, 2013 at 9:45 AM, L.C. Karssen <lennart at karssen.org
>     <mailto:lennart at karssen.org>> wrote:
> 
>         Hi Yurii,
> 
>         The quick and easy thing to do is to at least upload the PDF
>         version, of
>         course. I think we should do that asap (based on the version in
>         SVN).
> 
>         As the the HTML, I may have done that once when we just set up
>         Drupal,
>         but I'm not sure. It would take me some time to figure it out
>         again. If
>         Anatolij could help us out that would be great!
> 
> 
>         Lennart.
> 
>         On 16/03/13 14:35, Yurii Aulchenko wrote:
>         > Dear All,
>         >
>         > Some of you may have noticed that I have 'suspended' the "GenABEL
>         > tutorial" on http://www.genabel.org/tutorials with message
>         >
>         > General extensive tutorial on GenABEL suite [ TEMPORARILY
>         UNAVAILABLE,
>         > EXPECTED TO BE BACK ON MARCH 18, 2013]
>         >
>         > - the idea being that by that time we already switch to the
>         new public
>         > version.
>         >
>         > Should I compile what we have as current version and then we
>         publish?
>         >
>         > A bit of problem is that I never did that (import large
>         > HTML documentation files) before - if I send the bundled
>         HTML/PNG could
>         > someone help me with importing that in a proper way?
>         >
>         > best wishes,
>         > Yurii
>         >
>         > --
>         > -----------------------------------------------------
>         > Yurii S. Aulchenko
>         >
>         > [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
>         > <http://twitter.com/YuriiAulchenko> ] [ Blog
>         > <http://yurii-aulchenko.blogspot.nl/> ]
>         >
>         >
>         > _______________________________________________
>         > 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
>         >
> 
>         --
>         -----------------------------------------------------------------
>         L.C. Karssen
>         Utrecht
>         The Netherlands
> 
>         lennart at karssen.org <mailto: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
>         <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
> 

-- 
-----------------------------------------------------------------
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 Mar 20 11:54:29 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 20 Mar 2013 11:54:29 +0100
Subject: [GenABEL-dev] GenABEL project style guide
In-Reply-To: <5146D111.7050604@karssen.org>
References: <5146D111.7050604@karssen.org>
Message-ID: <CAHX9t6Jh3rPHEq0W=DMJOvoiYnxjUTHPP1dTjh+dZC9YecyNxw@mail.gmail.com>

Hi Lennart,

Indeed, why do not we set up piratpad; or we can use our SVN, the same
section we have tutorials in - then it will go directly to
http://genabel.r-forge.r-project.org/

I think it is important to have guidelines  and I personally will try to
follow them as much as I could.

At the same time, I would like to emphasize that we had the idea that rules
and guidelines should be suggestive, so that even if I do not comply 100% I
can still make it into the project, and then can improve on the way. See
the quote below.

best, Yurii

Quote from

http://www.genabel.org/developers:

Rules of the game
The documents provided here are meant to help. We are scared to think of a
situation when 'guidelines' and 'rules' prevent people from contributing to
the project, and a willing contributor is discouraged by just looking at
the pile of 'rules'.

On Mon, Mar 18, 2013 at 9:32 AM, L.C. Karssen <lennart at karssen.org> wrote:

> Dear all,
>
> I'd like to follow up on something Yurii wrote in the discussion on the
> GenABEL tutorial:
>
> On 03/14/2013 09:38 AM, Yurii Aulchenko wrote:
> > I agree that full argument names should be preferred. I was just being
> > lazy; I am trying to improve. If other people come up with things
> > which are "not in good style" we should probably think of a "good
> > style rules" document and then ask people to please to follow them.
> >
>
> I completely agree with Yurii. In fact, I think we should not only set
> guidelines for the style of the code in the tutorial, but more generally
> for all R and C/C++ code in the GenABEL project.
>
> What about setting up a shared editing environment (e.g. on
> piratepad.net) to work on an initial draft of these quidelines? Once
> they are more or less fixed we can move the document to SVN as part of
> the developer documentation.
>
> From my experience over the last few years I think the following points
> are the most commonly occurring ones (for any language) that need
> harmonisation:
> - comma's should be followed by a space
> - operators (= + - * etc.) should be surrounded by a space (and in R the
> <- operator too)
> - a file should always have a newline at the end
> - don't use tabs (as everyone seems to have a different setting for the
> tab stop): use spaces. How many spaces is up for debate. Of course
> Makefiles are exempt from this rule as tabs are mandatory
> - style of brackets: is the opening bracket on the same line as the name
> of the loop/function or on a new line on its own? (e.g. K&R, Allman or
> bsd style)
> - always use {} in if clauses/for loops (even if there is only one
> statement in the clause/loop
> - lines should not be longer than 80 characters (you may call me old
> fashioned ;-))
>
> I think most of these can be set as options in modern development
> environment. I'm not an Eclipse user, like many of you, but in Emacs
> these can easily be set in your .emacs file. We should also provide info
> on how to implement these settings in various DEs in our guidelines
> document so that new developers can easily use them.
>
>
> 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
> ------------------------------------------------------------------
>
>
> _______________________________________________
> 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  Wed Mar 20 12:00:16 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 20 Mar 2013 12:00:16 +0100
Subject: [GenABEL-dev] ld-based pruning
In-Reply-To: <5146D341.303@karssen.org>
References: <E6EBBA81BC4F6F4988D93E600F485C2E09677B@EXCH-RX02.erasmusmc.nl>
 <CAHX9t6JP+ea_N3Y8ndTs9BKH1wABDVkL_5EwJGhabUoQaUGkUg@mail.gmail.com>
 <5146D341.303@karssen.org>
Message-ID: <CAHX9t6KwwKpBQHd9XMmj71djSJO3XJ_bruTVzyb34_8bLftw3Q@mail.gmail.com>

> Technically, if we make it part of GenABEL would that mean that GenABEL
> depends on DatABEL (now it is only a suggested dependency) since Paul's
> function 'require()'s DatABEL? Are there any other R packages that have
> functionality that only works if a given package is installed (that is
> not in the dependency list but only in the suggested list)?
>
>

I do not see a big problem with above - e.g. there are functions like
minimac2databel in the GenA. They start with (
https://r-forge.r-project.org/scm/viewvc.php/pkg/GenABEL/R/minimac2databel.R?view=markup&root=genabel
)

minimac2databel <- function(imputedgenofile, infofile, outfile, cachesizeMb=64)
{
  if (!require(DatABEL))
    stop("This function requires DatABEL package to be installed")


This seems to be accepted practice

Yurii
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From lennart at karssen.org  Thu Mar 21 19:49:25 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 21 Mar 2013 19:49:25 +0100
Subject: [GenABEL-dev] GenABEL project style guide
In-Reply-To: <CAHX9t6Jh3rPHEq0W=DMJOvoiYnxjUTHPP1dTjh+dZC9YecyNxw@mail.gmail.com>
References: <5146D111.7050604@karssen.org>
 <CAHX9t6Jh3rPHEq0W=DMJOvoiYnxjUTHPP1dTjh+dZC9YecyNxw@mail.gmail.com>
Message-ID: <514B5635.4050309@karssen.org>

Dear all,

Maarten started an etherpad instance at http://openetherpad.org/oxx0htdP47
I've updated the text he and I came up with and reformatted it in Emacs
org-mode, which allows easy export to PDF and HTML (so that we can
easily integrated it in the development website on r-forge as per
Yurii's suggestion).

If I don't see much change in the EtherPad document in the coming days
I'll put the org file and its HTML export in SVN.


Lennart.

On 20/03/13 11:54, Yurii Aulchenko wrote:
> Hi Lennart,
> 
> Indeed, why do not we set up piratpad; or we can use our SVN, the same
> section we have tutorials in - then it will go directly
> to http://genabel.r-forge.r-project.org/
> 
> I think it is important to have guidelines  and I personally will try to
> follow them as much as I could.
> 
> At the same time, I would like to emphasize that we had the idea that
> rules and guidelines should be suggestive, so that even if I do not
> comply 100% I can still make it into the project, and then can improve
> on the way. See the quote below.
> 
> best, Yurii
> 
> Quote from
> 
> http://www.genabel.org/developers:
> 
> Rules of the game
> The documents provided here are meant to help. We are scared to think of
> a situation when 'guidelines' and 'rules' prevent people from
> contributing to the project, and a willing contributor is discouraged by
> just looking at the pile of 'rules'.
> 
> On Mon, Mar 18, 2013 at 9:32 AM, L.C. Karssen <lennart at karssen.org
> <mailto:lennart at karssen.org>> wrote:
> 
>     Dear all,
> 
>     I'd like to follow up on something Yurii wrote in the discussion on the
>     GenABEL tutorial:
> 
>     On 03/14/2013 09:38 AM, Yurii Aulchenko wrote:
>     > I agree that full argument names should be preferred. I was just being
>     > lazy; I am trying to improve. If other people come up with things
>     > which are "not in good style" we should probably think of a "good
>     > style rules" document and then ask people to please to follow them.
>     >
> 
>     I completely agree with Yurii. In fact, I think we should not only set
>     guidelines for the style of the code in the tutorial, but more generally
>     for all R and C/C++ code in the GenABEL project.
> 
>     What about setting up a shared editing environment (e.g. on
>     piratepad.net <http://piratepad.net>) to work on an initial draft of
>     these quidelines? Once
>     they are more or less fixed we can move the document to SVN as part of
>     the developer documentation.
> 
>     From my experience over the last few years I think the following points
>     are the most commonly occurring ones (for any language) that need
>     harmonisation:
>     - comma's should be followed by a space
>     - operators (= + - * etc.) should be surrounded by a space (and in R the
>     <- operator too)
>     - a file should always have a newline at the end
>     - don't use tabs (as everyone seems to have a different setting for the
>     tab stop): use spaces. How many spaces is up for debate. Of course
>     Makefiles are exempt from this rule as tabs are mandatory
>     - style of brackets: is the opening bracket on the same line as the name
>     of the loop/function or on a new line on its own? (e.g. K&R, Allman or
>     bsd style)
>     - always use {} in if clauses/for loops (even if there is only one
>     statement in the clause/loop
>     - lines should not be longer than 80 characters (you may call me old
>     fashioned ;-))
> 
>     I think most of these can be set as options in modern development
>     environment. I'm not an Eclipse user, like many of you, but in Emacs
>     these can easily be set in your .emacs file. We should also provide info
>     on how to implement these settings in various DEs in our guidelines
>     document so that new developers can easily use them.
> 
> 
>     Lennart.
>     --
>     -----------------------------------------------------------------
>     L.C. Karssen
>     Utrecht
>     The Netherlands
> 
>     lennart at karssen.org <mailto: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
>     <mailto: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/> ]

-- 
-----------------------------------------------------------------
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 lennart at karssen.org  Thu Mar 21 19:53:57 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 21 Mar 2013 19:53:57 +0100
Subject: [GenABEL-dev] ld-based pruning
In-Reply-To: <CAHX9t6KwwKpBQHd9XMmj71djSJO3XJ_bruTVzyb34_8bLftw3Q@mail.gmail.com>
References: <E6EBBA81BC4F6F4988D93E600F485C2E09677B@EXCH-RX02.erasmusmc.nl>
 <CAHX9t6JP+ea_N3Y8ndTs9BKH1wABDVkL_5EwJGhabUoQaUGkUg@mail.gmail.com>
 <5146D341.303@karssen.org>
 <CAHX9t6KwwKpBQHd9XMmj71djSJO3XJ_bruTVzyb34_8bLftw3Q@mail.gmail.com>
Message-ID: <514B5745.60401@karssen.org>

Hi Yurii,

That's an excellent suggestion. This makes me more inclined to put
Paul's function in GenABEL. Most users already have that package
installed and if we would make separate ProbABEL-R-tools package it
would mean yet another package people need to install and keep up to
date on their systems.

The only thing that remains in terms of input checking is a check for
the existence of the ProbABEL config file. But that's easy.


Lennart.

On 20/03/13 12:00, Yurii Aulchenko wrote:
> 
>     Technically, if we make it part of GenABEL would that mean that GenABEL
>     depends on DatABEL (now it is only a suggested dependency) since Paul's
>     function 'require()'s DatABEL? Are there any other R packages that have
>     functionality that only works if a given package is installed (that is
>     not in the dependency list but only in the suggested list)?
> 
> 
> 
> I do not see a big problem with above - e.g. there are functions like
> minimac2databel in the GenA. They start with
> (https://r-forge.r-project.org/scm/viewvc.php/pkg/GenABEL/R/minimac2databel.R?view=markup&root=genabel)
> 
> minimac2databel <- function(imputedgenofile, infofile, outfile, cachesizeMb=64)
> {
>   if (!require(DatABEL))
>     stop("This function requires DatABEL package to be installed")
> 
> 
> This seems to be accepted practice
> 
> 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 lennart at karssen.org  Thu Mar 21 19:56:02 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 21 Mar 2013 19:56:02 +0100
Subject: [GenABEL-dev] ld-based pruning
In-Reply-To: <514B5745.60401@karssen.org>
References: <E6EBBA81BC4F6F4988D93E600F485C2E09677B@EXCH-RX02.erasmusmc.nl>
 <CAHX9t6JP+ea_N3Y8ndTs9BKH1wABDVkL_5EwJGhabUoQaUGkUg@mail.gmail.com>
 <5146D341.303@karssen.org>
 <CAHX9t6KwwKpBQHd9XMmj71djSJO3XJ_bruTVzyb34_8bLftw3Q@mail.gmail.com>
 <514B5745.60401@karssen.org>
Message-ID: <514B57C2.6050707@karssen.org>


On 21/03/13 19:53, L.C. Karssen wrote:
> The only thing that remains in terms of input checking is a check for
> the existence of the ProbABEL config file. But that's easy.

Oops, I should check first before I write. A check for the existence of
the config file is already present.


Lennart.

> 
> 
> Lennart.
> 
> On 20/03/13 12:00, Yurii Aulchenko wrote:
>>
>>     Technically, if we make it part of GenABEL would that mean that GenABEL
>>     depends on DatABEL (now it is only a suggested dependency) since Paul's
>>     function 'require()'s DatABEL? Are there any other R packages that have
>>     functionality that only works if a given package is installed (that is
>>     not in the dependency list but only in the suggested list)?
>>
>>
>>
>> I do not see a big problem with above - e.g. there are functions like
>> minimac2databel in the GenA. They start with
>> (https://r-forge.r-project.org/scm/viewvc.php/pkg/GenABEL/R/minimac2databel.R?view=markup&root=genabel)
>>
>> minimac2databel <- function(imputedgenofile, infofile, outfile, cachesizeMb=64)
>> {
>>   if (!require(DatABEL))
>>     stop("This function requires DatABEL package to be installed")
>>
>>
>> This seems to be accepted practice
>>
>> 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 kooyman at gmail.com  Sat Mar 23 16:39:46 2013
From: kooyman at gmail.com (Maarten Kooyman)
Date: Sat, 23 Mar 2013 16:39:46 +0100
Subject: [GenABEL-dev] GenABEL project style guide
In-Reply-To: <514B5635.4050309@karssen.org>
References: <5146D111.7050604@karssen.org>
 <CAHX9t6Jh3rPHEq0W=DMJOvoiYnxjUTHPP1dTjh+dZC9YecyNxw@mail.gmail.com>
 <514B5635.4050309@karssen.org>
Message-ID: <514DCCC2.1040003@gmail.com>

Dear all,

Google made a page with styles for different languages they use for 
there opensource projects. There is nice documentation for c++ and also 
(a less annotated ) part for R.

This and more can be found at:
https://code.google.com/p/google-styleguide/

The links to the programming  languages can be found in the left bottom 
table on this page.

I think this information can add valuable information  to the discussion 
and enriches your knowledge about programming languages.

Kind regards,

Maarten


On 03/21/2013 07:49 PM, L.C. Karssen wrote:
> Dear all,
>
> Maarten started an etherpad instance at http://openetherpad.org/oxx0htdP47
> I've updated the text he and I came up with and reformatted it in Emacs
> org-mode, which allows easy export to PDF and HTML (so that we can
> easily integrated it in the development website on r-forge as per
> Yurii's suggestion).
>
> If I don't see much change in the EtherPad document in the coming days
> I'll put the org file and its HTML export in SVN.
>
>
> Lennart.
>
> On 20/03/13 11:54, Yurii Aulchenko wrote:
>> Hi Lennart,
>>
>> Indeed, why do not we set up piratpad; or we can use our SVN, the same
>> section we have tutorials in - then it will go directly
>> to http://genabel.r-forge.r-project.org/
>>
>> I think it is important to have guidelines  and I personally will try to
>> follow them as much as I could.
>>
>> At the same time, I would like to emphasize that we had the idea that
>> rules and guidelines should be suggestive, so that even if I do not
>> comply 100% I can still make it into the project, and then can improve
>> on the way. See the quote below.
>>
>> best, Yurii
>>
>> Quote from
>>
>> http://www.genabel.org/developers:
>>
>> Rules of the game
>> The documents provided here are meant to help. We are scared to think of
>> a situation when 'guidelines' and 'rules' prevent people from
>> contributing to the project, and a willing contributor is discouraged by
>> just looking at the pile of 'rules'.
>>
>> On Mon, Mar 18, 2013 at 9:32 AM, L.C. Karssen <lennart at karssen.org
>> <mailto:lennart at karssen.org>> wrote:
>>
>>      Dear all,
>>
>>      I'd like to follow up on something Yurii wrote in the discussion on the
>>      GenABEL tutorial:
>>
>>      On 03/14/2013 09:38 AM, Yurii Aulchenko wrote:
>>      > I agree that full argument names should be preferred. I was just being
>>      > lazy; I am trying to improve. If other people come up with things
>>      > which are "not in good style" we should probably think of a "good
>>      > style rules" document and then ask people to please to follow them.
>>      >
>>
>>      I completely agree with Yurii. In fact, I think we should not only set
>>      guidelines for the style of the code in the tutorial, but more generally
>>      for all R and C/C++ code in the GenABEL project.
>>
>>      What about setting up a shared editing environment (e.g. on
>>      piratepad.net <http://piratepad.net>) to work on an initial draft of
>>      these quidelines? Once
>>      they are more or less fixed we can move the document to SVN as part of
>>      the developer documentation.
>>
>>      From my experience over the last few years I think the following points
>>      are the most commonly occurring ones (for any language) that need
>>      harmonisation:
>>      - comma's should be followed by a space
>>      - operators (= + - * etc.) should be surrounded by a space (and in R the
>>      <- operator too)
>>      - a file should always have a newline at the end
>>      - don't use tabs (as everyone seems to have a different setting for the
>>      tab stop): use spaces. How many spaces is up for debate. Of course
>>      Makefiles are exempt from this rule as tabs are mandatory
>>      - style of brackets: is the opening bracket on the same line as the name
>>      of the loop/function or on a new line on its own? (e.g. K&R, Allman or
>>      bsd style)
>>      - always use {} in if clauses/for loops (even if there is only one
>>      statement in the clause/loop
>>      - lines should not be longer than 80 characters (you may call me old
>>      fashioned ;-))
>>
>>      I think most of these can be set as options in modern development
>>      environment. I'm not an Eclipse user, like many of you, but in Emacs
>>      these can easily be set in your .emacs file. We should also provide info
>>      on how to implement these settings in various DEs in our guidelines
>>      document so that new developers can easily use them.
>>
>>
>>      Lennart.
>>      --
>>      -----------------------------------------------------------------
>>      L.C. Karssen
>>      Utrecht
>>      The Netherlands
>>
>>      lennart at karssen.org <mailto: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
>>      <mailto: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/> ]
>
>
> _______________________________________________
> 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  Sat Mar 23 16:58:46 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Sat, 23 Mar 2013 16:58:46 +0100
Subject: [GenABEL-dev] GenABEL project style guide
In-Reply-To: <514DCCC2.1040003@gmail.com>
References: <5146D111.7050604@karssen.org>
 <CAHX9t6Jh3rPHEq0W=DMJOvoiYnxjUTHPP1dTjh+dZC9YecyNxw@mail.gmail.com>
 <514B5635.4050309@karssen.org> <514DCCC2.1040003@gmail.com>
Message-ID: <514DD136.9080803@karssen.org>

Thanks for the link Maarten! I've been wanting to take a look at Googles
guide for a long time, but never took the time.

This can save considerable time. Looking at the R guide I agree with
almost all of the guidelines. We should either copy them or simple link
to them (maybe with a brief summary of the most important points).

The C++ guide is much more involved... I've already found some
interesting things in there.
For our own guide I think we should make a selection, mostly related to
code layout, which we want to incorporate into our own document. The
other parts can probably be linked to.


Oh, and... they even have an Emacs config file that helps conforming to
their style! ;-)


Lennart.


On 23-03-13 16:39, Maarten Kooyman wrote:
> Dear all,
> 
> Google made a page with styles for different languages they use for
> there opensource projects. There is nice documentation for c++ and also
> (a less annotated ) part for R.
> 
> This and more can be found at:
> https://code.google.com/p/google-styleguide/
> 
> The links to the programming  languages can be found in the left bottom
> table on this page.
> 
> I think this information can add valuable information  to the discussion
> and enriches your knowledge about programming languages.
> 
> Kind regards,
> 
> Maarten
> 
> 
> On 03/21/2013 07:49 PM, L.C. Karssen wrote:
>> Dear all,
>>
>> Maarten started an etherpad instance at http://openetherpad.org/oxx0htdP47
>> I've updated the text he and I came up with and reformatted it in Emacs
>> org-mode, which allows easy export to PDF and HTML (so that we can
>> easily integrated it in the development website on r-forge as per
>> Yurii's suggestion).
>>
>> If I don't see much change in the EtherPad document in the coming days
>> I'll put the org file and its HTML export in SVN.
>>
>>
>> Lennart.
>>
>> On 20/03/13 11:54, Yurii Aulchenko wrote:
>>> Hi Lennart,
>>>
>>> Indeed, why do not we set up piratpad; or we can use our SVN, the same
>>> section we have tutorials in - then it will go directly
>>> to http://genabel.r-forge.r-project.org/
>>>
>>> I think it is important to have guidelines  and I personally will try to
>>> follow them as much as I could.
>>>
>>> At the same time, I would like to emphasize that we had the idea that
>>> rules and guidelines should be suggestive, so that even if I do not
>>> comply 100% I can still make it into the project, and then can improve
>>> on the way. See the quote below.
>>>
>>> best, Yurii
>>>
>>> Quote from
>>>
>>> http://www.genabel.org/developers:
>>>
>>> Rules of the game
>>> The documents provided here are meant to help. We are scared to think of
>>> a situation when 'guidelines' and 'rules' prevent people from
>>> contributing to the project, and a willing contributor is discouraged by
>>> just looking at the pile of 'rules'.
>>>
>>> On Mon, Mar 18, 2013 at 9:32 AM, L.C. Karssen <lennart at karssen.org
>>> <mailto:lennart at karssen.org>> wrote:
>>>
>>>     Dear all,
>>>
>>>     I'd like to follow up on something Yurii wrote in the discussion on the
>>>     GenABEL tutorial:
>>>
>>>     On 03/14/2013 09:38 AM, Yurii Aulchenko wrote:
>>>     > I agree that full argument names should be preferred. I was just being
>>>     > lazy; I am trying to improve. If other people come up with things
>>>     > which are "not in good style" we should probably think of a "good
>>>     > style rules" document and then ask people to please to follow them.
>>>     >
>>>
>>>     I completely agree with Yurii. In fact, I think we should not only set
>>>     guidelines for the style of the code in the tutorial, but more generally
>>>     for all R and C/C++ code in the GenABEL project.
>>>
>>>     What about setting up a shared editing environment (e.g. on
>>>     piratepad.net <http://piratepad.net>) to work on an initial draft of
>>>     these quidelines? Once
>>>     they are more or less fixed we can move the document to SVN as part of
>>>     the developer documentation.
>>>
>>>     From my experience over the last few years I think the following points
>>>     are the most commonly occurring ones (for any language) that need
>>>     harmonisation:
>>>     - comma's should be followed by a space
>>>     - operators (= + - * etc.) should be surrounded by a space (and in R the
>>>     <- operator too)
>>>     - a file should always have a newline at the end
>>>     - don't use tabs (as everyone seems to have a different setting for the
>>>     tab stop): use spaces. How many spaces is up for debate. Of course
>>>     Makefiles are exempt from this rule as tabs are mandatory
>>>     - style of brackets: is the opening bracket on the same line as the name
>>>     of the loop/function or on a new line on its own? (e.g. K&R, Allman or
>>>     bsd style)
>>>     - always use {} in if clauses/for loops (even if there is only one
>>>     statement in the clause/loop
>>>     - lines should not be longer than 80 characters (you may call me old
>>>     fashioned ;-))
>>>
>>>     I think most of these can be set as options in modern development
>>>     environment. I'm not an Eclipse user, like many of you, but in Emacs
>>>     these can easily be set in your .emacs file. We should also provide info
>>>     on how to implement these settings in various DEs in our guidelines
>>>     document so that new developers can easily use them.
>>>
>>>
>>>     Lennart.
>>>     --
>>>     -----------------------------------------------------------------
>>>     L.C. Karssen
>>>     Utrecht
>>>     The Netherlands
>>>
>>>     lennart at karssen.org <mailto: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
>>>     <mailto: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/> ]
>>
>>
>> _______________________________________________
>> 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 Mar 27 16:58:41 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 27 Mar 2013 16:58:41 +0100
Subject: [GenABEL-dev] abstract for UseR! 2013
Message-ID: <CAHX9t6J-dDAf2+AtNgPpbmMNVnv6+37jiQC36chH8bpgdkefZg@mail.gmail.com>

Dear All,

Please find below an abstract I am going to send for the UseR! 2013
meeting.

Comments and suggestions are welcome! - the deadline is March 31

Yurii

\title{The GenABEL suite for genome-wide association analyses}

\begin{center}
  {\bf Yurii S Aulchenko$^{1,2,3,^\star}$, on behalf of the GenABEL project}
\end{center}

\keywords genome-wide association scans, SNP, complex traits,
statistical genomics

\vskip 0.8cm

Genome-wide association (GWA) analysis is a widely recognized
technique for identification of genomic regions
(loci) in which changes in DNA sequence lead to changes in complex
phenotype. In GWA scans, genomes of thousands of individuals are
assessed by use of single nucleotide polymorphisms (SNP) arrays or
whole-genome resequencing to gather information on hundreds of
thousands to millions of genetic variants. The trait values of
genotyped individuals are then tested for association with this
genetic variation. During last eight years, hundreds of loci for dozens of
human common disease and other complex traits were identified using
GWA scans.

The \pkg{GenABEL} project aims to provide a free framework for
collaborative, robust, transparent, open-source based development of
statistical genomics methodology.
In the framework of this project we have developed a suite of
packages facilitating different semi-independent types of GWA analyses.
The suite currently includes nine packages, of which seven are \proglang{R}
libraries, such as the
\pkg{GenABEL} for generic GWA quality control and analyzes, \pkg{MetABEL}
for meta-analysis,
\pkg{DatABEL} for large data sets management, \pkg{VariABEL} for
identification of potentially interacting variants, and others. The packages
are distributed under GPL or LGPL and are available at the
\pkg{GenABEL} project home page, \url{http://www.genabel.org}.
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From lennart at karssen.org  Thu Mar 28 09:21:08 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 28 Mar 2013 09:21:08 +0100
Subject: [GenABEL-dev] abstract for UseR! 2013
In-Reply-To: <CAHX9t6J-dDAf2+AtNgPpbmMNVnv6+37jiQC36chH8bpgdkefZg@mail.gmail.com>
References: <CAHX9t6J-dDAf2+AtNgPpbmMNVnv6+37jiQC36chH8bpgdkefZg@mail.gmail.com>
Message-ID: <5153FD74.7030907@karssen.org>

Hi Yurii,

Looks good! The only thing I'm missing is a sentence that explains what
you are going to show. Something along the lines of "I will show results
obtained with GenABEL/show how to analyse a dataset using
GenABEL/introduce each of the packages in the suite/...".


Good luck in Spain!

Lennart.


On 27/03/13 16:58, Yurii Aulchenko wrote:
> Dear All,
> 
> Please find below an abstract I am going to send for the UseR! 2013
> meeting. 
> 
> Comments and suggestions are welcome! - the deadline is March 31
> 
> Yurii
> 
> \title{The GenABEL suite for genome-wide association analyses}
> 
> \begin{center}
>   {\bf Yurii S Aulchenko$^{1,2,3,^\star}$, on behalf of the GenABEL project}
> \end{center}
> 
> \keywords genome-wide association scans, SNP, complex traits,
> statistical genomics
> 
> \vskip 0.8cm
> 
> Genome-wide association (GWA) analysis is a widely recognized 
> technique for identification of genomic regions
> (loci) in which changes in DNA sequence lead to changes in complex 
> phenotype. In GWA scans, genomes of thousands of individuals are
> assessed by use of single nucleotide polymorphisms (SNP) arrays or 
> whole-genome resequencing to gather information on hundreds of
> thousands to millions of genetic variants. The trait values of
> genotyped individuals are then tested for association with this
> genetic variation. During last eight years, hundreds of loci for dozens of
> human common disease and other complex traits were identified using
> GWA scans. 
> 
> The \pkg{GenABEL} project aims to provide a free framework for
> collaborative, robust, transparent, open-source based development of
> statistical genomics methodology. 
> In the framework of this project we have developed a suite of
> packages facilitating different semi-independent types of GWA analyses. 
> The suite currently includes nine packages, of which seven are
> \proglang{R} libraries, such as the
> \pkg{GenABEL} for generic GWA quality control and analyzes,
> \pkg{MetABEL} for meta-analysis,
> \pkg{DatABEL} for large data sets management, \pkg{VariABEL} for
> identification of potentially interacting variants, and others. The packages
> are distributed under GPL or LGPL and are available at the
> \pkg{GenABEL} project home page, \url{http://www.genabel.org}. 
> 
> 
> 
> _______________________________________________
> 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 C.Wangdee1 at uu.nl  Thu Mar 28 10:05:02 2013
From: C.Wangdee1 at uu.nl (Wangdee, C.)
Date: Thu, 28 Mar 2013 09:05:02 +0000
Subject: [GenABEL-dev] a problem of illegal genotype (three alleles)
Message-ID: <9E2FF58C4F4AEE4D87822AF9763F86C1101C52FE@ICTSC-W-S205.soliscom.uu.nl>

Dear,

I am working with the data set of GWAS on GenABEL. I found a problem when I run a command convert.snp.ped.
The program said "Error in convert.snp.ped("pedin1.txt", "map.txt", "genokooi.raw") :
  illegal genotype (three alleles) snp 'BICF2G630100019' file 'pedin1.txt' line 91 !"
I tried to manage and get new pedin but the problem cannot solve.
Could you please help me on this problem?

Best regards,
Chalika
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From yurii.aulchenko at gmail.com  Thu Mar 28 12:57:33 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 28 Mar 2013 12:57:33 +0100
Subject: [GenABEL-dev] a problem of illegal genotype (three alleles)
In-Reply-To: <9E2FF58C4F4AEE4D87822AF9763F86C1101C52FE@ICTSC-W-S205.soliscom.uu.nl>
References: <9E2FF58C4F4AEE4D87822AF9763F86C1101C52FE@ICTSC-W-S205.soliscom.uu.nl>
Message-ID: <CAHX9t6K82BFi-R6=oDFRXL9JqzAdcHJD-35AQuz8CtqXJsmEMg@mail.gmail.com>

Dear Chalika,

This list is dedicated to the discussion related to the development of the
GenABEL suite and project, but not to the user support.

Therefore I think you question is better suited for the forum.genabel.org.
It is also quite likely that you will find some information answering your
question over there.

best regards,
Yurii

On Thu, Mar 28, 2013 at 10:05 AM, Wangdee, C. <C.Wangdee1 at uu.nl> wrote:

>  Dear,****
>
> ** **
>
> I am working with the data set of GWAS on GenABEL. I found a problem when
> I run a command convert.snp.ped.****
>
> The program said ?Error in convert.snp.ped("pedin1.txt", "map.txt",
> "genokooi.raw") : ****
>
>   illegal genotype (three alleles) snp 'BICF2G630100019' file 'pedin1.txt'
> line 91 !?****
>
> I tried to manage and get new pedin but the problem cannot solve.****
>
> Could you please help me on this problem?****
>
> ** **
>
> Best regards,****
>
> Chalika****
>
> _______________________________________________
> 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 marcin.kierczak at slu.se  Thu Mar 28 13:25:10 2013
From: marcin.kierczak at slu.se (Marcin Kierczak)
Date: Thu, 28 Mar 2013 12:25:10 +0000
Subject: [GenABEL-dev] a problem of illegal genotype (three alleles)
In-Reply-To: <CAHX9t6K82BFi-R6=oDFRXL9JqzAdcHJD-35AQuz8CtqXJsmEMg@mail.gmail.com>
References: <9E2FF58C4F4AEE4D87822AF9763F86C1101C52FE@ICTSC-W-S205.soliscom.uu.nl>
 <CAHX9t6K82BFi-R6=oDFRXL9JqzAdcHJD-35AQuz8CtqXJsmEMg@mail.gmail.com>
Message-ID: <E5DFDE9F825FBA4F9240A8B6F24BF7E72652E10A@exchange2-2>

Dear Chalika,

this is a common problem -- often it is caused by some weird character in ped file which makes GenABEL think that there are more than two alleles. Often this is caused by:

- you do not have 6 columns in front of the first genotype column in your file and GenABEL takes phenotype column as the first genotype
- letter case , e.g. you have alleles "A", "T" and "a" in your column
- often it is white-character-related issue, i.e. you have mixed tabs and spaces in your file. This is the most difficult to spot but also the most common thing. It is often caused by the fact that white characters are differently encoded and interpreted by different OS. If you are using Linux machine and your file was created by a Windows program, it may result in such error.

I think it would be a tremendous help if GenABEL printed these three alleles and I suppose it is a very easy add-on for one of the next releases.

Good luck!

Marcin

______________________________________________________________________________

Swedish University of Agricultural Sciences
Department of Clinical Sciences

Mailing address:
Box 7023
SE-75007 Uppsala
Sweden

email: marcin.kierczak at slu.se<mailto:orjan.carlborg at slu.se>
phone: +46 72 516 76 36


web: http://www.computationalgenetics.se<http://www.computationalgenetics.se/>
http://www.kierczak.net

facebook: http://www.facebook.com/pages/Computationalgenetics/174216822622706
______________________________________________________________________________







On Mar 28, 2013, at 12:57 PM, Yurii Aulchenko <yurii.aulchenko at gmail.com<mailto:yurii.aulchenko at gmail.com>>
 wrote:

Dear Chalika,

This list is dedicated to the discussion related to the development of the
GenABEL suite and project, but not to the user support.

Therefore I think you question is better suited for the forum.genabel.org<http://forum.genabel.org>.
It is also quite likely that you will find some information answering your
question over there.

best regards,
Yurii

On Thu, Mar 28, 2013 at 10:05 AM, Wangdee, C. <C.Wangdee1 at uu.nl<mailto:C.Wangdee1 at uu.nl>> wrote:

Dear,****

** **

I am working with the data set of GWAS on GenABEL. I found a problem when
I run a command convert.snp.ped.****

The program said ?Error in convert.snp.ped("pedin1.txt", "map.txt",
"genokooi.raw") : ****

 illegal genotype (three alleles) snp 'BICF2G630100019' file 'pedin1.txt'
line 91 !?****

I tried to manage and get new pedin but the problem cannot solve.****

Could you please help me on this problem?****

** **

Best regards,****

Chalika****

_______________________________________________
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




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

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
_______________________________________________
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

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From lennart at karssen.org  Thu Mar 28 14:34:20 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 28 Mar 2013 14:34:20 +0100
Subject: [GenABEL-dev] export.plink bug: should we change the default?
Message-ID: <515446DC.6040602@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
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Fri Mar 29 12:16:07 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 29 Mar 2013 12:16:07 +0100
Subject: [GenABEL-dev] abstract for UseR! 2013
In-Reply-To: <5153FD74.7030907@karssen.org>
References: <CAHX9t6J-dDAf2+AtNgPpbmMNVnv6+37jiQC36chH8bpgdkefZg@mail.gmail.com>
 <5153FD74.7030907@karssen.org>
Message-ID: <CAHX9t6JdHRjwUA4SBeF+nU9Q5J9kqtk6iGrgjH73-dDknurWHQ@mail.gmail.com>

Thanks for comments Lennart!

I am going to add

In this talk, I will describe the \pkg{GenABEL} project in general
and will also introduce some of the packages of the suite.

A bit of problem being using 'in this talk' while I am not sure if I am
getting a poster :)

Yurii

On Thu, Mar 28, 2013 at 9:21 AM, L.C. Karssen <lennart at karssen.org> wrote:

> Hi Yurii,
>
> Looks good! The only thing I'm missing is a sentence that explains what
> you are going to show. Something along the lines of "I will show results
> obtained with GenABEL/show how to analyse a dataset using
> GenABEL/introduce each of the packages in the suite/...".
>
>
> Good luck in Spain!
>
> Lennart.
>
>
> On 27/03/13 16:58, Yurii Aulchenko wrote:
> > Dear All,
> >
> > Please find below an abstract I am going to send for the UseR! 2013
> > meeting.
> >
> > Comments and suggestions are welcome! - the deadline is March 31
> >
> > Yurii
> >
> > \title{The GenABEL suite for genome-wide association analyses}
> >
> > \begin{center}
> >   {\bf Yurii S Aulchenko$^{1,2,3,^\star}$, on behalf of the GenABEL
> project}
> > \end{center}
> >
> > \keywords genome-wide association scans, SNP, complex traits,
> > statistical genomics
> >
> > \vskip 0.8cm
> >
> > Genome-wide association (GWA) analysis is a widely recognized
> > technique for identification of genomic regions
> > (loci) in which changes in DNA sequence lead to changes in complex
> > phenotype. In GWA scans, genomes of thousands of individuals are
> > assessed by use of single nucleotide polymorphisms (SNP) arrays or
> > whole-genome resequencing to gather information on hundreds of
> > thousands to millions of genetic variants. The trait values of
> > genotyped individuals are then tested for association with this
> > genetic variation. During last eight years, hundreds of loci for dozens
> of
> > human common disease and other complex traits were identified using
> > GWA scans.
> >
> > The \pkg{GenABEL} project aims to provide a free framework for
> > collaborative, robust, transparent, open-source based development of
> > statistical genomics methodology.
> > In the framework of this project we have developed a suite of
> > packages facilitating different semi-independent types of GWA analyses.
> > The suite currently includes nine packages, of which seven are
> > \proglang{R} libraries, such as the
> > \pkg{GenABEL} for generic GWA quality control and analyzes,
> > \pkg{MetABEL} for meta-analysis,
> > \pkg{DatABEL} for large data sets management, \pkg{VariABEL} for
> > identification of potentially interacting variants, and others. The
> packages
> > are distributed under GPL or LGPL and are available at the
> > \pkg{GenABEL} project home page, \url{http://www.genabel.org}.
> >
> >
> >
> > _______________________________________________
> > 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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