From yurii.aulchenko at gmail.com  Mon Dec  2 09:32:55 2013
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Mon, 2 Dec 2013 09:32:55 +0100
Subject: [GenABEL-dev] [genabel-Bugs][2608] GenABEL-package loads too
	long if there is no internet connection
In-Reply-To: <20131202082607.B661E186243@r-forge.r-project.org>
References: <20131202082607.B661E186243@r-forge.r-project.org>
Message-ID: <50DC46B3-5A3F-4BC0-BCCC-1094EFDCEB03@gmail.com>

CRAN continues changing the layout of the page, and therefore these functions were disabled (see the beginning of the code). And for the moment quality of the code does not guarantee that the package starts if this happens. 

I do not know how we can easily solve this...

Y


On Dec 2, 2013, at 09:26 AM, <genabel-bugs at r-forge.r-project.org> <genabel-bugs at r-forge.r-project.org> wrote:

> Bugs item #2608, was changed at 2013-03-12 09:14 by Lennart Karssen
> You can respond by visiting: 
> https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=2608&group_id=505
> 
> Status: Open
> Priority: 2
> Submitted By: Yurii Aulchenko (yurii)
> Assigned to: Nobody (None)
> Summary: GenABEL-package loads too long if there is no internet connection 
> Resolution: None
> Operating System: None
> Severity: trivial
> Hardware: None
> Version: None
> Component: GenABEL
> URL: 
> 
> 
> Initial Comment:
> Try loading the GenA-package ('library(GenABEL)") in R with and without internet connection. There is a clear difference. This is something to do with the (multiple???) 'timeout' argument - probably need to do quicker. 
> 
> ----------------------------------------------------------------------
> 
>> Comment By: Lennart Karssen (lckarssen)
> Date: 2013-12-02 09:26
> 
> Message:
> Maybe we can also add an option that allows the users to bypass the check completely. For example by setting an option in their ~/.Rprofile file like this:
> 
> options(GenABEL.update.check = FALSE)
> 
> 
> ----------------------------------------------------------------------
> 
> Comment By: Maksim Struchalin (maksim)
> Date: 2013-11-30 10:30
> 
> Message:
> I studied this problem a bit today. The delay is caused by R function readLines() in the .onAttach() function from file R/zzz.R. This function tries to read from a site without (!) checking whether this site is opened sucessfuly by function 'url()'. If there is no internet connection, then the readLines() get stuck for 20 seconds and return "try-error" (through try()). There are 3 calls of readLines() that should cause a total delay of 60 sec.
> 
> I see two possible solutions:
> 1) Use R package "RCurl" which provide more complex instruments for work with internet (hopefuly it will solve the problem). But, unfortunatelly, I can not install it. 
> 2) Try to 'ping' sites and see response. In this case, we check out whether sites are responding to our ping request and then read from those which reacted on our ping. It should work on win/max/linux as all of them have 'ping' system function. Disadvantages: This apporoach will not work if the site's mainteners will forbid ping response.
> 
> 
> 
> ----------------------------------------------------------------------
> 
> Comment By: Yurii Aulchenko (yurii)
> Date: 2013-03-12 10:23
> 
> Message:
> starting point: 
> function '.onAttach' in GenABEL/R/zzz.R
> 
> ----------------------------------------------------------------------
> 
> You can respond by visiting: 
> https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=2608&group_id=505


From lennart at karssen.org  Mon Dec  2 09:40:03 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 02 Dec 2013 09:40:03 +0100
Subject: [GenABEL-dev] Preparing for ProbABEL v4.2 release
Message-ID: <529C4763.4090905@karssen.org>

Dear all,

I'm preparing to release ProbABEL v0.4.2 this week. If you have any
patches that you'd like to submit/commit, please do so as soon as possible.
Please don't commit large changes that need extensive testing. These can
be committed for the release after that.


Thanks,

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

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From lennart at karssen.org  Mon Dec  2 12:03:10 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 02 Dec 2013 12:03:10 +0100
Subject: [GenABEL-dev] Jenkins continuous integration server available
In-Reply-To: <5298A717.1060705@karssen.org>
References: <528A1410.8010802@karssen.org> <529890E2.1000008@mail.ru>
 <5298A717.1060705@karssen.org>
Message-ID: <529C68EE.8080509@karssen.org>

Dear all,

The Jenkins server can now be reached via jenkins.genabel.org (which
still points to the old URL on my home server). Note that there will be
an SSL certificate warning (since the certificate is signed for
*.karssen.org, not *.genabel.org). If I have time, I'll fix that in the
future.

As per Maksim's suggestion I also added a link in the Developer section
of www.genabel.org, as well as on http://genabel.r-forge.r-project.org/


Let me know if you notice any odd behaviour.


Lennart.

On 29-11-13 15:39, L.C. Karssen wrote:
> Good suggestion!
> I'll do that.
> 
> 
> Lennart.
> 
> On 11/29/2013 02:04 PM, Maksim Struchalin wrote:
>> Hi Lennart,
>>
>> Is it possible to make a reference to http://www.karssen.org/jenkins/
>> from http://www.genabel.org/developers or from r-forge (or better from
>> both)? It would be more convinient to acess to it + future new
>> developres will know that such an instrument exists. Now, I have to look
>> for your email to figure out the ref to Jenkins.
>>
>> best,
>> Maksim
>>
>>  
>> On 18/11/2013 20:20, L.C. Karssen wrote:
>>> Dear all,
>>>
>>> In order to keep an eye on the build stability of the various C/C++
>>> packages in the GenABEL suite, I've taken some time in the past weeks to
>>> set up a Jenkins server [1] at http://www.karssen.org/jenkins/
>>>
>>> Jenkins checks out the source code from R-forge, runs several static
>>> code analysis tools and tries to compile the code. Any errors or
>>> warnings that pop up are listed. This way we can make sure that the code
>>> is always in a proper (compilable) state and also provides hints on how
>>> to improve the code.
>>>
>>> Maarten Kooyman piloted the use of Jenkins at my previous employer. Many
>>> of the things we learned from that setup have been incorporated in this
>>> Jenkins install. Thanks a lot Maarten!
>>>
>>> The ProbABEL project is configured in most detail with checks of the
>>> C/C++ style, violations of the Google coding standards and Valgrind
>>> checks for memory leaks. More checks still need to be added for ProbABEL
>>> and other projects. Consider this a work in progress.
>>>
>>> Have a look around and let me know if you have any questions or
>>> suggestions.
>>>
>>>
>>> Best regards,
>>>
>>> Lennart.
>>>
>>>
>>> [1] http://jenkins-ci.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
>>
>>
>>
>> _______________________________________________
>> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From yurii.aulchenko at gmail.com  Mon Dec  2 12:39:45 2013
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Mon, 2 Dec 2013 12:39:45 +0100
Subject: [GenABEL-dev] Jenkins continuous integration server available
In-Reply-To: <529C68EE.8080509@karssen.org>
References: <528A1410.8010802@karssen.org> <529890E2.1000008@mail.ru>
 <5298A717.1060705@karssen.org> <529C68EE.8080509@karssen.org>
Message-ID: <1142A492-2E60-4883-844F-55C18B0F93BA@gmail.com>

wowowow!

Y

On Dec 2, 2013, at 12:03 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Dear all,
> 
> The Jenkins server can now be reached via jenkins.genabel.org (which
> still points to the old URL on my home server). Note that there will be
> an SSL certificate warning (since the certificate is signed for
> *.karssen.org, not *.genabel.org). If I have time, I'll fix that in the
> future.
> 
> As per Maksim's suggestion I also added a link in the Developer section
> of www.genabel.org, as well as on http://genabel.r-forge.r-project.org/
> 
> 
> Let me know if you notice any odd behaviour.
> 
> 
> Lennart.
> 
> On 29-11-13 15:39, L.C. Karssen wrote:
>> Good suggestion!
>> I'll do that.
>> 
>> 
>> Lennart.
>> 
>> On 11/29/2013 02:04 PM, Maksim Struchalin wrote:
>>> Hi Lennart,
>>> 
>>> Is it possible to make a reference to http://www.karssen.org/jenkins/
>>> from http://www.genabel.org/developers or from r-forge (or better from
>>> both)? It would be more convinient to acess to it + future new
>>> developres will know that such an instrument exists. Now, I have to look
>>> for your email to figure out the ref to Jenkins.
>>> 
>>> best,
>>> Maksim
>>> 
>>> 
>>> On 18/11/2013 20:20, L.C. Karssen wrote:
>>>> Dear all,
>>>> 
>>>> In order to keep an eye on the build stability of the various C/C++
>>>> packages in the GenABEL suite, I've taken some time in the past weeks to
>>>> set up a Jenkins server [1] at http://www.karssen.org/jenkins/
>>>> 
>>>> Jenkins checks out the source code from R-forge, runs several static
>>>> code analysis tools and tries to compile the code. Any errors or
>>>> warnings that pop up are listed. This way we can make sure that the code
>>>> is always in a proper (compilable) state and also provides hints on how
>>>> to improve the code.
>>>> 
>>>> Maarten Kooyman piloted the use of Jenkins at my previous employer. Many
>>>> of the things we learned from that setup have been incorporated in this
>>>> Jenkins install. Thanks a lot Maarten!
>>>> 
>>>> The ProbABEL project is configured in most detail with checks of the
>>>> C/C++ style, violations of the Google coding standards and Valgrind
>>>> checks for memory leaks. More checks still need to be added for ProbABEL
>>>> and other projects. Consider this a work in progress.
>>>> 
>>>> Have a look around and let me know if you have any questions or
>>>> suggestions.
>>>> 
>>>> 
>>>> Best regards,
>>>> 
>>>> Lennart.
>>>> 
>>>> 
>>>> [1] http://jenkins-ci.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
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
> 
> _______________________________________________
> 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  Thu Dec  5 00:27:18 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 5 Dec 2013 00:27:18 +0100
Subject: [GenABEL-dev] Jenkins continuous integration server available
In-Reply-To: <529C68EE.8080509@karssen.org>
References: <528A1410.8010802@karssen.org> <529890E2.1000008@mail.ru>
 <5298A717.1060705@karssen.org> <529C68EE.8080509@karssen.org>
Message-ID: <CAHX9t6+weiD1N2mCawtESBRTR1-OyiKVULzRfhjCvPD5oaOS1w@mail.gmail.com>

do you think jenkins is worth a short message in our news-line? (I think it
is)

Y


On Mon, Dec 2, 2013 at 12:03 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Dear all,
>
> The Jenkins server can now be reached via jenkins.genabel.org (which
> still points to the old URL on my home server). Note that there will be
> an SSL certificate warning (since the certificate is signed for
> *.karssen.org, not *.genabel.org). If I have time, I'll fix that in the
> future.
>
> As per Maksim's suggestion I also added a link in the Developer section
> of www.genabel.org, as well as on http://genabel.r-forge.r-project.org/
>
>
> Let me know if you notice any odd behaviour.
>
>
> Lennart.
>
> On 29-11-13 15:39, L.C. Karssen wrote:
> > Good suggestion!
> > I'll do that.
> >
> >
> > Lennart.
> >
> > On 11/29/2013 02:04 PM, Maksim Struchalin wrote:
> >> Hi Lennart,
> >>
> >> Is it possible to make a reference to http://www.karssen.org/jenkins/
> >> from http://www.genabel.org/developers or from r-forge (or better from
> >> both)? It would be more convinient to acess to it + future new
> >> developres will know that such an instrument exists. Now, I have to look
> >> for your email to figure out the ref to Jenkins.
> >>
> >> best,
> >> Maksim
> >>
> >>
> >> On 18/11/2013 20:20, L.C. Karssen wrote:
> >>> Dear all,
> >>>
> >>> In order to keep an eye on the build stability of the various C/C++
> >>> packages in the GenABEL suite, I've taken some time in the past weeks
> to
> >>> set up a Jenkins server [1] at http://www.karssen.org/jenkins/
> >>>
> >>> Jenkins checks out the source code from R-forge, runs several static
> >>> code analysis tools and tries to compile the code. Any errors or
> >>> warnings that pop up are listed. This way we can make sure that the
> code
> >>> is always in a proper (compilable) state and also provides hints on how
> >>> to improve the code.
> >>>
> >>> Maarten Kooyman piloted the use of Jenkins at my previous employer.
> Many
> >>> of the things we learned from that setup have been incorporated in this
> >>> Jenkins install. Thanks a lot Maarten!
> >>>
> >>> The ProbABEL project is configured in most detail with checks of the
> >>> C/C++ style, violations of the Google coding standards and Valgrind
> >>> checks for memory leaks. More checks still need to be added for
> ProbABEL
> >>> and other projects. Consider this a work in progress.
> >>>
> >>> Have a look around and let me know if you have any questions or
> >>> suggestions.
> >>>
> >>>
> >>> Best regards,
> >>>
> >>> Lennart.
> >>>
> >>>
> >>> [1] http://jenkins-ci.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
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
>
> _______________________________________________
> 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 lennart at karssen.org  Thu Dec  5 08:13:50 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 05 Dec 2013 08:13:50 +0100
Subject: [GenABEL-dev] Jenkins continuous integration server available
In-Reply-To: <CAHX9t6+weiD1N2mCawtESBRTR1-OyiKVULzRfhjCvPD5oaOS1w@mail.gmail.com>
References: <528A1410.8010802@karssen.org> <529890E2.1000008@mail.ru>
 <5298A717.1060705@karssen.org> <529C68EE.8080509@karssen.org>
 <CAHX9t6+weiD1N2mCawtESBRTR1-OyiKVULzRfhjCvPD5oaOS1w@mail.gmail.com>
Message-ID: <216f4ff1-37fc-4e42-8286-d86a456a58e9@email.android.com>

Good idea! Thanks for the suggestion.  I'll announce it today.

Lennart. 

Yurii Aulchenko <yurii.aulchenko at gmail.com> schreef:
>do you think jenkins is worth a short message in our news-line? (I
>think it
>is)
>
>Y
>
>
>On Mon, Dec 2, 2013 at 12:03 PM, L.C. Karssen <lennart at karssen.org>
>wrote:
>
>> Dear all,
>>
>> The Jenkins server can now be reached via jenkins.genabel.org (which
>> still points to the old URL on my home server). Note that there will
>be
>> an SSL certificate warning (since the certificate is signed for
>> *.karssen.org, not *.genabel.org). If I have time, I'll fix that in
>the
>> future.
>>
>> As per Maksim's suggestion I also added a link in the Developer
>section
>> of www.genabel.org, as well as on
>http://genabel.r-forge.r-project.org/
>>
>>
>> Let me know if you notice any odd behaviour.
>>
>>
>> Lennart.
>>
>> On 29-11-13 15:39, L.C. Karssen wrote:
>> > Good suggestion!
>> > I'll do that.
>> >
>> >
>> > Lennart.
>> >
>> > On 11/29/2013 02:04 PM, Maksim Struchalin wrote:
>> >> Hi Lennart,
>> >>
>> >> Is it possible to make a reference to
>http://www.karssen.org/jenkins/
>> >> from http://www.genabel.org/developers or from r-forge (or better
>from
>> >> both)? It would be more convinient to acess to it + future new
>> >> developres will know that such an instrument exists. Now, I have
>to look
>> >> for your email to figure out the ref to Jenkins.
>> >>
>> >> best,
>> >> Maksim
>> >>
>> >>
>> >> On 18/11/2013 20:20, L.C. Karssen wrote:
>> >>> Dear all,
>> >>>
>> >>> In order to keep an eye on the build stability of the various
>C/C++
>> >>> packages in the GenABEL suite, I've taken some time in the past
>weeks
>> to
>> >>> set up a Jenkins server [1] at http://www.karssen.org/jenkins/
>> >>>
>> >>> Jenkins checks out the source code from R-forge, runs several
>static
>> >>> code analysis tools and tries to compile the code. Any errors or
>> >>> warnings that pop up are listed. This way we can make sure that
>the
>> code
>> >>> is always in a proper (compilable) state and also provides hints
>on how
>> >>> to improve the code.
>> >>>
>> >>> Maarten Kooyman piloted the use of Jenkins at my previous
>employer.
>> Many
>> >>> of the things we learned from that setup have been incorporated
>in this
>> >>> Jenkins install. Thanks a lot Maarten!
>> >>>
>> >>> The ProbABEL project is configured in most detail with checks of
>the
>> >>> C/C++ style, violations of the Google coding standards and
>Valgrind
>> >>> checks for memory leaks. More checks still need to be added for
>> ProbABEL
>> >>> and other projects. Consider this a work in progress.
>> >>>
>> >>> Have a look around and let me know if you have any questions or
>> >>> suggestions.
>> >>>
>> >>>
>> >>> Best regards,
>> >>>
>> >>> Lennart.
>> >>>
>> >>>
>> >>> [1] http://jenkins-ci.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
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> 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
>> GPG key ID: A88F554A
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>
>>
>> _______________________________________________
>> 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/> ]

L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.org
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From yurii.aulchenko at gmail.com  Thu Dec  5 09:35:27 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 5 Dec 2013 09:35:27 +0100
Subject: [GenABEL-dev] Jenkins continuous integration server available
In-Reply-To: <216f4ff1-37fc-4e42-8286-d86a456a58e9@email.android.com>
References: <528A1410.8010802@karssen.org> <529890E2.1000008@mail.ru>
 <5298A717.1060705@karssen.org> <529C68EE.8080509@karssen.org>
 <CAHX9t6+weiD1N2mCawtESBRTR1-OyiKVULzRfhjCvPD5oaOS1w@mail.gmail.com>
 <216f4ff1-37fc-4e42-8286-d86a456a58e9@email.android.com>
Message-ID: <CAHX9t6+_p5ns9aW+VWnoy8cifZhs6XWZkmJK7CUkXj0jHm-PJw@mail.gmail.com>

great! please let me know - I will push it to my social networks


On Thu, Dec 5, 2013 at 8:13 AM, L.C. Karssen <lennart at karssen.org> wrote:

> Good idea! Thanks for the suggestion. I'll announce it today.
>
> Lennart.
>
> Yurii Aulchenko <yurii.aulchenko at gmail.com> schreef:
>
>> do you think jenkins is worth a short message in our news-line? (I think
>> it is)
>>
>> Y
>>
>>
>> On Mon, Dec 2, 2013 at 12:03 PM, L.C. Karssen <lennart at karssen.org>wrote:
>>
>>> Dear all,
>>>
>>> The Jenkins server can now be reached via jenkins.genabel.org (which
>>> still points to the old URL on my home server). Note that there will be
>>> an SSL certificate warning (since the certificate is signed for
>>> *.karssen.org, not *.genabel.org). If I have time, I'll fix that in the
>>> future.
>>>
>>> As per Maksim's suggestion I also added a link in the Developer section
>>> of www.genabel.org, as well as on http://genabel.r-forge.r-project.org/
>>>
>>>
>>> Let me know if you notice any odd behaviour.
>>>
>>>
>>> Lennart.
>>>
>>> On 29-11-13 15:39, L.C. Karssen wrote:
>>> > Good suggestion!
>>> > I'll do that.
>>> >
>>> >
>>> > Lennart.
>>> >
>>> > On 11/29/2013 02:04 PM, Maksim Struchalin wrote:
>>> >> Hi Lennart,
>>> >>
>>> >> Is it possible to make a reference to http://www.karssen.org/jenkins/
>>> >> from http://www.genabel.org/developers or from r-forge (or better
>>> from
>>> >> both)? It would be more convinient to acess to it + future new
>>> >> developres will know that such an instrument exists. Now, I have to
>>> look
>>> >> for your email to figure out the ref to Jenkins.
>>> >>
>>> >> best,
>>> >> Maksim
>>> >>
>>> >>
>>> >> On 18/11/2013 20:20, L.C. Karssen wrote:
>>> >>> Dear all,
>>> >>>
>>> >>> In order to keep an eye on the build stability of the various C/C++
>>> >>> packages in the GenABEL suite, I've taken some time in the past
>>> weeks to
>>> >>> set up a Jenkins server [1] at http://www.karssen.org/jenkins/
>>> >>>
>>> >>> Jenkins checks out the source code from R-forge, runs several static
>>> >>> code analysis tools and tries to compile the code. Any errors or
>>> >>> warnings that pop up are listed. This way we can make sure that the
>>> code
>>> >>> is always in a proper (compilable) state and also provides hints on
>>> how
>>> >>> to improve the code.
>>> >>>
>>> >>> Maarten Kooyman piloted the use of Jenkins at my previous employer.
>>> Many
>>> >>> of the things we learned from that setup have been incorporated in
>>> this
>>> >>> Jenkins install. Thanks a lot Maarten!
>>> >>>
>>> >>> The ProbABEL project is configured in most detail with checks of the
>>> >>> C/C++ style, violations of the Google coding standards and Valgrind
>>> >>> checks for memory leaks. More checks still need to be added for
>>> ProbABEL
>>> >>> and other projects. Consider this a work in progress.
>>> >>>
>>> >>> Have a look around and let me know if you have any questions or
>>> >>> suggestions.
>>> >>>
>>> >>>
>>> >>> Best regards,
>>> >>>
>>> >>> Lennart.
>>> >>>
>>> >>>
>>> >>> [1] http://jenkins-ci.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
>>> >>
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >> 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
>>> GPG key ID: A88F554A
>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>
>>>
>>> _______________________________________________
>>> 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/> ]
>>
>
> L.C. Karssen
> Utrecht
> The Netherlands
> lennart at karssen.org
>



-- 
-----------------------------------------------------
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 m.kooijman at erasmusmc.nl  Thu Dec  5 10:21:31 2013
From: m.kooijman at erasmusmc.nl (Maarten Kooyman)
Date: Thu, 05 Dec 2013 10:21:31 +0100
Subject: [GenABEL-dev] Jenkins continuous integration server available
In-Reply-To: <CAHX9t6+_p5ns9aW+VWnoy8cifZhs6XWZkmJK7CUkXj0jHm-PJw@mail.gmail.com>
References: <528A1410.8010802@karssen.org> <529890E2.1000008@mail.ru>
 <5298A717.1060705@karssen.org> <529C68EE.8080509@karssen.org>
 <CAHX9t6+weiD1N2mCawtESBRTR1-OyiKVULzRfhjCvPD5oaOS1w@mail.gmail.com>
 <216f4ff1-37fc-4e42-8286-d86a456a58e9@email.android.com>
 <CAHX9t6+_p5ns9aW+VWnoy8cifZhs6XWZkmJK7CUkXj0jHm-PJw@mail.gmail.com>
Message-ID: <52A0459B.8070804@erasmusmc.nl>

Hi Yurii and Lennart,

I think it is a good idea to integrate |"R CMD check" in jenkins for all
R packages. This will spot problems when they are committed. |
Maarten




On 12/05/2013 09:35 AM, Yurii Aulchenko wrote:

> great! please let me know - I will push it to my social networks
>
>
> On Thu, Dec 5, 2013 at 8:13 AM, L.C. Karssen <lennart at karssen.org
> <mailto:lennart at karssen.org>> wrote:
>
>     Good idea! Thanks for the suggestion. I'll announce it today.
>
>     Lennart.
>
>     Yurii Aulchenko <yurii.aulchenko at gmail.com
>     <mailto:yurii.aulchenko at gmail.com>> schreef:
>
>         do you think jenkins is worth a short message in our
>         news-line? (I think it is)
>
>         Y
>
>
>         On Mon, Dec 2, 2013 at 12:03 PM, L.C. Karssen
>         <lennart at karssen.org <mailto:lennart at karssen.org>> wrote:
>
>             Dear all,
>
>             The Jenkins server can now be reached via
>             jenkins.genabel.org <http://jenkins.genabel.org> (which
>             still points to the old URL on my home server). Note that
>             there will be
>             an SSL certificate warning (since the certificate is
>             signed for
>             *.karssen.org <http://karssen.org>, not *.genabel.org
>             <http://genabel.org>). If I have time, I'll fix that in the
>             future.
>
>             As per Maksim's suggestion I also added a link in the
>             Developer section
>             of www.genabel.org <http://www.genabel.org>, as well as on
>             http://genabel.r-forge.r-project.org/
>
>
>             Let me know if you notice any odd behaviour.
>
>
>             Lennart.
>
>             On 29-11-13 15:39, L.C. Karssen wrote:
>             > Good suggestion!
>             > I'll do that.
>             >
>             >
>             > Lennart.
>             >
>             > On 11/29/2013 02:04 PM, Maksim Struchalin wrote:
>             >> Hi Lennart,
>             >>
>             >> Is it possible to make a reference to
>             http://www.karssen.org/jenkins/
>             >> from http://www.genabel.org/developers or from r-forge
>             (or better from
>             >> both)? It would be more convinient to acess to it +
>             future new
>             >> developres will know that such an instrument exists.
>             Now, I have to look
>             >> for your email to figure out the ref to Jenkins.
>             >>
>             >> best,
>             >> Maksim
>             >>
>             >>
>             >> On 18/11/2013 20:20, L.C. Karssen wrote:
>             >>> Dear all,
>             >>>
>             >>> In order to keep an eye on the build stability of the
>             various C/C++
>             >>> packages in the GenABEL suite, I've taken some time in
>             the past weeks to
>             >>> set up a Jenkins server [1] at
>             http://www.karssen.org/jenkins/
>             >>>
>             >>> Jenkins checks out the source code from R-forge, runs
>             several static
>             >>> code analysis tools and tries to compile the code. Any
>             errors or
>             >>> warnings that pop up are listed. This way we can make
>             sure that the code
>             >>> is always in a proper (compilable) state and also
>             provides hints on how
>             >>> to improve the code.
>             >>>
>             >>> Maarten Kooyman piloted the use of Jenkins at my
>             previous employer. Many
>             >>> of the things we learned from that setup have been
>             incorporated in this
>             >>> Jenkins install. Thanks a lot Maarten!
>             >>>
>             >>> The ProbABEL project is configured in most detail with
>             checks of the
>             >>> C/C++ style, violations of the Google coding standards
>             and Valgrind
>             >>> checks for memory leaks. More checks still need to be
>             added for ProbABEL
>             >>> and other projects. Consider this a work in progress.
>             >>>
>             >>> Have a look around and let me know if you have any
>             questions or
>             >>> suggestions.
>             >>>
>             >>>
>             >>> Best regards,
>             >>>
>             >>> Lennart.
>             >>>
>             >>>
>             >>> [1] http://jenkins-ci.org/
>             >>>
>             >>>
>             >>>
>             >>> _______________________________________________
>             >>> genabel-devel mailing list
>             >>> genabel-devel at lists.r-forge.r-project.org
>             <mailto:genabel-devel at lists.r-forge.r-project.org>
>             >>>
>             https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>             >>
>             >>
>             >>
>             >> _______________________________________________
>             >> genabel-devel mailing list
>             >> genabel-devel at lists.r-forge.r-project.org
>             <mailto:genabel-devel at lists.r-forge.r-project.org>
>             >>
>             https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>             >>
>             >
>             >
>             >
>             > _______________________________________________
>             > genabel-devel mailing list
>             > genabel-devel at lists.r-forge.r-project.org
>             <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
>             GPG key ID: A88F554A
>             -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
>
>             _______________________________________________
>             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 <mailto:lennart at karssen.org>
>
>
>
>
> -- 
> -----------------------------------------------------
> 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  Thu Dec  5 13:24:17 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 05 Dec 2013 13:24:17 +0100
Subject: [GenABEL-dev] Jenkins continuous integration server available
In-Reply-To: <CAHX9t6+_p5ns9aW+VWnoy8cifZhs6XWZkmJK7CUkXj0jHm-PJw@mail.gmail.com>
References: <528A1410.8010802@karssen.org>	<529890E2.1000008@mail.ru>	<5298A717.1060705@karssen.org>	<529C68EE.8080509@karssen.org>	<CAHX9t6+weiD1N2mCawtESBRTR1-OyiKVULzRfhjCvPD5oaOS1w@mail.gmail.com>	<216f4ff1-37fc-4e42-8286-d86a456a58e9@email.android.com>
 <CAHX9t6+_p5ns9aW+VWnoy8cifZhs6XWZkmJK7CUkXj0jHm-PJw@mail.gmail.com>
Message-ID: <52A07071.9040008@karssen.org>

Dear all,

At Yurii's suggestion I've added an announcement on our web page:
http://genabel.org/node/288.


Best,

Lennart.

On 05-12-13 09:35, Yurii Aulchenko wrote:
> great! please let me know - I will push it to my social networks
> 
> 
> On Thu, Dec 5, 2013 at 8:13 AM, L.C. Karssen <lennart at karssen.org
> <mailto:lennart at karssen.org>> wrote:
> 
>     Good idea! Thanks for the suggestion. I'll announce it today.
> 
>     Lennart.
> 
>     Yurii Aulchenko <yurii.aulchenko at gmail.com
>     <mailto:yurii.aulchenko at gmail.com>> schreef:
> 
>         do you think jenkins is worth a short message in our news-line?
>         (I think it is)
> 
>         Y
> 
> 
>         On Mon, Dec 2, 2013 at 12:03 PM, L.C. Karssen
>         <lennart at karssen.org <mailto:lennart at karssen.org>> wrote:
> 
>             Dear all,
> 
>             The Jenkins server can now be reached via
>             jenkins.genabel.org <http://jenkins.genabel.org> (which
>             still points to the old URL on my home server). Note that
>             there will be
>             an SSL certificate warning (since the certificate is signed for
>             *.karssen.org <http://karssen.org>, not *.genabel.org
>             <http://genabel.org>). If I have time, I'll fix that in the
>             future.
> 
>             As per Maksim's suggestion I also added a link in the
>             Developer section
>             of www.genabel.org <http://www.genabel.org>, as well as on
>             http://genabel.r-forge.r-project.org/
> 
> 
>             Let me know if you notice any odd behaviour.
> 
> 
>             Lennart.
> 
>             On 29-11-13 15:39, L.C. Karssen wrote:
>             > Good suggestion!
>             > I'll do that.
>             >
>             >
>             > Lennart.
>             >
>             > On 11/29/2013 02:04 PM, Maksim Struchalin wrote:
>             >> Hi Lennart,
>             >>
>             >> Is it possible to make a reference to
>             http://www.karssen.org/jenkins/
>             >> from http://www.genabel.org/developers or from r-forge
>             (or better from
>             >> both)? It would be more convinient to acess to it +
>             future new
>             >> developres will know that such an instrument exists. Now,
>             I have to look
>             >> for your email to figure out the ref to Jenkins.
>             >>
>             >> best,
>             >> Maksim
>             >>
>             >>
>             >> On 18/11/2013 20:20, L.C. Karssen wrote:
>             >>> Dear all,
>             >>>
>             >>> In order to keep an eye on the build stability of the
>             various C/C++
>             >>> packages in the GenABEL suite, I've taken some time in
>             the past weeks to
>             >>> set up a Jenkins server [1] at
>             http://www.karssen.org/jenkins/
>             >>>
>             >>> Jenkins checks out the source code from R-forge, runs
>             several static
>             >>> code analysis tools and tries to compile the code. Any
>             errors or
>             >>> warnings that pop up are listed. This way we can make
>             sure that the code
>             >>> is always in a proper (compilable) state and also
>             provides hints on how
>             >>> to improve the code.
>             >>>
>             >>> Maarten Kooyman piloted the use of Jenkins at my
>             previous employer. Many
>             >>> of the things we learned from that setup have been
>             incorporated in this
>             >>> Jenkins install. Thanks a lot Maarten!
>             >>>
>             >>> The ProbABEL project is configured in most detail with
>             checks of the
>             >>> C/C++ style, violations of the Google coding standards
>             and Valgrind
>             >>> checks for memory leaks. More checks still need to be
>             added for ProbABEL
>             >>> and other projects. Consider this a work in progress.
>             >>>
>             >>> Have a look around and let me know if you have any
>             questions or
>             >>> suggestions.
>             >>>
>             >>>
>             >>> Best regards,
>             >>>
>             >>> Lennart.
>             >>>
>             >>>
>             >>> [1] http://jenkins-ci.org/
>             >>>
>             >>>
>             >>>
>             >>> _______________________________________________
>             >>> genabel-devel mailing list
>             >>> genabel-devel at lists.r-forge.r-project.org
>             <mailto:genabel-devel at lists.r-forge.r-project.org>
>             >>>
>             https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>             >>
>             >>
>             >>
>             >> _______________________________________________
>             >> genabel-devel mailing list
>             >> genabel-devel at lists.r-forge.r-project.org
>             <mailto:genabel-devel at lists.r-forge.r-project.org>
>             >>
>             https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>             >>
>             >
>             >
>             >
>             > _______________________________________________
>             > genabel-devel mailing list
>             > genabel-devel at lists.r-forge.r-project.org
>             <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
>             GPG key ID: A88F554A
>             -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
> 
> 
>             _______________________________________________
>             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 <mailto:lennart at karssen.org>
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From m.v.struchalin at mail.ru  Fri Dec  6 07:40:58 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Fri, 06 Dec 2013 13:40:58 +0700
Subject: [GenABEL-dev] new release of GenABEL is coming
Message-ID: <52A1717A.3000309@mail.ru>

Dear All,

I am going to submit a new version of GenABEL (and GenABEL.data) on 
CRAN. If anyone here has any objections to this version being submitted, 
let them speak now or forever hold your peace :-).

best,
Maksim

From lennart at karssen.org  Fri Dec  6 09:26:38 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 06 Dec 2013 09:26:38 +0100
Subject: [GenABEL-dev] new release of GenABEL is coming
In-Reply-To: <52A1717A.3000309@mail.ru>
References: <52A1717A.3000309@mail.ru>
Message-ID: <52A18A3E.8090805@karssen.org>

Hi Maksim,

Good luck with the CRAN submission! Let's see if it all works as planned.


Lennart.

On 06-12-13 07:40, Maksim Struchalin wrote:
> Dear All,
> 
> I am going to submit a new version of GenABEL (and GenABEL.data) on
> CRAN. If anyone here has any objections to this version being submitted,
> let them speak now or forever hold your peace :-).
> 
> best,
> Maksim
> _______________________________________________
> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From m.v.struchalin at mail.ru  Fri Dec  6 12:27:22 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Fri, 06 Dec 2013 18:27:22 +0700
Subject: [GenABEL-dev] GenABEL-tutorial.pdf
Message-ID: <52A1B49A.50908@mail.ru>

Hi Yurii & Others

I am trying to build GenABEL for the final submission to CRAN but I am 
stuck in making GenABEL-tutorial.pdf. After running 
GenABEL-general/scripts/makedistrib_GenABEL.sh I got a message that 
MixABL is not installed. I am trying to install it and it fails. Is it 
neccassary to make other ABEL* pakages compilable to just submit GenABEL 
on CRAN?

best,
Maksim

From yurii.aulchenko at gmail.com  Fri Dec  6 12:37:33 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 6 Dec 2013 12:37:33 +0100
Subject: [GenABEL-dev] GenABEL-tutorial.pdf
In-Reply-To: <52A1B49A.50908@mail.ru>
References: <52A1B49A.50908@mail.ru>
Message-ID: <CAHX9t6JNH9+X+T0wPkcYAFGuz0MH-KFmb_1sDbOfFkmr5XBjMw@mail.gmail.com>

in principle building the GenA-tutorial could be skipped, but....

- of course it is good to have tutorial updated (it is included with
distrib)

- when trying to build tutorial, it works as testing, - some errors may pop
up

so I would definitely recommend installing MixABEL, but at then end this is
up to you.

Y


On Fri, Dec 6, 2013 at 12:27 PM, Maksim Struchalin
<m.v.struchalin at mail.ru>wrote:

> Hi Yurii & Others
>
> I am trying to build GenABEL for the final submission to CRAN but I am
> stuck in making GenABEL-tutorial.pdf. After running GenABEL-general/scripts/makedistrib_GenABEL.sh
> I got a message that MixABL is not installed. I am trying to install it and
> it fails. Is it neccassary to make other ABEL* pakages compilable to just
> submit GenABEL on CRAN?
>
> best,
> Maksim
> _______________________________________________
> 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  Mon Dec  9 09:12:02 2013
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Mon, 9 Dec 2013 09:12:02 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1458 - in pkg: GenABEL
	GenABEL.data
In-Reply-To: <20131209080052.0C175186A6D@r-forge.r-project.org>
References: <20131209080052.0C175186A6D@r-forge.r-project.org>
Message-ID: <5A329EB3-F43B-4369-96F6-2A220402BD38@gmail.com>

I am very glad to see these last touches!

Maxim, if you/others have no objections I would recommend to put you as the Maintainer - this saves some trouble during submission, and easily changed afterwards if necessary

but this is up to you of cause  - I thought it may easier with submission and then for you be nice to have a line on CV, like "GenABEL-package maintainer, 2013" :) )

the moment you do not want it anymore, I can take back over as the maintainer

Yurii

On Dec 9, 2013, at 09:00 AM, noreply at r-forge.r-project.org wrote:

> Author: maksim
> Date: 2013-12-09 09:00:51 +0100 (Mon, 09 Dec 2013)
> New Revision: 1458
> 
> Modified:
>   pkg/GenABEL.data/DESCRIPTION
>   pkg/GenABEL/DESCRIPTION
> Log:
> The final-final update before sunbission to CRAN
> 
> Modified: pkg/GenABEL/DESCRIPTION
> ===================================================================
> --- pkg/GenABEL/DESCRIPTION	2013-12-09 06:46:45 UTC (rev 1457)
> +++ pkg/GenABEL/DESCRIPTION	2013-12-09 08:00:51 UTC (rev 1458)
> @@ -2,7 +2,7 @@
> Type: Package
> Title: genome-wide SNP association analysis
> Version: 1.8-0
> -Date: 2013-12-06
> +Date: 2013-12-09
> Author: GenABEL project developers
> Contact: GenABEL project developers <genabel.project at gmail.com>
> Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru>
> 
> Modified: pkg/GenABEL.data/DESCRIPTION
> ===================================================================
> --- pkg/GenABEL.data/DESCRIPTION	2013-12-09 06:46:45 UTC (rev 1457)
> +++ pkg/GenABEL.data/DESCRIPTION	2013-12-09 08:00:51 UTC (rev 1458)
> @@ -2,7 +2,7 @@
> Type: Package
> Title: Package contains data which is used by GenABEL example and test functions
> Version: 1.0
> -Date: 2013-12-06
> +Date: 2013-12-09
> Authors at R: c(person("Maksim Struchalin", "Developer", role = c("aut", "cre"), email = "m.v.struchalin at mail.ru"),
> 					   person("GenABEL project developers", "Developer", role = "aut", email = "genabel.project at gmail.com"))
> Depends: R (>= 2.15.0)
> 
> _______________________________________________
> Genabel-commits mailing list
> Genabel-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits


From yurii.aulchenko at gmail.com  Mon Dec  9 12:42:58 2013
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Mon, 9 Dec 2013 12:42:58 +0100
Subject: [GenABEL-dev] Fwd: CRAN submission GenABEL 1.8-0
References: <52A5A94F.9060104@stats.ox.ac.uk>
Message-ID: <16B1D7C9-4E21-4B1F-B9E0-E3FA36DC36FC@gmail.com>

Getting many comments from prof. Ripley

he does not sound very happy

Yurii

Begin forwarded message:

> From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
> Subject: Re: CRAN submission GenABEL 1.8-0
> Date: December 9, 2013 at 12:28:15 PM GMT+1
> To: Yurii Aulchenko <yurii at bionet.nsc.ru>, CRAN <cran at r-project.org>
> 
> On 09/12/2013 09:49, Yurii Aulchenko wrote:
>> [This was generated from CRAN.R-project.org/submit.html]
>> 
>> The following package was uploaded to CRAN:
>> ===========================================
>> 
>> Package Information:
>> Package: GenABEL
>> Version: 1.8-0
>> Title: genome-wide SNP association analysis
>> Author(s): GenABEL project developers
>> Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru>
>> Depends: R (>= 2.15.0), methods, MASS, utils, GenABEL.data
>> Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm,
>>   MetABEL, PredictABEL, VariABEL, bigRR
>> Description: a package for genome-wide association analysis between
>>   quantitative or binary traits and single-nucleotide
>>   polymorphisms (SNPs).
>> License: GPL (>= 2)
>> 
>> 
>> The maintainer confirms that he or she
>> has read and agrees to the CRAN policies.
>> 
>> Submitter's comment: In this version of GenABEL, the data is moved to a
>>   specially created new packaged called GenABEL.data
>>   (which was uploaded on CRAN earlier today).
>>   Additioanlly, memory leak is fixed for a number of
>>   functions and unused variables are deleted.
> 
> That package did not comply with the CRAN policies.  You need to re-submit if it is accepted.
> 
> We see
> 
> * checking foreign function calls ... NOTE
> Foreign function call to a different package:
>  .Call("iterator", ..., PACKAGE = "DatABEL")
> 
> Why can an R wrapper not be exported from DatABEL?
> 
> * checking sizes of PDF files under ?inst/doc? ... WARNING
>  ?gs+qpdf? made some significant size reductions:
>     compacted ?GenABEL-tutorial.pdf? from 4.2Mb to 2.2Mb
>  consider running tools::compactPDF(gs_quality = "ebook") on these files
> 
> which is a lot.  Please re-think your use of figures: at least one (ca p188) is full of overlapping symbols.
> 
> And this fails to install with clang/libcxx as reported before:
> 
> clang++ -std=c++11 -stdlib=libc++ -fsanitize=undefined -fno-omit-frame-pointer -I/data/gannet/ripley/R/R-clang2/include -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -Wall -pedantic -mtune=native  -c convert_snp_illumina.cpp -o convert_snp_illumina.o
> convert_snp_illumina.cpp:70:14: warning: comparison between NULL and non-pointer ('ifstream' (aka 'basic_ifstream<char>') and NULL) [-Wnull-arithmetic]
>        if (illfile == NULL) {
>            ~~~~~~~ ^  ~~~~
> convert_snp_illumina.cpp:70:14: error: invalid operands to binary expression ('ifstream' (aka 'basic_ifstream<char>') and 'long')
>        if (illfile == NULL) {
>            ~~~~~~~ ^  ~~~~
> convert_snp_illumina.cpp:270:14: warning: comparison between NULL and non-pointer ('ofstream' (aka 'basic_ofstream<char>') and NULL) [-Wnull-arithmetic]
>        if (outfile == NULL) {
>            ~~~~~~~ ^  ~~~~
> convert_snp_illumina.cpp:270:14: error: invalid operands to binary expression ('ofstream' (aka 'basic_ofstream<char>') and 'long')
>        if (outfile == NULL) {
>            ~~~~~~~ ^  ~~~~
> 2 warnings and 2 errors generated.
> 
> You really do need to do this as per the C++ standard (check outfile.bad()?)
> 
> Please show more respect for our time: all of these reports could have been avoided by following the CRAN policies.
> 
> 
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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From m.kooijman at erasmusmc.nl  Mon Dec  9 13:02:02 2013
From: m.kooijman at erasmusmc.nl (Maarten Kooyman)
Date: Mon, 09 Dec 2013 13:02:02 +0100
Subject: [GenABEL-dev] Fwd: CRAN submission GenABEL 1.8-0
In-Reply-To: <16B1D7C9-4E21-4B1F-B9E0-E3FA36DC36FC@gmail.com>
References: <52A5A94F.9060104@stats.ox.ac.uk>
 <16B1D7C9-4E21-4B1F-B9E0-E3FA36DC36FC@gmail.com>
Message-ID: <52A5B13A.7070908@erasmusmc.nl>

Dear all,

I think it is a smart move to add a clang/libcxx pipeline in Jenkins.
This prevents future rejection of CRAN submissions because something
does not build (Wich is pretty good and easy to test). It is inhuman to 
ask that every developer compiles their software with a bunch of
different compilers. But you can let a butler named Jenkins do this kind
of work.(a pic of our butler is visible at the left side of
http://www.karssen.org/jenkins/)

Kind regards,

Maarten Kooyman
Erasmus MC
Department of Epidemiology

On 12/09/2013 12:42 PM, Yury Aulchenko wrote:
> Getting many comments from prof. Ripley
>
> he does not sound very happy
>
> Yurii
>
> Begin forwarded message:
>
>> *From: *Prof Brian Ripley <ripley at stats.ox.ac.uk
>> <mailto:ripley at stats.ox.ac.uk>>
>> *Subject: **Re: CRAN submission GenABEL 1.8-0*
>> *Date: *December 9, 2013 at 12:28:15 PM GMT+1
>> *To: *Yurii Aulchenko <yurii at bionet.nsc.ru
>> <mailto:yurii at bionet.nsc.ru>>, CRAN <cran at r-project.org
>> <mailto:cran at r-project.org>>
>>
>> On 09/12/2013 09:49, Yurii Aulchenko wrote:
>>> [This was generated from CRAN.R-project.org/submit.html]
>>> <http://CRAN.R-project.org/submit.html]>
>>>
>>> The following package was uploaded to CRAN:
>>> ===========================================
>>>
>>> Package Information:
>>> Package: GenABEL
>>> Version: 1.8-0
>>> Title: genome-wide SNP association analysis
>>> Author(s): GenABEL project developers
>>> Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru
>>> <mailto:yurii at bionet.nsc.ru>>
>>> Depends: R (>= 2.15.0), methods, MASS, utils, GenABEL.data
>>> Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm,
>>>   MetABEL, PredictABEL, VariABEL, bigRR
>>> Description: a package for genome-wide association analysis between
>>>   quantitative or binary traits and single-nucleotide
>>>   polymorphisms (SNPs).
>>> License: GPL (>= 2)
>>>
>>>
>>> The maintainer confirms that he or she
>>> has read and agrees to the CRAN policies.
>>>
>>> Submitter's comment: In this version of GenABEL, the data is moved to a
>>>   specially created new packaged called GenABEL.data
>>>   (which was uploaded on CRAN earlier today).
>>>   Additioanlly, memory leak is fixed for a number of
>>>   functions and unused variables are deleted.
>>
>> That package did not comply with the CRAN policies.  You need to
>> re-submit if it is accepted.
>>
>> We see
>>
>> * checking foreign function calls ... NOTE
>> Foreign function call to a different package:
>>  .Call("iterator", ..., PACKAGE = "DatABEL")
>>
>> Why can an R wrapper not be exported from DatABEL?
>>
>> * checking sizes of PDF files under 'inst/doc' ... WARNING
>>  'gs+qpdf' made some significant size reductions:
>>     compacted 'GenABEL-tutorial.pdf' from 4.2Mb to 2.2Mb
>>  consider running tools::compactPDF(gs_quality = "ebook") on these files
>>
>> which is a lot.  Please re-think your use of figures: at least one
>> (ca p188) is full of overlapping symbols.
>>
>> And this fails to install with clang/libcxx as reported before:
>>
>> clang++ -std=c++11 -stdlib=libc++ -fsanitize=undefined
>> -fno-omit-frame-pointer -I/data/gannet/ripley/R/R-clang2/include
>> -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -Wall
>> -pedantic -mtune=native  -c convert_snp_illumina.cpp -o
>> convert_snp_illumina.o
>> convert_snp_illumina.cpp:70:14: warning: comparison between NULL and
>> non-pointer ('ifstream' (aka 'basic_ifstream<char>') and NULL)
>> [-Wnull-arithmetic]
>>        if (illfile == NULL) {
>>            ~~~~~~~ ^  ~~~~
>> convert_snp_illumina.cpp:70:14: error: invalid operands to binary
>> expression ('ifstream' (aka 'basic_ifstream<char>') and 'long')
>>        if (illfile == NULL) {
>>            ~~~~~~~ ^  ~~~~
>> convert_snp_illumina.cpp:270:14: warning: comparison between NULL and
>> non-pointer ('ofstream' (aka 'basic_ofstream<char>') and NULL)
>> [-Wnull-arithmetic]
>>        if (outfile == NULL) {
>>            ~~~~~~~ ^  ~~~~
>> convert_snp_illumina.cpp:270:14: error: invalid operands to binary
>> expression ('ofstream' (aka 'basic_ofstream<char>') and 'long')
>>        if (outfile == NULL) {
>>            ~~~~~~~ ^  ~~~~
>> 2 warnings and 2 errors generated.
>>
>> You really do need to do this as per the C++ standard (check
>> outfile.bad()?)
>>
>> Please show more respect for our time: all of these reports could
>> have been avoided by following the CRAN policies.
>>
>>
>> -- 
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> <mailto:ripley at stats.ox.ac.uk>
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> <http://www.stats.ox.ac.uk/%7Eripley/>
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>
>
>
> _______________________________________________
> 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  Mon Dec  9 13:23:12 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 09 Dec 2013 13:23:12 +0100
Subject: [GenABEL-dev] Fwd: CRAN submission GenABEL 1.8-0
In-Reply-To: <52A5B13A.7070908@erasmusmc.nl>
References: <52A5A94F.9060104@stats.ox.ac.uk>
 <16B1D7C9-4E21-4B1F-B9E0-E3FA36DC36FC@gmail.com>
 <52A5B13A.7070908@erasmusmc.nl>
Message-ID: <52A5B630.9010409@karssen.org>

Good point Maarten. IIRC you had this working in your test installation
of Jenkins.
For me, as admin of the externally viewable Jenkins, that probably means
I have to deploy a separate virtual machine for Jenkins (the one it runs
on now may have the latest packages for CLANG.
I'll try to set up a new VM tomorrow, maybe Wednesday.


Best,

Lennart.

On 09-12-13 13:02, Maarten Kooyman wrote:
> Dear all,
> 
> I think it is a smart move to add a clang/libcxx pipeline in Jenkins.
> This prevents future rejection of CRAN submissions because something
> does not build (Wich is pretty good and easy to test). It is inhuman to 
> ask that every developer compiles their software with a bunch of
> different compilers. But you can let a butler named Jenkins do this kind
> of work.(a pic of our butler is visible at the left side of
> http://www.karssen.org/jenkins/)
> 
> Kind regards,
> 
> Maarten Kooyman
> Erasmus MC
> Department of Epidemiology
> 
> On 12/09/2013 12:42 PM, Yury Aulchenko wrote:
>> Getting many comments from prof. Ripley
>>
>> he does not sound very happy
>>
>> Yurii
>>
>> Begin forwarded message:
>>
>>> *From: *Prof Brian Ripley <ripley at stats.ox.ac.uk
>>> <mailto:ripley at stats.ox.ac.uk>>
>>> *Subject: **Re: CRAN submission GenABEL 1.8-0*
>>> *Date: *December 9, 2013 at 12:28:15 PM GMT+1
>>> *To: *Yurii Aulchenko <yurii at bionet.nsc.ru
>>> <mailto:yurii at bionet.nsc.ru>>, CRAN <cran at r-project.org
>>> <mailto:cran at r-project.org>>
>>>
>>> On 09/12/2013 09:49, Yurii Aulchenko wrote:
>>>> [This was generated from CRAN.R-project.org/submit.html]
>>>> <http://CRAN.R-project.org/submit.html]>
>>>>
>>>> The following package was uploaded to CRAN:
>>>> ===========================================
>>>>
>>>> Package Information:
>>>> Package: GenABEL
>>>> Version: 1.8-0
>>>> Title: genome-wide SNP association analysis
>>>> Author(s): GenABEL project developers
>>>> Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru
>>>> <mailto:yurii at bionet.nsc.ru>>
>>>> Depends: R (>= 2.15.0), methods, MASS, utils, GenABEL.data
>>>> Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm,
>>>>   MetABEL, PredictABEL, VariABEL, bigRR
>>>> Description: a package for genome-wide association analysis between
>>>>   quantitative or binary traits and single-nucleotide
>>>>   polymorphisms (SNPs).
>>>> License: GPL (>= 2)
>>>>
>>>>
>>>> The maintainer confirms that he or she
>>>> has read and agrees to the CRAN policies.
>>>>
>>>> Submitter's comment: In this version of GenABEL, the data is moved to a
>>>>   specially created new packaged called GenABEL.data
>>>>   (which was uploaded on CRAN earlier today).
>>>>   Additioanlly, memory leak is fixed for a number of
>>>>   functions and unused variables are deleted.
>>>
>>> That package did not comply with the CRAN policies.  You need to
>>> re-submit if it is accepted.
>>>
>>> We see
>>>
>>> * checking foreign function calls ... NOTE
>>> Foreign function call to a different package:
>>>  .Call("iterator", ..., PACKAGE = "DatABEL")
>>>
>>> Why can an R wrapper not be exported from DatABEL?
>>>
>>> * checking sizes of PDF files under ?inst/doc? ... WARNING
>>>  ?gs+qpdf? made some significant size reductions:
>>>     compacted ?GenABEL-tutorial.pdf? from 4.2Mb to 2.2Mb
>>>  consider running tools::compactPDF(gs_quality = "ebook") on these files
>>>
>>> which is a lot.  Please re-think your use of figures: at least one
>>> (ca p188) is full of overlapping symbols.
>>>
>>> And this fails to install with clang/libcxx as reported before:
>>>
>>> clang++ -std=c++11 -stdlib=libc++ -fsanitize=undefined
>>> -fno-omit-frame-pointer -I/data/gannet/ripley/R/R-clang2/include
>>> -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -Wall
>>> -pedantic -mtune=native  -c convert_snp_illumina.cpp -o
>>> convert_snp_illumina.o
>>> convert_snp_illumina.cpp:70:14: warning: comparison between NULL and
>>> non-pointer ('ifstream' (aka 'basic_ifstream<char>') and NULL)
>>> [-Wnull-arithmetic]
>>>        if (illfile == NULL) {
>>>            ~~~~~~~ ^  ~~~~
>>> convert_snp_illumina.cpp:70:14: error: invalid operands to binary
>>> expression ('ifstream' (aka 'basic_ifstream<char>') and 'long')
>>>        if (illfile == NULL) {
>>>            ~~~~~~~ ^  ~~~~
>>> convert_snp_illumina.cpp:270:14: warning: comparison between NULL and
>>> non-pointer ('ofstream' (aka 'basic_ofstream<char>') and NULL)
>>> [-Wnull-arithmetic]
>>>        if (outfile == NULL) {
>>>            ~~~~~~~ ^  ~~~~
>>> convert_snp_illumina.cpp:270:14: error: invalid operands to binary
>>> expression ('ofstream' (aka 'basic_ofstream<char>') and 'long')
>>>        if (outfile == NULL) {
>>>            ~~~~~~~ ^  ~~~~
>>> 2 warnings and 2 errors generated.
>>>
>>> You really do need to do this as per the C++ standard (check
>>> outfile.bad()?)
>>>
>>> Please show more respect for our time: all of these reports could
>>> have been avoided by following the CRAN policies.
>>>
>>>
>>> -- 
>>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>>> <mailto:ripley at stats.ox.ac.uk>
>>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>>> <http://www.stats.ox.ac.uk/%7Eripley/>
>>> University of Oxford,             Tel:  +44 1865 272861 (self)
>>> 1 South Parks Road,                     +44 1865 272866 (PA)
>>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
>>
>>
>> _______________________________________________
>> 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 lennart at karssen.org  Mon Dec  9 13:39:48 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 09 Dec 2013 13:39:48 +0100
Subject: [GenABEL-dev] Trying to get ProbABEL packaged in Debian
Message-ID: <52A5BA14.2010508@karssen.org>

Dear list,

Last week I applied for membership of the Debian-med team [1], this can
be seen as a subproject (a so-called blend) of Debian which focusses on
getting software for the fields of medicine and life sciences packaged
into the default Debian repositories.

The people in Debian-med are very helpful and I'm now in the process of
getting ProbABEL v0.4.1 packaged according to the Debian guidelines.
Luckily I had my Ubuntu PPA package to start from, so a lot of the
learning had already been done. They have already packaged GenABEL
(r-cran-genabel) [2,3], so that's a good starting point for those who
want to package other R-base packages in the GenABEL suite.

I hope to get ProbABEL accepted soon, hopefully in time so that it makes
it into Ubuntu 14.04, which will be an LTS (long term support) release
(Debian Import Freeze is Feb 6th 2014 [4]).


I'll keep the list updated on progress.

Lennart.


[1] https://wiki.debian.org/DebianMed
[2] http://packages.debian.org/search?keywords=r-cran-genabel
[3] http://packages.qa.debian.org/r/r-cran-genabel.html
[4] https://wiki.ubuntu.com/TrustyTahr/ReleaseSchedule
-- 
-----------------------------------------------------------------
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 m.v.struchalin at mail.ru  Mon Dec  9 14:09:59 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Mon, 09 Dec 2013 20:09:59 +0700
Subject: [GenABEL-dev] Fwd: CRAN submission GenABEL 1.8-0
In-Reply-To: <52A5B13A.7070908@erasmusmc.nl>
References: <52A5A94F.9060104@stats.ox.ac.uk>
 <16B1D7C9-4E21-4B1F-B9E0-E3FA36DC36FC@gmail.com>
 <52A5B13A.7070908@erasmusmc.nl>
Message-ID: <52A5C127.6040007@mail.ru>

Looks like this is how we should deal with it. If they use clang/libcxx 
for compiling GenABEL code then we have to do the same.

best,
Maksim

On 09/12/2013 19:02, Maarten Kooyman wrote:
> Dear all,
>
> I think it is a smart move to add a clang/libcxx pipeline in Jenkins. 
> This prevents future rejection of CRAN submissions because something 
> does not build (Wich is pretty good and easy to test). It is inhuman 
> to  ask that every developer compiles their software with a bunch of 
> different compilers. But you can let a butler named Jenkins do this 
> kind of work.(a pic of our butler is visible at the left side of 
> http://www.karssen.org/jenkins/)
>
> Kind regards,
>
> Maarten Kooyman
> Erasmus MC
> Department of Epidemiology
> On 12/09/2013 12:42 PM, Yury Aulchenko wrote:
>> Getting many comments from prof. Ripley
>>
>> he does not sound very happy
>>
>> Yurii
>>
>> Begin forwarded message:
>>
>>> *From: *Prof Brian Ripley <ripley at stats.ox.ac.uk 
>>> <mailto:ripley at stats.ox.ac.uk>>
>>> *Subject: **Re: CRAN submission GenABEL 1.8-0*
>>> *Date: *December 9, 2013 at 12:28:15 PM GMT+1
>>> *To: *Yurii Aulchenko <yurii at bionet.nsc.ru 
>>> <mailto:yurii at bionet.nsc.ru>>, CRAN <cran at r-project.org 
>>> <mailto:cran at r-project.org>>
>>>
>>> On 09/12/2013 09:49, Yurii Aulchenko wrote:
>>>> [This was generated from CRAN.R-project.org/submit.html] 
>>>> <http://CRAN.R-project.org/submit.html]>
>>>>
>>>> The following package was uploaded to CRAN:
>>>> ===========================================
>>>>
>>>> Package Information:
>>>> Package: GenABEL
>>>> Version: 1.8-0
>>>> Title: genome-wide SNP association analysis
>>>> Author(s): GenABEL project developers
>>>> Maintainer: Yurii Aulchenko <yurii at bionet.nsc.ru 
>>>> <mailto:yurii at bionet.nsc.ru>>
>>>> Depends: R (>= 2.15.0), methods, MASS, utils, GenABEL.data
>>>> Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0), hglm,
>>>>   MetABEL, PredictABEL, VariABEL, bigRR
>>>> Description: a package for genome-wide association analysis between
>>>>   quantitative or binary traits and single-nucleotide
>>>>   polymorphisms (SNPs).
>>>> License: GPL (>= 2)
>>>>
>>>>
>>>> The maintainer confirms that he or she
>>>> has read and agrees to the CRAN policies.
>>>>
>>>> Submitter's comment: In this version of GenABEL, the data is moved to a
>>>>   specially created new packaged called GenABEL.data
>>>>   (which was uploaded on CRAN earlier today).
>>>>   Additioanlly, memory leak is fixed for a number of
>>>>   functions and unused variables are deleted.
>>>
>>> That package did not comply with the CRAN policies.  You need to 
>>> re-submit if it is accepted.
>>>
>>> We see
>>>
>>> * checking foreign function calls ... NOTE
>>> Foreign function call to a different package:
>>>  .Call("iterator", ..., PACKAGE = "DatABEL")
>>>
>>> Why can an R wrapper not be exported from DatABEL?
>>>
>>> * checking sizes of PDF files under 'inst/doc' ... WARNING
>>>  'gs+qpdf' made some significant size reductions:
>>>     compacted 'GenABEL-tutorial.pdf' from 4.2Mb to 2.2Mb
>>>  consider running tools::compactPDF(gs_quality = "ebook") on these files
>>>
>>> which is a lot.  Please re-think your use of figures: at least one 
>>> (ca p188) is full of overlapping symbols.
>>>
>>> And this fails to install with clang/libcxx as reported before:
>>>
>>> clang++ -std=c++11 -stdlib=libc++ -fsanitize=undefined 
>>> -fno-omit-frame-pointer -I/data/gannet/ripley/R/R-clang2/include 
>>> -DNDEBUG  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 
>>> -Wall -pedantic -mtune=native  -c convert_snp_illumina.cpp -o 
>>> convert_snp_illumina.o
>>> convert_snp_illumina.cpp:70:14: warning: comparison between NULL and 
>>> non-pointer ('ifstream' (aka 'basic_ifstream<char>') and NULL) 
>>> [-Wnull-arithmetic]
>>>        if (illfile == NULL) {
>>>            ~~~~~~~ ^  ~~~~
>>> convert_snp_illumina.cpp:70:14: error: invalid operands to binary 
>>> expression ('ifstream' (aka 'basic_ifstream<char>') and 'long')
>>>        if (illfile == NULL) {
>>>            ~~~~~~~ ^  ~~~~
>>> convert_snp_illumina.cpp:270:14: warning: comparison between NULL 
>>> and non-pointer ('ofstream' (aka 'basic_ofstream<char>') and NULL) 
>>> [-Wnull-arithmetic]
>>>        if (outfile == NULL) {
>>>            ~~~~~~~ ^  ~~~~
>>> convert_snp_illumina.cpp:270:14: error: invalid operands to binary 
>>> expression ('ofstream' (aka 'basic_ofstream<char>') and 'long')
>>>        if (outfile == NULL) {
>>>            ~~~~~~~ ^  ~~~~
>>> 2 warnings and 2 errors generated.
>>>
>>> You really do need to do this as per the C++ standard (check 
>>> outfile.bad()?)
>>>
>>> Please show more respect for our time: all of these reports could 
>>> have been avoided by following the CRAN policies.
>>>
>>>
>>> -- 
>>> Brian D. Ripley, ripley at stats.ox.ac.uk <mailto:ripley at stats.ox.ac.uk>
>>> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ 
>>> <http://www.stats.ox.ac.uk/%7Eripley/>
>>> University of Oxford,             Tel:  +44 1865 272861 (self)
>>> 1 South Parks Road,                     +44 1865 272866 (PA)
>>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

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From m.v.struchalin at mail.ru  Tue Dec 10 12:00:34 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Tue, 10 Dec 2013 18:00:34 +0700
Subject: [GenABEL-dev] clang
Message-ID: <52A6F452.7050907@mail.ru>

Hi Maarten & Lennart,

Following Maarten suggestion to add support of clang in Jenkins, I tried 
to intsall clang on my UBUNTU and here I want to share what I got.
We duscused something separatly already but I thik it is better to move 
in the list so we can trace the dialog back in the future.


I installed 'clang' and 'llvm' (both precompiled). And I run in a 
command line:

clang++ -std=c++11 -stdlib=libc++ -fsanitize=undefined 
-fno-omit-frame-pointer -I/usr/share/R/include/  -DNDEBUG 
-I/home/maksim/distrib/libcxx/include   -DCOMPILE_WITH_R -fpic  -g -O2 
-Wall -pedantic -mtune=native  -c convert_snp_illumina.cpp -o 
convert_snp_illumina.o

it spit out:


  convert_snp_illumina.cpp:70:14: warning: comparison between NULL and
  non-pointer ('ifstream' (aka 'basic_ifstream<char>') and NULL)
  [-Wnull-arithmetic]
           if (illfile == NULL) {
               ~~~~~~~ ^  ~~~~
  convert_snp_illumina.cpp:70:14: error: invalid operands to binary
  expression ('ifstream' (aka 'basic_ifstream<char>') and 'long')
           if (illfile == NULL) {
               ~~~~~~~ ^  ~~~~
  convert_snp_illumina.cpp:270:14: warning: comparison between NULL and
  non-pointer ('ofstream' (aka 'basic_ofstream<char>') and NULL)
  [-Wnull-arithmetic]
           if (outfile == NULL) {
               ~~~~~~~ ^  ~~~~
  convert_snp_illumina.cpp:270:14: error: invalid operands to binary
  expression ('ofstream' (aka 'basic_ofstream<char>') and 'long')
           if (outfile == NULL) {
               ~~~~~~~ ^  ~~~~

Here -I/home/maksim/distrib/libcxx/include is a standard library for 
clang ('libcxx' was downloaded from http://libcxx.llvm.org/).


This is exactly the warinings/errors which CRAN people sent us. To run 
it as R CMD INSTALL, we need to change /etc/R/Makeconf (as Maarten 
mentioned already) appropraitelly and compile the library 'libcxx' (now, 
I just downloaded it and used headers files only). I tried 'sudo apt-get 
install libc++-dev' as Maarten suggested but got many conflicts with 
other packages and could not install it.

That's what I got by now.

p.s. It seems we always should use 'clang' for compiling R packages 
because as I understand it makes more extensive diagnostic of C++ code 
before compiling. What do you think?

best,
Maksim



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From kooyman at gmail.com  Tue Dec 10 14:49:51 2013
From: kooyman at gmail.com (Maarten Kooyman)
Date: Tue, 10 Dec 2013 14:49:51 +0100
Subject: [GenABEL-dev] clang
In-Reply-To: <52A6F452.7050907@mail.ru>
References: <52A6F452.7050907@mail.ru>
Message-ID: <52A71BFF.8000207@gmail.com>

Hi Maksim,

It seems that libcxx has stricter rules the lib we "normally" use.


replace


  if (illfile == NULL) {

with

if (!illfile.is_open()) {

and it should compile again. I did not do functional testing!  In my 
opion the is_open() variant looks cleaner then the ==NULL construction.


 >p.s. It seems we always should use 'clang' for compiling R packages 
because as I understand it makes more extensive >diagnostic of C++ code 
before compiling. What do you think?

Most computers do have the GCC pipeline as default (except MacOS), so 
building it with GCC pipeline by default would be good enough. LLVM and 
GCC do both have there strengths and weaknesses. So the best way is to 
test both pipeline in Jenkins. CRAN does use a trunk version of R to 
test the packages so it would be wise to compile a fresh R on the 
jenkins server once in a while. It is in general a good idea to use the 
latest version(maybe even bleeding edge) to find error in our software 
before people have running this software on there production machine.

@maksim: were you able to fix all comment of CRAN?

Kind regards,

Maarten


On 12/10/2013 12:00 PM, Maksim Struchalin wrote:
> Hi Maarten & Lennart,
>
> Following Maarten suggestion to add support of clang in Jenkins, I 
> tried to intsall clang on my UBUNTU and here I want to share what I got.
> We duscused something separatly already but I thik it is better to 
> move in the list so we can trace the dialog back in the future.
>
>
> I installed 'clang' and 'llvm' (both precompiled). And I run in a 
> command line:
>
> clang++ -std=c++11 -stdlib=libc++ -fsanitize=undefined 
> -fno-omit-frame-pointer -I/usr/share/R/include/  -DNDEBUG 
> -I/home/maksim/distrib/libcxx/include   -DCOMPILE_WITH_R -fpic  -g -O2 
> -Wall -pedantic -mtune=native  -c convert_snp_illumina.cpp -o 
> convert_snp_illumina.o
>
> it spit out:
>
>
>   convert_snp_illumina.cpp:70:14: warning: comparison between NULL and
>   non-pointer ('ifstream' (aka 'basic_ifstream<char>') and NULL)
>   [-Wnull-arithmetic]
>
>               ~~~~~~~ ^  ~~~~
>   convert_snp_illumina.cpp:70:14: error: invalid operands to binary
>   expression ('ifstream' (aka 'basic_ifstream<char>') and 'long')
>           if (illfile == NULL) {
>               ~~~~~~~ ^  ~~~~
>   convert_snp_illumina.cpp:270:14: warning: comparison between NULL
>   and non-pointer ('ofstream' (aka 'basic_ofstream<char>') and NULL)
>   [-Wnull-arithmetic]
>           if (outfile == NULL) {
>               ~~~~~~~ ^  ~~~~
>   convert_snp_illumina.cpp:270:14: error: invalid operands to binary
>   expression ('ofstream' (aka 'basic_ofstream<char>') and 'long')
>           if (outfile == NULL) {
>               ~~~~~~~ ^  ~~~~
>
> Here -I/home/maksim/distrib/libcxx/include is a standard library for 
> clang ('libcxx' was downloaded from http://libcxx.llvm.org/).
>
>
> This is exactly the warinings/errors which CRAN people sent us. To run 
> it as R CMD INSTALL, we need to change /etc/R/Makeconf (as Maarten 
> mentioned already) appropraitelly and compile the library 'libcxx' 
> (now, I just downloaded it and used headers files only). I tried 'sudo 
> apt-get install libc++-dev' as Maarten suggested but got many 
> conflicts with other packages and could not install it.
>
> That's what I got by now.
>
>
> best,
> Maksim
>
>
>
>
>
> _______________________________________________
> 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 m.v.struchalin at mail.ru  Wed Dec 11 06:24:52 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Wed, 11 Dec 2013 12:24:52 +0700
Subject: [GenABEL-dev] clang
In-Reply-To: <52A71BFF.8000207@gmail.com>
References: <52A6F452.7050907@mail.ru> <52A71BFF.8000207@gmail.com>
Message-ID: <52A7F724.9040801@mail.ru>

Hi Maarten,

Thanks for suggesting how to fix these warnings/errors but at the 
current stage I am trying to figure out how to get a complete report on 
all warnings/errors in the code. Yurii forwarded an email from CRAN with 
'warning/error' report on convert_snp_illumina.cpp file only. But, there 
are more warnings I guess. To fix them, we need first to find a way how 
CRAN people gets these warnings/errors. The version which I submited to 
CRAN was 'free' of warnings/errors' according to gcc-4.6 (there was only 
one warning on export_plink.cpp as I reported as a bug on r-forge). CRAN 
is unhappy with this version. This is beacuse the CRAN's pipline which 
is used for checking R packages is more complicated then just compiling 
by 'gcc' and I would like to find a way how they do it.

I think we need to follow your suggestion and add support of 'clan' in 
Jenkins, at least. More: following an email from prof. Ripley (from 
November 16, 2013), I think, we need to add support of
clang and g++ 4.8.1 in C++98 and C++11 modes. Also: probably add support 
of Undefined Behaviour Sanitizer because they use it. We need to read 
carefully 'Writing R Extensions' manual and change GenABEL code 
according to CRAN policy.

Yury: Do you have more comments on GenABEL from Ripley? They might help 
to understand what to do.

best,
Maksim


On 10/12/2013 20:49, Maarten Kooyman wrote:
> Hi Maksim,
>
> It seems that libcxx has stricter rules the lib we "normally" use.
>
>
> replace
>
>
>   if (illfile == NULL) {
>
> with
>
> if (!illfile.is_open()) {
>
> and it should compile again. I did not do functional testing! In my 
> opion the is_open() variant looks cleaner then the ==NULL construction.
>
>
> >p.s. It seems we always should use 'clang' for compiling R packages 
> because as I understand it makes more extensive >diagnostic of C++ 
> code before compiling. What do you think?
>
> Most computers do have the GCC pipeline as default (except MacOS), so 
> building it with GCC pipeline by default would be good enough. LLVM 
> and GCC do both have there strengths and weaknesses. So the best way 
> is to test both pipeline in Jenkins. CRAN does use a trunk version of 
> R to test the packages so it would be wise to compile a fresh R on the 
> jenkins server once in a while. It is in general a good idea to use 
> the latest version(maybe even bleeding edge) to find error in our 
> software before people have running this software on there production 
> machine.
>
> @maksim: were you able to fix all comment of CRAN?
>
> Kind regards,
>
> Maarten
>
>
> On 12/10/2013 12:00 PM, Maksim Struchalin wrote:
>> Hi Maarten & Lennart,
>>
>> Following Maarten suggestion to add support of clang in Jenkins, I 
>> tried to intsall clang on my UBUNTU and here I want to share what I got.
>> We duscused something separatly already but I thik it is better to 
>> move in the list so we can trace the dialog back in the future.
>>
>>
>> I installed 'clang' and 'llvm' (both precompiled). And I run in a 
>> command line:
>>
>> clang++ -std=c++11 -stdlib=libc++ -fsanitize=undefined 
>> -fno-omit-frame-pointer -I/usr/share/R/include/  -DNDEBUG 
>> -I/home/maksim/distrib/libcxx/include   -DCOMPILE_WITH_R -fpic -g -O2 
>> -Wall -pedantic -mtune=native  -c convert_snp_illumina.cpp -o 
>> convert_snp_illumina.o
>>
>> it spit out:
>>
>>
>>   convert_snp_illumina.cpp:70:14: warning: comparison between NULL
>>   and non-pointer ('ifstream' (aka 'basic_ifstream<char>') and NULL)
>>   [-Wnull-arithmetic]
>>
>>               ~~~~~~~ ^  ~~~~
>>   convert_snp_illumina.cpp:70:14: error: invalid operands to binary
>>   expression ('ifstream' (aka 'basic_ifstream<char>') and 'long')
>>           if (illfile == NULL) {
>>               ~~~~~~~ ^  ~~~~
>>   convert_snp_illumina.cpp:270:14: warning: comparison between NULL
>>   and non-pointer ('ofstream' (aka 'basic_ofstream<char>') and NULL)
>>   [-Wnull-arithmetic]
>>           if (outfile == NULL) {
>>               ~~~~~~~ ^  ~~~~
>>   convert_snp_illumina.cpp:270:14: error: invalid operands to binary
>>   expression ('ofstream' (aka 'basic_ofstream<char>') and 'long')
>>           if (outfile == NULL) {
>>               ~~~~~~~ ^  ~~~~
>>
>> Here -I/home/maksim/distrib/libcxx/include is a standard library for 
>> clang ('libcxx' was downloaded from http://libcxx.llvm.org/).
>>
>>
>> This is exactly the warinings/errors which CRAN people sent us. To 
>> run it as R CMD INSTALL, we need to change /etc/R/Makeconf (as 
>> Maarten mentioned already) appropraitelly and compile the library 
>> 'libcxx' (now, I just downloaded it and used headers files only). I 
>> tried 'sudo apt-get install libc++-dev' as Maarten suggested but got 
>> many conflicts with other packages and could not install it.
>>
>> That's what I got by now.
>>
>>
>> best,
>> Maksim
>>
>>
>>
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

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From lennart at karssen.org  Wed Dec 11 11:55:24 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 11 Dec 2013 11:55:24 +0100
Subject: [GenABEL-dev] Preparing for ProbABEL v0.4.2 release
In-Reply-To: <529C4763.4090905@karssen.org>
References: <529C4763.4090905@karssen.org>
Message-ID: <52A8449C.9050109@karssen.org>

Dear all,

This is just to inform you that I've decided to put off releasing v0.4.2
a bit. This will allow me to incorporate (some of) the changes requested
by the Debian packaging in this upcoming release.


Best regards,

Lennart.

On 02-12-13 09:40, L.C. Karssen wrote:
> Dear all,
> 
> I'm preparing to release ProbABEL v0.4.2 this week. If you have any
> patches that you'd like to submit/commit, please do so as soon as possible.
> Please don't commit large changes that need extensive testing. These can
> be committed for the release after that.
> 
> 
> Thanks,
> 
> Lennart.
> 
> 
> 
> _______________________________________________
> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From lennart at karssen.org  Wed Dec 11 12:08:33 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 11 Dec 2013 12:08:33 +0100
Subject: [GenABEL-dev] ProbABEL: Binaries without extension
Message-ID: <52A847B1.2090201@karssen.org>

Dear list,

While working on packaging ProbABEL for inclusion in Debian, I came
across the following warning in the Debian package check (using the
lintian program):

W: probabel: script-with-language-extension usr/bin/extIDS.pl
W: probabel: script-with-language-extension usr/bin/probabel.pl

The short explanation is this:
    When scripts are installed into a directory in the system PATH, the
    script name should not include an extension such as .sh or .pl that
    denotes the scripting language currently used to implement it. The
    implementation language may change; if it does, leaving the name the
    same would be confusing and changing it would be disruptive.


The reasoning behind this warning is the following:
There are several reasons for not having an extension in the name of a
binary/script, nicely listed in this post:
    http://lists.debian.org/debian-med/2012/04/msg00103.html
The most important one to me is:
    I do not see what actual information such extensions are
    providing to the end user.  A user expects a program to do a job.
    Fullstop.  The user does not need to care about the language a
    program is written in if it just does what it is expected to do.


So, for ProbABEL I propose the following:
- extIDS.pl is not used a lot, so we can safely remove the .pl extension
there (and update the manual, mention it in the ChangeLog and release notes)
- For probabel.pl this is different. Many people use it exclusively
instead of calling pa{linear,logist,coxph} directly and changing this
would mean breaking user experience completely. I think we do need to
remove the extension at some point in the future, but that would be in a
'large' update, say v0.5, not in a minor one like the upcoming v0.4.2.


What do you think of this?

Lennart.


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

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From m.v.struchalin at mail.ru  Wed Dec 11 13:22:41 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Wed, 11 Dec 2013 19:22:41 +0700
Subject: [GenABEL-dev] ProbABEL: Binaries without extension
In-Reply-To: <52A847B1.2090201@karssen.org>
References: <52A847B1.2090201@karssen.org>
Message-ID: <52A85911.2070407@mail.ru>

Hi Lennart,

For me, it sounds reasonable to remove the file extensions.
About probabel.pl: we can provide both 'probabel.pl' and 'probabel' for 
the next few revisions (if it is possible). In this case, if users run 
'probabel.pl', we show a warning messages saying that they need to use 
'probabel' instead of 'proabbel.pl' and that 'probabel.pl' will be 
removed soon. Later, when most of users switched to 'probabel', we 
remove 'probabel.pl'.

best,
Maksim




On 11/12/2013 18:08, L.C. Karssen wrote:
> Dear list,
>
> While working on packaging ProbABEL for inclusion in Debian, I came
> across the following warning in the Debian package check (using the
> lintian program):
>
> W: probabel: script-with-language-extension usr/bin/extIDS.pl
> W: probabel: script-with-language-extension usr/bin/probabel.pl
>
> The short explanation is this:
>      When scripts are installed into a directory in the system PATH, the
>      script name should not include an extension such as .sh or .pl that
>      denotes the scripting language currently used to implement it. The
>      implementation language may change; if it does, leaving the name the
>      same would be confusing and changing it would be disruptive.
>
>
> The reasoning behind this warning is the following:
> There are several reasons for not having an extension in the name of a
> binary/script, nicely listed in this post:
>      http://lists.debian.org/debian-med/2012/04/msg00103.html
> The most important one to me is:
>      I do not see what actual information such extensions are
>      providing to the end user.  A user expects a program to do a job.
>      Fullstop.  The user does not need to care about the language a
>      program is written in if it just does what it is expected to do.
>
>
> So, for ProbABEL I propose the following:
> - extIDS.pl is not used a lot, so we can safely remove the .pl extension
> there (and update the manual, mention it in the ChangeLog and release notes)
> - For probabel.pl this is different. Many people use it exclusively
> instead of calling pa{linear,logist,coxph} directly and changing this
> would mean breaking user experience completely. I think we do need to
> remove the extension at some point in the future, but that would be in a
> 'large' update, say v0.5, not in a minor one like the upcoming v0.4.2.
>
>
> What do you think of this?
>
> Lennart.
>
>
> --
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
>
>
> _______________________________________________
> 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 Dec 11 13:53:06 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 11 Dec 2013 13:53:06 +0100
Subject: [GenABEL-dev] ProbABEL: Binaries without extension
In-Reply-To: <52A85911.2070407@mail.ru>
References: <52A847B1.2090201@karssen.org> <52A85911.2070407@mail.ru>
Message-ID: <1152651267260974754@unknownmsgid>

Question which probably supports Maxim's suggestion: How will this affect
existing user pipelines?

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

On Dec 11, 2013, at 13:22, Maksim Struchalin <m.v.struchalin at mail.ru> wrote:

 Hi Lennart,

For me, it sounds reasonable to remove the file extensions.
About probabel.pl: we can provide both 'probabel.pl' and 'probabel' for the
next few revisions (if it is possible). In this case, if users run '
probabel.pl', we show a warning messages saying that they need to use
'probabel' instead of 'proabbel.pl' and that 'probabel.pl' will be removed
soon. Later, when most of users switched to 'probabel', we remove '
probabel.pl'.

best,
Maksim




On 11/12/2013 18:08, L.C. Karssen wrote:

Dear list,

While working on packaging ProbABEL for inclusion in Debian, I came
across the following warning in the Debian package check (using the
lintian program):

W: probabel: script-with-language-extension usr/bin/extIDS.pl
W: probabel: script-with-language-extension usr/bin/probabel.pl

The short explanation is this:
    When scripts are installed into a directory in the system PATH, the
    script name should not include an extension such as .sh or .pl that
    denotes the scripting language currently used to implement it. The
    implementation language may change; if it does, leaving the name the
    same would be confusing and changing it would be disruptive.


The reasoning behind this warning is the following:
There are several reasons for not having an extension in the name of a
binary/script, nicely listed in this post:
    http://lists.debian.org/debian-med/2012/04/msg00103.html
The most important one to me is:
    I do not see what actual information such extensions are
    providing to the end user.  A user expects a program to do a job.
    Fullstop.  The user does not need to care about the language a
    program is written in if it just does what it is expected to do.


So, for ProbABEL I propose the following:
- extIDS.pl is not used a lot, so we can safely remove the .pl extension
there (and update the manual, mention it in the ChangeLog and release notes)
- For probabel.pl this is different. Many people use it exclusively
instead of calling pa{linear,logist,coxph} directly and changing this
would mean breaking user experience completely. I think we do need to
remove the extension at some point in the future, but that would be in a
'large' update, say v0.5, not in a minor one like the upcoming v0.4.2.


What do you think of this?

Lennart.


--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.orghttp://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-




_______________________________________________
genabel-devel mailing
listgenabel-devel at lists.r-forge.r-project.orghttps://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel


_______________________________________________
genabel-devel mailing list
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https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
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From m.kooijman at erasmusmc.nl  Wed Dec 11 13:58:22 2013
From: m.kooijman at erasmusmc.nl (Maarten Kooyman)
Date: Wed, 11 Dec 2013 13:58:22 +0100
Subject: [GenABEL-dev] ProbABEL: Binaries without extension
In-Reply-To: <1152651267260974754@unknownmsgid>
References: <52A847B1.2090201@karssen.org> <52A85911.2070407@mail.ru>
 <1152651267260974754@unknownmsgid>
Message-ID: <52A8616E.60404@erasmusmc.nl>


I think the solution of Maksim is quite workable. The minimal time to
push this change is at least a half year: this buys time for users to
update their pipeline.

Maarten Kooyman
 On 12/11/2013 01:53 PM, Yurii Aulchenko wrote:

> Question which probably supports Maxim's suggestion: How will this
> affect existing user pipelines?
>
> ----------------------
> Yurii Aulchenko 
> (sent from mobile device)
>
> On Dec 11, 2013, at 13:22, Maksim Struchalin <m.v.struchalin at mail.ru
> <mailto:m.v.struchalin at mail.ru>> wrote:
>
>> Hi Lennart,
>>
>> For me, it sounds reasonable to remove the file extensions.
>> About probabel.pl <http://probabel.pl>: we can provide both
>> 'probabel.pl <http://probabel.pl>' and 'probabel' for the next few
>> revisions (if it is possible). In this case, if users run
>> 'probabel.pl <http://probabel.pl>', we show a warning messages saying
>> that they need to use 'probabel' instead of 'proabbel.pl
>> <http://proabbel.pl>' and that 'probabel.pl <http://probabel.pl>'
>> will be removed soon. Later, when most of users switched to
>> 'probabel', we remove 'probabel.pl <http://probabel.pl>'.
>>
>> best,
>> Maksim
>>
>>
>>
>>
>> On 11/12/2013 18:08, L.C. Karssen wrote:
>>> Dear list,
>>>
>>> While working on packaging ProbABEL for inclusion in Debian, I came
>>> across the following warning in the Debian package check (using the
>>> lintian program):
>>>
>>> W: probabel: script-with-language-extension usr/bin/extIDS.pl
>>> W: probabel: script-with-language-extension usr/bin/probabel.pl <http://probabel.pl>
>>>
>>> The short explanation is this:
>>>     When scripts are installed into a directory in the system PATH, the
>>>     script name should not include an extension such as .sh or .pl that
>>>     denotes the scripting language currently used to implement it. The
>>>     implementation language may change; if it does, leaving the name the
>>>     same would be confusing and changing it would be disruptive.
>>>
>>>
>>> The reasoning behind this warning is the following:
>>> There are several reasons for not having an extension in the name of a
>>> binary/script, nicely listed in this post:
>>>     http://lists.debian.org/debian-med/2012/04/msg00103.html
>>> The most important one to me is:
>>>     I do not see what actual information such extensions are
>>>     providing to the end user.  A user expects a program to do a job.
>>>     Fullstop.  The user does not need to care about the language a
>>>     program is written in if it just does what it is expected to do.
>>>
>>>
>>> So, for ProbABEL I propose the following:
>>> - extIDS.pl is not used a lot, so we can safely remove the .pl extension
>>> there (and update the manual, mention it in the ChangeLog and release notes)
>>> - For probabel.pl <http://probabel.pl> this is different. Many people use it exclusively
>>> instead of calling pa{linear,logist,coxph} directly and changing this
>>> would mean breaking user experience completely. I think we do need to
>>> remove the extension at some point in the future, but that would be in a
>>> 'large' update, say v0.5, not in a minor one like the upcoming v0.4.2.
>>>
>>>
>>> What do you think of this?
>>>
>>> Lennart.
>>>
>>>
>>> --
>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>> L.C. Karssen
>>> Utrecht
>>> The Netherlands
>>>
>>> lennart at karssen.org
>>> http://blog.karssen.org
>>> GPG key ID: A88F554A
>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
>
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

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From yurii.aulchenko at gmail.com  Wed Dec 11 13:58:41 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 11 Dec 2013 13:58:41 +0100
Subject: [GenABEL-dev] Fwd: CRAN package maintainer check
References: <21160.19434.966306.39780@fangorn.hornik.net>
Message-ID: <5671711241854569534@unknownmsgid>

FYI

Some of the points (eg API) are highly relevant to us as far as I can see

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

Begin forwarded message:

*From:* Kurt Hornik <Kurt.Hornik at wu.ac.at>
*Date:* December 11, 2013 at 12:26:34 GMT+1
*To:* Kurt Hornik <Kurt.Hornik at wu.ac.at>
*Cc:* Brian Ripley <ripley at stats.ox.ac.uk>, Uwe Ligges <
uwe.ligges at tu-dortmund.de>
*Subject:* *CRAN package maintainer check*
*Reply-To:* Kurt.Hornik at wu.ac.at


Dear CRAN package maintainer,

We email all CRAN maintainers periodically to check that the email
address is still active and to remind them of the CRAN policies at
<http://CRAN.R-project.org/web/packages/policies.html>.

Changes to those policies in the last 4 months are given below.

Please check whether your maintainer address needs updating (in
particular in case you moved, or received multiple copies of this
message).

Best,
-k

***********************************************************************

Index: CRAN_policies.texi
===================================================================
--- CRAN_policies.texi    (revision 2906)
+++ CRAN_policies.texi    (working copy)
@@ -236,15 +236,23 @@
into which they are loaded.

@item
- at acronym{CRAN} packages should use only the public API.  Hence they should
-not use entry points not declared as API in installed headers nor
- at code{.Internal()} nor @code{.Call()} etc calls to base packages.  Such
-usages can cause packages to break at any time, even in patched versions
-of R.
+ at acronym{CRAN} packages should use only the public API.  Hence they
+should not use entry points not declared as API in installed headers nor
+ at code{.Internal()} nor @code{.Call()} etc calls to base packages. Also,
+ at code{:::} should not be used to access undocumented/internal functions
+in base packages.  Such usages can cause packages to break at any time,
+even in patched versions of R.

+ at end itemize

+ at item
+Changes to @acronym{CRAN} packages causing significant disruption to
+other packages must be agreed with the @acronym{CRAN} maintainers well
+in advance of any publicity.  Introduction of new packages providing
+back-compatibility versions of already available packages is not
+allowed.
+
@end itemize
- at end itemize

@node Binary packages, Submission, Source packages, Top
@unnumbered Binary packages
@@ -280,12 +288,16 @@
@node Submission,  , Binary packages, Top
@unnumbered Submission

-When submitting a package to CRAN you should either
+When submitting a package to CRAN you should @strong{either}
@itemize

@item
-use the submission form at @uref{http://CRAN.R-project.org/submit.html}, or
+use the submission form at @uref{http://CRAN.R-project.org/submit.html}
+(and not send an email).  You will be sent a confirmation email which
+needs to be accepted.

+ at strong{or}
+
@item
upload by anonymous @command{ftp} to
@uref{ftp://CRAN.R-project.org/@/incoming/} and send a (plain text ASCII)
@@ -293,29 +305,28 @@

@end itemize

+In either case, you can check that the submission was received by
+looking at @uref{ftp://cran.r-project.org/incoming/}.
+
In more detail:

@itemize

@item
-Uploads must be source tarballs as created by @command{R CMD build} and
-follow the @file{@var{PACKAGE}_ at var{VERSION}.tar.gz} naming scheme.
+Uploads must be source tarballs created by @command{R CMD build} and
+following the @file{@var{PACKAGE}_ at var{VERSION}.tar.gz} naming scheme.

@item
Please ensure that @command{R CMD check --as-cran} has been run @emph{on
the tarball to be uploaded} before submission.  This should be done with
-the current release of R or (preferably) R-devel or R-patched. As
-``Writing R Extensions'' used to say
+the current version of R-devel (or if that is not possible, current
+R-patched or the current release of R.)

- at quotation
-Please ensure that you can run through the complete procedure with only
-warnings that you understand and have reasons not to eliminate.  In
-principle, packages must pass @code{R CMD check} without warnings or
+In principle, packages must pass @code{R CMD check} without warnings or
significant notes to be admitted to the main @acronym{CRAN} package
area.  If there are warnings or notes you cannot eliminate (for example
because you believe them to be spurious) send an explanatory note as
-part of your covering email.
- at end quotation
+part of your covering email, or as a comment on the submission form.

@item
For a package update, please check that any packages depending on this
@@ -325,17 +336,18 @@
for the package.

@item
-A submission upload  should be accompanied by an email to
- at email{CRAN@@R-project.org} sent from the maintainer
-address listed in the package, and  using the subject line
-`CRAN submission @var{PACKAGE} @var{VERSION}', where @var{PACKAGE} and
- at var{VERSION} are the package name and version, respectively.  Plain
-text ASCII emails should be used if at all possible.
+An @command{ftp} upload should be accompanied by an email to
+ at email{CRAN@@R-project.org} sent from the maintainer address listed in
+the package, and using the subject line `CRAN submission @var{PACKAGE}
+ at var{VERSION}', where @var{PACKAGE} and @var{VERSION} are the package
+name and version, respectively.  Plain text ASCII emails should be used
+if at all possible.

If for some reason the submission has to be made by someone else (for
example, a co-author) this needs to be explained, and the designated
maintainer will need to confirm the submission.  Explain any change in
-the maintainer's email address.
+the maintainer's email address and if possible send confirmation from
+the previous address.

For a new submission, confirm in your email that you have read and agree
to these policies.  (This includes new versions of previously archived
@@ -343,7 +355,7 @@

If the package needs special treatment (for example if vignettes can
only be run or re-built on the maintainer's machine or take a very long
-time), say so in the submission email.
+time), say so in the submission email or on the submission form.

Do not email the package itself.

@@ -373,6 +385,12 @@
writing portable packages in @url{../../doc/manuals/R-exts.html,
``Writing R Extensions''}.

+Before submitting a package update, consult the CRAN check page at
+ at uref{http://cran.r-project.org/web/checks/check_results_NAME.html},
+substituting NAME by the name of your package.  In particular, wait for
+that page to be fully updated after publication of a version (which can
+take at least 48 hours) before submitting any corrections.
+
@item
If an update will change the package's API and hence affect packages
depending on it, it is expected that you will contact the maintainers of
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From lennart at karssen.org  Wed Dec 11 13:59:28 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 11 Dec 2013 13:59:28 +0100
Subject: [GenABEL-dev] ProbABEL: Binaries without extension
In-Reply-To: <52A85911.2070407@mail.ru>
References: <52A847B1.2090201@karssen.org> <52A85911.2070407@mail.ru>
Message-ID: <52A861B0.2070107@karssen.org>

Dear Maksim,

On 11-12-13 13:22, Maksim Struchalin wrote:
> Hi Lennart,
> 
> For me, it sounds reasonable to remove the file extensions.
> About probabel.pl: we can provide both 'probabel.pl' and 'probabel' for
> the next few revisions (if it is possible). 

Good suggestion. That should be possible.

> In this case, if users run
> 'probabel.pl', we show a warning messages saying that they need to use
> 'probabel' instead of 'proabbel.pl' and that 'probabel.pl' will be
> removed soon. 

Also a good point! I think it would be easy to implement such a warning
and it will help getting the users adapted to the change.


Thanks,

Lennart.

> Later, when most of users switched to 'probabel', we
> remove 'probabel.pl'.
> 
> best,
> Maksim
> 
> 
> 
> 
> On 11/12/2013 18:08, L.C. Karssen wrote:
>> Dear list,
>>
>> While working on packaging ProbABEL for inclusion in Debian, I came
>> across the following warning in the Debian package check (using the
>> lintian program):
>>
>> W: probabel: script-with-language-extension usr/bin/extIDS.pl
>> W: probabel: script-with-language-extension usr/bin/probabel.pl
>>
>> The short explanation is this:
>>     When scripts are installed into a directory in the system PATH, the
>>     script name should not include an extension such as .sh or .pl that
>>     denotes the scripting language currently used to implement it. The
>>     implementation language may change; if it does, leaving the name the
>>     same would be confusing and changing it would be disruptive.
>>
>>
>> The reasoning behind this warning is the following:
>> There are several reasons for not having an extension in the name of a
>> binary/script, nicely listed in this post:
>>     http://lists.debian.org/debian-med/2012/04/msg00103.html
>> The most important one to me is:
>>     I do not see what actual information such extensions are
>>     providing to the end user.  A user expects a program to do a job.
>>     Fullstop.  The user does not need to care about the language a
>>     program is written in if it just does what it is expected to do.
>>
>>
>> So, for ProbABEL I propose the following:
>> - extIDS.pl is not used a lot, so we can safely remove the .pl extension
>> there (and update the manual, mention it in the ChangeLog and release notes)
>> - For probabel.pl this is different. Many people use it exclusively
>> instead of calling pa{linear,logist,coxph} directly and changing this
>> would mean breaking user experience completely. I think we do need to
>> remove the extension at some point in the future, but that would be in a
>> 'large' update, say v0.5, not in a minor one like the upcoming v0.4.2.
>>
>>
>> What do you think of this?
>>
>> Lennart.
>>
>>
>> --
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>>
>> lennart at karssen.org
>> http://blog.karssen.org
>> GPG key ID: A88F554A
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>
>>
>>
>> _______________________________________________
>> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From lennart at karssen.org  Wed Dec 11 14:34:07 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 11 Dec 2013 14:34:07 +0100
Subject: [GenABEL-dev] ProbABEL: Binaries without extension
In-Reply-To: <52A8616E.60404@erasmusmc.nl>
References: <52A847B1.2090201@karssen.org> <52A85911.2070407@mail.ru>
 <1152651267260974754@unknownmsgid> <52A8616E.60404@erasmusmc.nl>
Message-ID: <52A869CF.3010604@karssen.org>

On 11-12-13 13:58, Maarten Kooyman wrote:
> 
> I think the solution of Maksim is quite workable. The minimal time to
> push this change is at least a half year: this buys time for users to
> update their pipeline.

I agree.


Lennart.

> 
> Maarten Kooyman
>  On 12/11/2013 01:53 PM, Yurii Aulchenko wrote:
> 
>> Question which probably supports Maxim's suggestion: How will this
>> affect existing user pipelines?
>>
>> ----------------------
>> Yurii Aulchenko 
>> (sent from mobile device)
>>
>> On Dec 11, 2013, at 13:22, Maksim Struchalin <m.v.struchalin at mail.ru
>> <mailto:m.v.struchalin at mail.ru>> wrote:
>>
>>> Hi Lennart,
>>>
>>> For me, it sounds reasonable to remove the file extensions.
>>> About probabel.pl <http://probabel.pl>: we can provide both
>>> 'probabel.pl <http://probabel.pl>' and 'probabel' for the next few
>>> revisions (if it is possible). In this case, if users run
>>> 'probabel.pl <http://probabel.pl>', we show a warning messages saying
>>> that they need to use 'probabel' instead of 'proabbel.pl
>>> <http://proabbel.pl>' and that 'probabel.pl <http://probabel.pl>'
>>> will be removed soon. Later, when most of users switched to
>>> 'probabel', we remove 'probabel.pl <http://probabel.pl>'.
>>>
>>> best,
>>> Maksim
>>>
>>>
>>>
>>>
>>> On 11/12/2013 18:08, L.C. Karssen wrote:
>>>> Dear list,
>>>>
>>>> While working on packaging ProbABEL for inclusion in Debian, I came
>>>> across the following warning in the Debian package check (using the
>>>> lintian program):
>>>>
>>>> W: probabel: script-with-language-extension usr/bin/extIDS.pl
>>>> W: probabel: script-with-language-extension usr/bin/probabel.pl <http://probabel.pl>
>>>>
>>>> The short explanation is this:
>>>>     When scripts are installed into a directory in the system PATH, the
>>>>     script name should not include an extension such as .sh or .pl that
>>>>     denotes the scripting language currently used to implement it. The
>>>>     implementation language may change; if it does, leaving the name the
>>>>     same would be confusing and changing it would be disruptive.
>>>>
>>>>
>>>> The reasoning behind this warning is the following:
>>>> There are several reasons for not having an extension in the name of a
>>>> binary/script, nicely listed in this post:
>>>>     http://lists.debian.org/debian-med/2012/04/msg00103.html
>>>> The most important one to me is:
>>>>     I do not see what actual information such extensions are
>>>>     providing to the end user.  A user expects a program to do a job.
>>>>     Fullstop.  The user does not need to care about the language a
>>>>     program is written in if it just does what it is expected to do.
>>>>
>>>>
>>>> So, for ProbABEL I propose the following:
>>>> - extIDS.pl is not used a lot, so we can safely remove the .pl extension
>>>> there (and update the manual, mention it in the ChangeLog and release notes)
>>>> - For probabel.pl <http://probabel.pl> this is different. Many people use it exclusively
>>>> instead of calling pa{linear,logist,coxph} directly and changing this
>>>> would mean breaking user experience completely. I think we do need to
>>>> remove the extension at some point in the future, but that would be in a
>>>> 'large' update, say v0.5, not in a minor one like the upcoming v0.4.2.
>>>>
>>>>
>>>> What do you think of this?
>>>>
>>>> Lennart.
>>>>
>>>>
>>>> --
>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>>> L.C. Karssen
>>>> Utrecht
>>>> The Netherlands
>>>>
>>>> lennart at karssen.org
>>>> http://blog.karssen.org
>>>> GPG key ID: A88F554A
>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>>
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

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

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From yurii.aulchenko at gmail.com  Fri Dec 13 08:57:12 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 13 Dec 2013 08:57:12 +0100
Subject: [GenABEL-dev] OmicA data type check?
Message-ID: <CAHX9t6+yvy7JaYExehX1zmQ6X=cD=tJAo-owds3_aFg101AdyA@mail.gmail.com>

Dear Diego,

In OmicA, can we check for the data type prior to the run and issue an
warning in case we have eg float and not double? To me it looks that it
must be relatively easy, because file vector format explicitly tells the
data type. May save quite some trouble for the user, as we can see from our
current experience...

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 fabregat at aices.rwth-aachen.de  Sun Dec 15 15:45:02 2013
From: fabregat at aices.rwth-aachen.de (Diego Fabregat Traver)
Date: Sun, 15 Dec 2013 15:45:02 +0100
Subject: [GenABEL-dev] OmicA data type check?
In-Reply-To: <CAHX9t6+yvy7JaYExehX1zmQ6X=cD=tJAo-owds3_aFg101AdyA@mail.gmail.com>
References: <CAHX9t6+yvy7JaYExehX1zmQ6X=cD=tJAo-owds3_aFg101AdyA@mail.gmail.com>
Message-ID: <fbb38f3c82420.52adce7e@aices.rwth-aachen.de>



On 13/12/13, Yurii Aulchenko  <yurii.aulchenko at gmail.com> wrote:

> Dear?Diego,
> 
> 
> In OmicA, can we check for the data type prior to the run?and issue an warning in case we have eg float and not double? To?me it looks that it must be relatively easy, because file vector format explicitly tells the data type. May save quite some trouble for the user, as we can see from our current experience...

In fact, I was convinced that this was already happening. I will look into this kind of details as soon as possible.

From lennart at karssen.org  Mon Dec 16 15:05:02 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 16 Dec 2013 15:05:02 +0100
Subject: [GenABEL-dev] Introducing OmicABELnoMM
Message-ID: <52AF088E.7030300@karssen.org>

Dear list,

As you may have noticed, I have committed a first version of
OmicABELnoMM to SVN on R-forge this morning.
OmicABELnoMM is the no-mixed-models version of OmicABEL, allowing rapid
genome-wide association analysis (linear regression), especially for
multiple traits ("omics" data).
OmicABELnoMM was written from scratch by Alvaro Jesus Frank so that the
algorithm is well tailored to the different mathematics. Alvaro works in
the same team at RWTH Aachen as Diego Fabregat Traver of OmicABEL fame,
under the supervision of Paolo Bientinesi, Yurii Aulchenko and,
recently, myself.

Please note that OmicABELnoMM is still under development (thanks Yakov
and Sodbo for your contributions!). Most notably, work is still being
done on the exact output file format. At present the output is stored in
a filevector-format file. This will probably remain the same, but the
order in which the information (betas, standard errors) is stored may
change.

These are the development plans we have for OmicABELnoMM in the near future:
- Implement autotools configuration
- Improve the output file format
- Add documentation


Best regards,

Lennart.


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

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From fabregat at aices.rwth-aachen.de  Mon Dec 16 15:17:46 2013
From: fabregat at aices.rwth-aachen.de (Diego Fabregat Traver)
Date: Mon, 16 Dec 2013 15:17:46 +0100
Subject: [GenABEL-dev] Introducing OmicABELnoMM
Message-ID: <fba496be41bb4.52af199a@aices.rwth-aachen.de>


Congrats guys! I didn't have the time to look at it carefully,
but from what I know it should be a pretty good piece of work ;)

Best,
Diego

On 16/12/13, "L.C. Karssen"  <lennart at karssen.org> wrote:

> Dear list,
> 
> As you may have noticed, I have committed a first version of
> OmicABELnoMM to SVN on R-forge this morning.
> OmicABELnoMM is the no-mixed-models version of OmicABEL, allowing rapid
> genome-wide association analysis (linear regression), especially for
> multiple traits ("omics" data).
> OmicABELnoMM was written from scratch by Alvaro Jesus Frank so that the
> algorithm is well tailored to the different mathematics. Alvaro works in
> the same team at RWTH Aachen as Diego Fabregat Traver of OmicABEL fame,
> under the supervision of Paolo Bientinesi, Yurii Aulchenko and,
> recently, myself.
> 
> Please note that OmicABELnoMM is still under development (thanks Yakov
> and Sodbo for your contributions!). Most notably, work is still being
> done on the exact output file format. At present the output is stored in
> a filevector-format file. This will probably remain the same, but the
> order in which the information (betas, standard errors) is stored may
> change.
> 
> These are the development plans we have for OmicABELnoMM in the near future:
> - Implement autotools configuration
> - Improve the output file format
> - Add documentation
> 
> 
> Best regards,
> 
> Lennart.
> 
> 
> -- 
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> L.C. Karssen
> Utrecht
> The Netherlands
> 
> lennart at karssen.org
> http://blog.karssen.org
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
> 
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel

From yurii.aulchenko at gmail.com  Tue Dec 17 16:32:11 2013
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Tue, 17 Dec 2013 16:32:11 +0100
Subject: [GenABEL-dev] announcement for genabel.org
Message-ID: <F7BC485C-9D82-4C7C-96BB-9386DB6D1874@gmail.com>

Dear All,

please find below the news we'd like to add on the GenABEL.org late today / tomorrow in the morning

best wishes,
Yurii


TC: Genomic control for non-additive models

A manuscript on <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0081431">?Development and application of genomic control methods for genome-wide association studies using non-additive models?</a> was recently published on-line (PLOS ONE). The work reported in the manuscript extends the genomic control method to non-additive models; all methods are implemented in GenABEL. [click on 'READ MORE' below for complete story]

With methods described, it is possible to correct the inflated statistic for non-additive models (such as recessive, dominant, over-dominant, and genotypic) in case a study population has genetic (sub)structure e.g. due to cryptic relatedness. Estimation of the correction coefficient is possible via the Variance Inflation Factor (VIF) and via polynomial of fixed degree (polynomial genomic control, PGC). The VIF estimation allows the corrections of 1df tests only, while PGC has more general application and also works for 2df genotypic test.

All methods reported in the manuscript are available in the GenABEL-package (part of the GenABEL suite) as functions PGC, VIFGC, VIFGC_ovedom.

We also take a chance to congratulate to Yakov Tsepilov - the first author of this study, and the GenABEL project contributor - on his first-as-first-author paper! Well done, and looking forward to see your next work!

From lennart at karssen.org  Wed Dec 18 11:06:06 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 18 Dec 2013 11:06:06 +0100
Subject: [GenABEL-dev] announcement for genabel.org
In-Reply-To: <F7BC485C-9D82-4C7C-96BB-9386DB6D1874@gmail.com>
References: <F7BC485C-9D82-4C7C-96BB-9386DB6D1874@gmail.com>
Message-ID: <52B1738E.3070904@karssen.org>

That's great news!

Congratulations to Yakov and the others!


Lennart.

On 17-12-13 16:32, Yury Aulchenko wrote:
> Dear All,
> 
> please find below the news we'd like to add on the GenABEL.org late today / tomorrow in the morning
> 
> best wishes,
> Yurii
> 
> 
> TC: Genomic control for non-additive models
> 
> A manuscript on <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0081431">?Development and application of genomic control methods for genome-wide association studies using non-additive models?</a> was recently published on-line (PLOS ONE). The work reported in the manuscript extends the genomic control method to non-additive models; all methods are implemented in GenABEL. [click on 'READ MORE' below for complete story]
> 
> With methods described, it is possible to correct the inflated statistic for non-additive models (such as recessive, dominant, over-dominant, and genotypic) in case a study population has genetic (sub)structure e.g. due to cryptic relatedness. Estimation of the correction coefficient is possible via the Variance Inflation Factor (VIF) and via polynomial of fixed degree (polynomial genomic control, PGC). The VIF estimation allows the corrections of 1df tests only, while PGC has more general application and also works for 2df genotypic test.
> 
> All methods reported in the manuscript are available in the GenABEL-package (part of the GenABEL suite) as functions PGC, VIFGC, VIFGC_ovedom.
> 
> We also take a chance to congratulate to Yakov Tsepilov - the first author of this study, and the GenABEL project contributor - on his first-as-first-author paper! Well done, and looking forward to see your next work!
> _______________________________________________
> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From lennart at karssen.org  Wed Dec 18 11:13:00 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Wed, 18 Dec 2013 11:13:00 +0100
Subject: [GenABEL-dev] Introducing OmicABELnoMM
In-Reply-To: <52AF088E.7030300@karssen.org>
References: <52AF088E.7030300@karssen.org>
Message-ID: <52B1752C.8020502@karssen.org>

Dear list,

Here's an update on my first steps with OmicABELnoMM after uploading it
to SVN:

1) I spent some time getting several files into better compliance with
our coding style guide.

2) I started implementing autoconf/automake. This is hampered by 3).

3) I tried using the openblas package that comes with Debian/Ubuntu, but
that doesn't seem to work. After digging a lot, I now think this is
because the Debian package is not compiled with the USE_OPENMP=1 flag
(which is needed according to Alvaro's instructions).
I'm going to investigate two ways to solve this:
- rebuild the Debian package with openMP support. If that helps I have a
stronger case to try and change the Debian package
- Include a copy of openblas 2.8.2 into the OmicABELnoMM package. I've
already verified that that works (basically following Alvaro's
instructions), but from a design point of view I don't like really it.
It would clutter SVN with components we're not interested in
maintaining. An alternative may be to have a
'download-and-compile-openblas' script.
Let me know if you have any suggestions or comments.

4) I've added OmicABELnoMM to Jenkins. It doesn't look good yet, given
that all the builds so far failed, but that will only improve in the
future :-)


Best,

Lennart.


On 16-12-13 15:05, L.C. Karssen wrote:
> Dear list,
> 
> As you may have noticed, I have committed a first version of
> OmicABELnoMM to SVN on R-forge this morning.
> OmicABELnoMM is the no-mixed-models version of OmicABEL, allowing rapid
> genome-wide association analysis (linear regression), especially for
> multiple traits ("omics" data).
> OmicABELnoMM was written from scratch by Alvaro Jesus Frank so that the
> algorithm is well tailored to the different mathematics. Alvaro works in
> the same team at RWTH Aachen as Diego Fabregat Traver of OmicABEL fame,
> under the supervision of Paolo Bientinesi, Yurii Aulchenko and,
> recently, myself.
> 
> Please note that OmicABELnoMM is still under development (thanks Yakov
> and Sodbo for your contributions!). Most notably, work is still being
> done on the exact output file format. At present the output is stored in
> a filevector-format file. This will probably remain the same, but the
> order in which the information (betas, standard errors) is stored may
> change.
> 
> These are the development plans we have for OmicABELnoMM in the near future:
> - Implement autotools configuration
> - Improve the output file format
> - Add documentation
> 
> 
> Best regards,
> 
> Lennart.
> 
> 
> 
> 
> _______________________________________________
> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From yurii.aulchenko at gmail.com  Wed Dec 18 13:00:45 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 18 Dec 2013 13:00:45 +0100
Subject: [GenABEL-dev] announcement for genabel.org
In-Reply-To: <52B1738E.3070904@karssen.org>
References: <F7BC485C-9D82-4C7C-96BB-9386DB6D1874@gmail.com>
 <52B1738E.3070904@karssen.org>
Message-ID: <CAHX9t6LyXE+NCDo3Te=asrfkKWnXuapYCFX5F1q5wLZo3u+ETg@mail.gmail.com>

Done!

http://www.genabel.org/news20131218

Please like on Facebook, re-tweet, like on scoop.it and LinkedIn...

http://www.scoop.it/t/statistical-omics/p/4012905113/2013/12/18/genomic-control-for-non-additive-models-genabel-org


On Wed, Dec 18, 2013 at 11:06 AM, L.C. Karssen <lennart at karssen.org> wrote:

> That's great news!
>
> Congratulations to Yakov and the others!
>
>
> Lennart.
>
> On 17-12-13 16:32, Yury Aulchenko wrote:
> > Dear All,
> >
> > please find below the news we'd like to add on the GenABEL.org late
> today / tomorrow in the morning
> >
> > best wishes,
> > Yurii
> >
> >
> > TC: Genomic control for non-additive models
> >
> > A manuscript on <a href="
> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0081431">?Development
> and application of genomic control methods for genome-wide association
> studies using non-additive models?</a> was recently published on-line (PLOS
> ONE). The work reported in the manuscript extends the genomic control
> method to non-additive models; all methods are implemented in GenABEL.
> [click on 'READ MORE' below for complete story]
> >
> > With methods described, it is possible to correct the inflated statistic
> for non-additive models (such as recessive, dominant, over-dominant, and
> genotypic) in case a study population has genetic (sub)structure e.g. due
> to cryptic relatedness. Estimation of the correction coefficient is
> possible via the Variance Inflation Factor (VIF) and via polynomial of
> fixed degree (polynomial genomic control, PGC). The VIF estimation allows
> the corrections of 1df tests only, while PGC has more general application
> and also works for 2df genotypic test.
> >
> > All methods reported in the manuscript are available in the
> GenABEL-package (part of the GenABEL suite) as functions PGC, VIFGC,
> VIFGC_ovedom.
> >
> > We also take a chance to congratulate to Yakov Tsepilov - the first
> author of this study, and the GenABEL project contributor - on his
> first-as-first-author paper! Well done, and looking forward to see your
> next work!
> > _______________________________________________
> > 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
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
>
> _______________________________________________
> 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 lennart at karssen.org  Thu Dec 19 00:26:55 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 19 Dec 2013 00:26:55 +0100
Subject: [GenABEL-dev] Introducing OmicABELnoMM
In-Reply-To: <52B1752C.8020502@karssen.org>
References: <52AF088E.7030300@karssen.org> <52B1752C.8020502@karssen.org>
Message-ID: <52B22F3F.6030607@karssen.org>

Dear list,

I've made some progress with compiling OmicABELnoMM. I've just uploaded
a working configure.ac.

I installed the following packages on my Ubuntu 13.10 system:
libopenblas-base
libopenblas-dev
liblapacke{,-dev}
liblapack-dev
liblapack3

If I then run
./configure LDFLAGS="-L/usr/lib/openblas-base"
make

Compilation works (lots of warnings though, due to -Wall) and a binary
is created. When running the example from the howtocompile.txt file I
get a bunch of the following warnings (although the program seems to run
fine with the example data):

OpenBLAS Warning : Detect OpenMP Loop and this application may hang.
Please rebuild the library with USE_OPENMP=1 option.


So, as I guessed, Ubuntu's libopenblas is not compiled with openMP support.
I've tried to created my own packages based on the instructions in
/usr/share/doc/libopenblas-base/README.Debian and adding USE_OPENMP=1 to
the make flags in the debian/rules file. That works, and after
recompiling the OpenBLAS warnings disappear.

On jenkins the build is still failing, because there is no lapacke
package for that machine...


Lennart.

On 18-12-13 11:13, L.C. Karssen wrote:
> Dear list,
> 
> Here's an update on my first steps with OmicABELnoMM after uploading it
> to SVN:
> 
> 1) I spent some time getting several files into better compliance with
> our coding style guide.
> 
> 2) I started implementing autoconf/automake. This is hampered by 3).
> 
> 3) I tried using the openblas package that comes with Debian/Ubuntu, but
> that doesn't seem to work. After digging a lot, I now think this is
> because the Debian package is not compiled with the USE_OPENMP=1 flag
> (which is needed according to Alvaro's instructions).
> I'm going to investigate two ways to solve this:
> - rebuild the Debian package with openMP support. If that helps I have a
> stronger case to try and change the Debian package
> - Include a copy of openblas 2.8.2 into the OmicABELnoMM package. I've
> already verified that that works (basically following Alvaro's
> instructions), but from a design point of view I don't like really it.
> It would clutter SVN with components we're not interested in
> maintaining. An alternative may be to have a
> 'download-and-compile-openblas' script.
> Let me know if you have any suggestions or comments.
> 
> 4) I've added OmicABELnoMM to Jenkins. It doesn't look good yet, given
> that all the builds so far failed, but that will only improve in the
> future :-)
> 
> 
> Best,
> 
> Lennart.
> 
> 
> On 16-12-13 15:05, L.C. Karssen wrote:
>> Dear list,
>>
>> As you may have noticed, I have committed a first version of
>> OmicABELnoMM to SVN on R-forge this morning.
>> OmicABELnoMM is the no-mixed-models version of OmicABEL, allowing rapid
>> genome-wide association analysis (linear regression), especially for
>> multiple traits ("omics" data).
>> OmicABELnoMM was written from scratch by Alvaro Jesus Frank so that the
>> algorithm is well tailored to the different mathematics. Alvaro works in
>> the same team at RWTH Aachen as Diego Fabregat Traver of OmicABEL fame,
>> under the supervision of Paolo Bientinesi, Yurii Aulchenko and,
>> recently, myself.
>>
>> Please note that OmicABELnoMM is still under development (thanks Yakov
>> and Sodbo for your contributions!). Most notably, work is still being
>> done on the exact output file format. At present the output is stored in
>> a filevector-format file. This will probably remain the same, but the
>> order in which the information (betas, standard errors) is stored may
>> change.
>>
>> These are the development plans we have for OmicABELnoMM in the near future:
>> - Implement autotools configuration
>> - Improve the output file format
>> - Add documentation
>>
>>
>> Best regards,
>>
>> Lennart.
>>
>>
>>
>>
>> _______________________________________________
>> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From lennart at karssen.org  Fri Dec 20 08:58:09 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 20 Dec 2013 08:58:09 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1496 -
	pkg/GenABEL-general/scripts
In-Reply-To: <20131220035617.5D17118652E@r-forge.r-project.org>
References: <20131220035617.5D17118652E@r-forge.r-project.org>
Message-ID: <52B3F891.8000301@karssen.org>

Hi Maksim,

Thanks for making this comprehensive script. Once I've got the new
Jenkins server up I will also incorporate it in there.

One suggestion: Instead of having all these lines like:
 echo "install.packages(\"pkg", repos='http.url')" > install.R
you can try the following (a so-called HERE document):

repo="http.url"   # Making a variable seems handy

cat <<EOF > install.R
install.packages("pkg", repos="$repo")
install.packages("pkg2", repos="$repo")
etc.
EOF

The idea behind a HERE document is that you continue adding to it until
you reached fixed string (EOF in this case, but you can use any string
you want).
Saves you a lot of typing and quotes.


Best,

Lennart.


On 20-12-13 04:56, noreply at r-forge.r-project.org wrote:
> Author: maksim
> Date: 2013-12-20 04:56:16 +0100 (Fri, 20 Dec 2013)
> New Revision: 1496
> 
> Modified:
>    pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
> Log:
> Some bugs fixed. The R package qvalue is installed from Bioconductor now because CRAN deleted it from its repository. Now the ready GenABEL distributive is in the GenABEL_DISTRIBUTIVE_IS_HERE directory after the script finished. You should check out all the warning messages in output before using the distributive.
> 
> Modified: pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
> ===================================================================
> --- pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-20 03:09:34 UTC (rev 1495)
> +++ pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-20 03:56:16 UTC (rev 1496)
> @@ -4,19 +4,15 @@
>  
>  
>  
> -echo
>  echo Remove GenABEL_version_for_submission...
> -echo
>  rm -rf $installation_dir
>  echo
>  echo Create GenABEL_version_for_submission...
> -echo
>  mkdir GenABEL_version_for_submission
>  cd GenABEL_version_for_submission
>  
>  echo
>  echo Extract packages from r-forge...
> -echo
>  svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/filevector
>  svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/DatABEL
>  svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/MetABEL
> @@ -29,31 +25,33 @@
>  
>  echo
>  echo Install the freshest R packages from CRAN repository...
> +
> +echo "install.packages(\"roxygen2\", repos='http://cran.xl-mirror.nl')" > install_fresh_R_packages.R
> +echo "install.packages(\"mvtnorm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +echo "install.packages(\"methods\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +echo "install.packages(\"MASS\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +echo "install.packages(\"utils\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>  echo
> +echo An R package qvalue is being installed from Bioconductor...
> +#echo "install.packages(\"qvalue\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +echo "source(\"http://bioconductor.org/biocLite.R\")" >> install_fresh_R_packages.R
> +echo "biocLite(\"qvalue\")" >> install_fresh_R_packages.R
> +echo "install.packages(\"genetics\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +echo "install.packages(\"haplo.stats\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +echo "install.packages(\"hglm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +echo "install.packages(\"PredictABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +echo "install.packages(\"VariABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +echo "install.packages(\"bigRR\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +R -f install_fresh_R_packages.R
> +rm -rf install_fresh_R_packages.R
>  
> -echo "install.packages(\"roxygen2\", repos='http://cran.us.r-project.org')" > install_roxygen_file.R
> -echo "install.packages(\"mvtnorm\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"methods\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"MASS\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"utils\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"qvalue\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"genetics\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"haplo.stats\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"hglm\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"PredictABEL\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"VariABEL\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -echo "install.packages(\"bigRR\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
> -R -f install_roxygen_file.R
> -rm -rf install_roxygen_file.R
>  
>  
>  
>  
>  
> -
>  echo
>  echo Build and install packages...
> -echo
>  
>  R CMD build DatABEL
>  R CMD INSTALL DatABEL_*
> @@ -72,8 +70,6 @@
>  PATH="$PATH:$probabel_src_location"
>  echo Search ProbABEL executive files in $probabel_src_location
>  
> -R CMD build MixABEL
> -R CMD INSTALL MixABEL_*
>  
>  cd GenABEL.data
>  rm -rf inst R
> @@ -86,10 +82,9 @@
>  
>  echo
>  echo Build, check and install GenABEL...
> -echo
>  # clean up the dev-version for distrib
>  cd GenABEL
> -rm cleanup* configure* *.R
> +rm -rf cleanup* configure* *.R
>  cd src
>  cp DAlib/*.c* .
>  cp DAlib/*.h* .
> @@ -110,22 +105,42 @@
>  # end cleanup
>  
>  R CMD check GenABEL
> -R CMD INSTALL GenABEL
> +R CMD build GenABEL
> +R CMD INSTALL GenABEL_*
>  
> +
> +
> +
> +R CMD build MixABEL
> +R CMD INSTALL MixABEL_*
> +
> +
>  echo
>  echo Build the tutorial...
> -echo
>  # build the tutorial
>  cd GenABEL_general
>  make
>  cd ..
> +
> +if [ -f GenABEL_general/GenABEL-tutorial.pdf ];
> +then
>  cp GenABEL_general/GenABEL-tutorial.pdf GenABEL/inst/doc/.
> -# end build the tutorial
> -
>  echo
>  echo Build the working version of GenABEL...
> -echo
>  R CMD build GenABEL
> +mkdir GenABEL_DISTRIBUTIVE_IS_HERE
> +cp GenABEL_*gz GenABEL_DISTRIBUTIVE_IS_HERE
> +echo "The distributive of GenABEL is in $installation_dir/GenABEL_DISTRIBUTIVE_IS_HERE directory. Check out that there were no errors/warnings during running this script."
> +echo "GenABEL building DONE!"
> +else
> +  echo "ERROR: File GenABEL_general/GenABEL-tutorial.pdf does not exist. It should have been generated after runing a make command in the GenABEL_general directory. Something did not work out."
> +  echo "Making GenABEL_general/GenABEL-tutorial.pdf was the last step in building GenABEL. Figure out what has happned, create GenABEL_general/GenABEL-tutorial.pdf by running the command make in the GenABEL_general dir, copy it in GenABEL/inst/doc/ and run R CMD build GenABEL."
> +fi
>  
> +
> +
> +# end build the tutorial
> +
> +
>  # and do not forget to run R CMD check --as-cran!
>  
> 
> _______________________________________________
> Genabel-commits mailing list
> Genabel-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
> 

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

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From lennart at karssen.org  Fri Dec 20 09:24:51 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 20 Dec 2013 09:24:51 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1498 -
	pkg/GenABEL-general/scripts tutorials/GenABEL_general
In-Reply-To: <20131220082209.76303186896@r-forge.r-project.org>
References: <20131220082209.76303186896@r-forge.r-project.org>
Message-ID: <52B3FED3.6010704@karssen.org>

Hi Maksim,

Cool! That's a quick implementation!


Thanks,

Lennart.

On 20-12-13 09:22, noreply at r-forge.r-project.org wrote:
> Author: maksim
> Date: 2013-12-20 09:22:09 +0100 (Fri, 20 Dec 2013)
> New Revision: 1498
> 
> Modified:
>    pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
>    tutorials/GenABEL_general/Makefile
> Log:
> Added instructions which reduce size of GenABEL-tutorial.pdf while runing Makfilein from GenABEL_general. Rewrote part for installation fresh R packages.
> 
> Modified: pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
> ===================================================================
> --- pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-20 06:28:26 UTC (rev 1497)
> +++ pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-20 08:22:09 UTC (rev 1498)
> @@ -24,24 +24,28 @@
>  
>  
>  echo
> -echo Install the freshest R packages from CRAN repository...
> +echo Install the freshest R packages from CRAN and Bioconductor repository...
>  
> -echo "install.packages(\"roxygen2\", repos='http://cran.xl-mirror.nl')" > install_fresh_R_packages.R
> -echo "install.packages(\"mvtnorm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"methods\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"MASS\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"utils\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo
> -echo An R package qvalue is being installed from Bioconductor...
> -#echo "install.packages(\"qvalue\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "source(\"http://bioconductor.org/biocLite.R\")" >> install_fresh_R_packages.R
> -echo "biocLite(\"qvalue\")" >> install_fresh_R_packages.R
> -echo "install.packages(\"genetics\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"haplo.stats\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"hglm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"PredictABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"VariABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"bigRR\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +CRAN_repo="\"http://cran.xl-mirror.nl\""
> +
> +cat <<EOF > install_fresh_R_packages.R
> +install.packages("roxygen2", repos=$CRAN_repo) 
> +install.packages("mvtnorm", repos=$CRAN_repo) 
> +install.packages("methods", repos=$CRAN_repo) 
> +install.packages("MASS", repos=$CRAN_repo) 
> +install.packages("utils", repos=$CRAN_repo) 
> +
> +source("http://bioconductor.org/biocLite.R") 
> +biocLite("qvalue") 
> +
> +install.packages("genetics", repos=$CRAN_repo) 
> +install.packages("haplo.stats", repos=$CRAN_repo) 
> +install.packages("hglm", repos=$CRAN_repo) 
> +install.packages("PredictABEL", repos=$CRAN_repo) 
> +install.packages("VariABEL", repos=$CRAN_repo) 
> +install.packages("bigRR", repos=$CRAN_repo) 
> +EOF
> +
>  R -f install_fresh_R_packages.R
>  rm -rf install_fresh_R_packages.R
>  
> @@ -124,9 +128,11 @@
>  
>  if [ -f GenABEL_general/GenABEL-tutorial.pdf ];
>  then
> -cp GenABEL_general/GenABEL-tutorial.pdf GenABEL/inst/doc/.
> -echo
> -echo Build the working version of GenABEL...
> +#echo Compressing GenABEL_general/GenABEL-tutorial.pdf...
> +#gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen -dNOPAUSE -dQUIET -dBATCH -sOutputFile=GenABEL_general/GenABEL-tutorial.pdf_compressed GenABEL_general/GenABEL-tutorial.pdf
> +#echo Copying GenABEL_general/GenABEL-tutorial.pdf in GenABEL/inst/doc/...
> +cp GenABEL_general/GenABEL-tutorial.pdf GenABEL/inst/doc/
> +echo Buildngd the GenABEL...
>  R CMD build GenABEL
>  mkdir GenABEL_DISTRIBUTIVE_IS_HERE
>  cp GenABEL_*gz GenABEL_DISTRIBUTIVE_IS_HERE
> 
> Modified: tutorials/GenABEL_general/Makefile
> ===================================================================
> --- tutorials/GenABEL_general/Makefile	2013-12-20 06:28:26 UTC (rev 1497)
> +++ tutorials/GenABEL_general/Makefile	2013-12-20 08:22:09 UTC (rev 1498)
> @@ -22,6 +22,8 @@
>  	makeindex $<
>  	pdflatex $<
>  	pdflatex $<
> +	gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dNOPAUSE -dQUIET -dBATCH -sOutputFile=$(MAIN).pdf_compressed $(MAIN).pdf
> +	mv $(MAIN).pdf_compressed $(MAIN).pdf
>  
>  html: all
>  	mk4ht htlatex GenABEL-tutorial.tex myxhtml
> 
> _______________________________________________
> Genabel-commits mailing list
> Genabel-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
> 

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

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From m.v.struchalin at mail.ru  Fri Dec 20 09:23:08 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Fri, 20 Dec 2013 15:23:08 +0700
Subject: [GenABEL-dev] [Genabel-commits] r1496 -
	pkg/GenABEL-general/scripts
In-Reply-To: <52B3F891.8000301@karssen.org>
References: <20131220035617.5D17118652E@r-forge.r-project.org>
 <52B3F891.8000301@karssen.org>
Message-ID: <52B3FE6C.90005@mail.ru>

Thanks Lennart. That's very usefull.
best,
Maksim

On 20/12/2013 14:58, L.C. Karssen wrote:
> Hi Maksim,
>
> Thanks for making this comprehensive script. Once I've got the new
> Jenkins server up I will also incorporate it in there.
>
> One suggestion: Instead of having all these lines like:
>   echo "install.packages(\"pkg", repos='http.url')" > install.R
> you can try the following (a so-called HERE document):
>
> repo="http.url"   # Making a variable seems handy
>
> cat <<EOF > install.R
> install.packages("pkg", repos="$repo")
> install.packages("pkg2", repos="$repo")
> etc.
> EOF
>
> The idea behind a HERE document is that you continue adding to it until
> you reached fixed string (EOF in this case, but you can use any string
> you want).
> Saves you a lot of typing and quotes.
>
>
> Best,
>
> Lennart.
>
>
> On 20-12-13 04:56, noreply at r-forge.r-project.org wrote:
>> Author: maksim
>> Date: 2013-12-20 04:56:16 +0100 (Fri, 20 Dec 2013)
>> New Revision: 1496
>>
>> Modified:
>>     pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
>> Log:
>> Some bugs fixed. The R package qvalue is installed from Bioconductor now because CRAN deleted it from its repository. Now the ready GenABEL distributive is in the GenABEL_DISTRIBUTIVE_IS_HERE directory after the script finished. You should check out all the warning messages in output before using the distributive.
>>
>> Modified: pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
>> ===================================================================
>> --- pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-20 03:09:34 UTC (rev 1495)
>> +++ pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-20 03:56:16 UTC (rev 1496)
>> @@ -4,19 +4,15 @@
>>   
>>   
>>   
>> -echo
>>   echo Remove GenABEL_version_for_submission...
>> -echo
>>   rm -rf $installation_dir
>>   echo
>>   echo Create GenABEL_version_for_submission...
>> -echo
>>   mkdir GenABEL_version_for_submission
>>   cd GenABEL_version_for_submission
>>   
>>   echo
>>   echo Extract packages from r-forge...
>> -echo
>>   svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/filevector
>>   svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/DatABEL
>>   svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/MetABEL
>> @@ -29,31 +25,33 @@
>>   
>>   echo
>>   echo Install the freshest R packages from CRAN repository...
>> +
>> +echo "install.packages(\"roxygen2\", repos='http://cran.xl-mirror.nl')" > install_fresh_R_packages.R
>> +echo "install.packages(\"mvtnorm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"methods\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"MASS\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"utils\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>>   echo
>> +echo An R package qvalue is being installed from Bioconductor...
>> +#echo "install.packages(\"qvalue\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "source(\"http://bioconductor.org/biocLite.R\")" >> install_fresh_R_packages.R
>> +echo "biocLite(\"qvalue\")" >> install_fresh_R_packages.R
>> +echo "install.packages(\"genetics\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"haplo.stats\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"hglm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"PredictABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"VariABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +echo "install.packages(\"bigRR\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
>> +R -f install_fresh_R_packages.R
>> +rm -rf install_fresh_R_packages.R
>>   
>> -echo "install.packages(\"roxygen2\", repos='http://cran.us.r-project.org')" > install_roxygen_file.R
>> -echo "install.packages(\"mvtnorm\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"methods\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"MASS\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"utils\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"qvalue\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"genetics\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"haplo.stats\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"hglm\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"PredictABEL\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"VariABEL\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -echo "install.packages(\"bigRR\", repos='http://cran.us.r-project.org')" >> install_roxygen_file.R
>> -R -f install_roxygen_file.R
>> -rm -rf install_roxygen_file.R
>>   
>>   
>>   
>>   
>>   
>> -
>>   echo
>>   echo Build and install packages...
>> -echo
>>   
>>   R CMD build DatABEL
>>   R CMD INSTALL DatABEL_*
>> @@ -72,8 +70,6 @@
>>   PATH="$PATH:$probabel_src_location"
>>   echo Search ProbABEL executive files in $probabel_src_location
>>   
>> -R CMD build MixABEL
>> -R CMD INSTALL MixABEL_*
>>   
>>   cd GenABEL.data
>>   rm -rf inst R
>> @@ -86,10 +82,9 @@
>>   
>>   echo
>>   echo Build, check and install GenABEL...
>> -echo
>>   # clean up the dev-version for distrib
>>   cd GenABEL
>> -rm cleanup* configure* *.R
>> +rm -rf cleanup* configure* *.R
>>   cd src
>>   cp DAlib/*.c* .
>>   cp DAlib/*.h* .
>> @@ -110,22 +105,42 @@
>>   # end cleanup
>>   
>>   R CMD check GenABEL
>> -R CMD INSTALL GenABEL
>> +R CMD build GenABEL
>> +R CMD INSTALL GenABEL_*
>>   
>> +
>> +
>> +
>> +R CMD build MixABEL
>> +R CMD INSTALL MixABEL_*
>> +
>> +
>>   echo
>>   echo Build the tutorial...
>> -echo
>>   # build the tutorial
>>   cd GenABEL_general
>>   make
>>   cd ..
>> +
>> +if [ -f GenABEL_general/GenABEL-tutorial.pdf ];
>> +then
>>   cp GenABEL_general/GenABEL-tutorial.pdf GenABEL/inst/doc/.
>> -# end build the tutorial
>> -
>>   echo
>>   echo Build the working version of GenABEL...
>> -echo
>>   R CMD build GenABEL
>> +mkdir GenABEL_DISTRIBUTIVE_IS_HERE
>> +cp GenABEL_*gz GenABEL_DISTRIBUTIVE_IS_HERE
>> +echo "The distributive of GenABEL is in $installation_dir/GenABEL_DISTRIBUTIVE_IS_HERE directory. Check out that there were no errors/warnings during running this script."
>> +echo "GenABEL building DONE!"
>> +else
>> +  echo "ERROR: File GenABEL_general/GenABEL-tutorial.pdf does not exist. It should have been generated after runing a make command in the GenABEL_general directory. Something did not work out."
>> +  echo "Making GenABEL_general/GenABEL-tutorial.pdf was the last step in building GenABEL. Figure out what has happned, create GenABEL_general/GenABEL-tutorial.pdf by running the command make in the GenABEL_general dir, copy it in GenABEL/inst/doc/ and run R CMD build GenABEL."
>> +fi
>>   
>> +
>> +
>> +# end build the tutorial
>> +
>> +
>>   # and do not forget to run R CMD check --as-cran!
>>   
>>
>> _______________________________________________
>> Genabel-commits mailing list
>> Genabel-commits at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
>>
>
>
> _______________________________________________
> 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 m.v.struchalin at mail.ru  Sat Dec 21 07:44:55 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Sat, 21 Dec 2013 13:44:55 +0700
Subject: [GenABEL-dev] Fwd: CRAN package MetABEL
In-Reply-To: <21172.48479.385656.257533@fangorn.hornik.net>
References: <21172.48479.385656.257533@fangorn.hornik.net>
Message-ID: <52B538E7.2050904@mail.ru>

Hi Yurii,

As I understand from the email below, we should resubmit MetABEL on CRAN 
with updated info.

best,
Maksim



-------- Original Message --------
Subject: 	CRAN package MetABEL
Date: 	Fri, 20 Dec 2013 22:57:51 +0100
From: 	Kurt Hornik <Kurt.Hornik at wu.ac.at>
Reply-To: 	Kurt.Hornik at wu.ac.at
To: 	m.v.struchalin at mail.ru
CC: 	Kurt Hornik <Kurt.Hornik at wu.ac.at>



This has

   m.struchalin at erasmusmc.nl

as maintainer address, which no longer works.

Can we pls asap have an update with a working maintainer email address?

Best
-k



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From yurii.aulchenko at gmail.com  Sat Dec 21 08:44:23 2013
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Sat, 21 Dec 2013 07:44:23 +0000
Subject: [GenABEL-dev] [Genabel-commits] r1495 - pkg/GenABEL
In-Reply-To: <20131220030937.2C4E4181085@r-forge.r-project.org>
References: <20131220030937.2C4E4181085@r-forge.r-project.org>
Message-ID: <5D5C971B-BABF-4A21-81F2-50EF9B90190F@gmail.com>

Not sure if the requirement may be that "data" is there always even if it is empty. It should be specified in their how to make packages (part of r extensions guide). 

Yurii

----------------
Sent from mobile device, please excuse possible typos

> On 20 Dec 2013, at 03:09, noreply at r-forge.r-project.org wrote:
> 
> Author: maksim
> Date: 2013-12-20 04:09:34 +0100 (Fri, 20 Dec 2013)
> New Revision: 1495
> 
> Removed:
>   pkg/GenABEL/data/
> Log:
> Remove the directory data because all of the data from this dir is moved to a new packages called GenABEL.data.
> 
> _______________________________________________
> Genabel-commits mailing list
> Genabel-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits

From m.v.struchalin at mail.ru  Sat Dec 21 10:36:45 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Sat, 21 Dec 2013 16:36:45 +0700
Subject: [GenABEL-dev] [Genabel-commits] r1495 - pkg/GenABEL
In-Reply-To: <5D5C971B-BABF-4A21-81F2-50EF9B90190F@gmail.com>
References: <20131220030937.2C4E4181085@r-forge.r-project.org>
 <5D5C971B-BABF-4A21-81F2-50EF9B90190F@gmail.com>
Message-ID: <4004EE49-DB46-40FE-A81B-E922B588EFFC@mail.ru>

R CMD check --as-cran told me delete this dir.

Maksim

Sent from my iPhone



> 21 ???. 2013 ?., ? 14:44, Yury Aulchenko <yurii.aulchenko at gmail.com> ???????(?):
> 
> Not sure if the requirement may be that "data" is there always even if it is empty. It should be specified in their how to make packages (part of r extensions guide). 
> 
> Yurii
> 
> ----------------
> Sent from mobile device, please excuse possible typos
> 
>> On 20 Dec 2013, at 03:09, noreply at r-forge.r-project.org wrote:
>> 
>> Author: maksim
>> Date: 2013-12-20 04:09:34 +0100 (Fri, 20 Dec 2013)
>> New Revision: 1495
>> 
>> Removed:
>>  pkg/GenABEL/data/
>> Log:
>> Remove the directory data because all of the data from this dir is moved to a new packages called GenABEL.data.
>> 
>> _______________________________________________
>> Genabel-commits mailing list
>> Genabel-commits at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

From yurii.aulchenko at gmail.com  Sat Dec 21 10:40:01 2013
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Sat, 21 Dec 2013 10:40:01 +0100
Subject: [GenABEL-dev] CRAN package MetABEL
In-Reply-To: <52B538E7.2050904@mail.ru>
References: <21172.48479.385656.257533@fangorn.hornik.net>
 <52B538E7.2050904@mail.ru>
Message-ID: <DD6E8D75-D881-4C7A-8E0C-1E51EA2055EE@gmail.com>

Yes, indeed. Can you please do this? - let me know in case you do not want to put yourself as maintainer for some reason. 

Best,
Yurii

----------------
Sent from mobile device, please excuse possible typos

> On 21 Dec 2013, at 07:44, Maksim Struchalin <m.v.struchalin at mail.ru> wrote:
> 
> Hi Yurii,
> 
> As I understand from the email below, we should resubmit MetABEL on CRAN with updated info.
> 
> best,
> Maksim
> 
> 
> 
> -------- Original Message --------
> Subject:	CRAN package MetABEL
> Date:	Fri, 20 Dec 2013 22:57:51 +0100
> From:	Kurt Hornik <Kurt.Hornik at wu.ac.at>
> Reply-To:	Kurt.Hornik at wu.ac.at
> To:	m.v.struchalin at mail.ru
> CC:	Kurt Hornik <Kurt.Hornik at wu.ac.at>
> 
> This has
> 
>   m.struchalin at erasmusmc.nl
> 
> as maintainer address, which no longer works.
> 
> Can we pls asap have an update with a working maintainer email address?
> 
> Best
> -k
> 
> 
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From yurii.aulchenko at gmail.com  Sat Dec 21 10:48:50 2013
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Sat, 21 Dec 2013 10:48:50 +0100
Subject: [GenABEL-dev] [Genabel-commits] r1495 - pkg/GenABEL
In-Reply-To: <4004EE49-DB46-40FE-A81B-E922B588EFFC@mail.ru>
References: <20131220030937.2C4E4181085@r-forge.r-project.org>
 <5D5C971B-BABF-4A21-81F2-50EF9B90190F@gmail.com>
 <4004EE49-DB46-40FE-A81B-E922B588EFFC@mail.ru>
Message-ID: <4EB45AF1-1E08-4A32-8829-6E65D5BF8E02@gmail.com>

Ah, this is really great! Thank you!

----------------
Sent from mobile device, please excuse possible typos

> On 21 Dec 2013, at 10:36, Maksim Struchalin <m.v.struchalin at mail.ru> wrote:
> 
> R CMD check --as-cran told me delete this dir.
> 
> Maksim
> 
> Sent from my iPhone
> 
> 
> 
>> 21 ???. 2013 ?., ? 14:44, Yury Aulchenko <yurii.aulchenko at gmail.com> ???????(?):
>> 
>> Not sure if the requirement may be that "data" is there always even if it is empty. It should be specified in their how to make packages (part of r extensions guide). 
>> 
>> Yurii
>> 
>> ----------------
>> Sent from mobile device, please excuse possible typos
>> 
>>> On 20 Dec 2013, at 03:09, noreply at r-forge.r-project.org wrote:
>>> 
>>> Author: maksim
>>> Date: 2013-12-20 04:09:34 +0100 (Fri, 20 Dec 2013)
>>> New Revision: 1495
>>> 
>>> Removed:
>>> pkg/GenABEL/data/
>>> Log:
>>> Remove the directory data because all of the data from this dir is moved to a new packages called GenABEL.data.
>>> 
>>> _______________________________________________
>>> Genabel-commits mailing list
>>> Genabel-commits at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
>> _______________________________________________
>> 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 m.v.struchalin at mail.ru  Mon Dec 23 12:13:31 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Mon, 23 Dec 2013 18:13:31 +0700
Subject: [GenABEL-dev] new GenA submision
Message-ID: <52B81ADB.907@mail.ru>

Hi Yurii,

I have considered the comments on GenABEL from CRAN after the last 
submission:

1) Fixed warnings from 'clang' compiler
2) Compressed the GenABEL tutorial down to 2.3Mb.
3) Changed the tutorial.
4) About itearator: By now, I can write an R function as CRAN suggested 
but it will take some time. I propose use GenABEL's iterator for this 
submission as it was before and make all the changes later.

I did not test GenABEL on Mac and win. Could someone do it? If these 
tests will pass ok, I can submit the GenABEL.

best,
Maksim

From yurii.aulchenko at gmail.com  Mon Dec 23 12:47:05 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Mon, 23 Dec 2013 12:47:05 +0100
Subject: [GenABEL-dev] new GenA submision
In-Reply-To: <52B81ADB.907@mail.ru>
References: <52B81ADB.907@mail.ru>
Message-ID: <CAHX9t6+9zDDQcREwz4kTzoZYW_WJOoLRnsBk9r_bZ3wQCuTsOw@mail.gmail.com>

I can run Mac tests

Should I use the makedistrib... on SVN to do it?

Yurii

On Monday, December 23, 2013, Maksim Struchalin wrote:

> Hi Yurii,
>
> I have considered the comments on GenABEL from CRAN after the last
> submission:
>
> 1) Fixed warnings from 'clang' compiler
> 2) Compressed the GenABEL tutorial down to 2.3Mb.
> 3) Changed the tutorial.
> 4) About itearator: By now, I can write an R function as CRAN suggested
> but it will take some time. I propose use GenABEL's iterator for this
> submission as it was before and make all the changes later.
>
> I did not test GenABEL on Mac and win. Could someone do it? If these tests
> will pass ok, I can submit the GenABEL.
>
> best,
> Maksim
>


-- 
-----------------------------------------------------
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 m.v.struchalin at mail.ru  Mon Dec 23 13:02:28 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Mon, 23 Dec 2013 19:02:28 +0700
Subject: [GenABEL-dev] new GenA submision
In-Reply-To: <CAHX9t6+9zDDQcREwz4kTzoZYW_WJOoLRnsBk9r_bZ3wQCuTsOw@mail.gmail.com>
References: <52B81ADB.907@mail.ru>
 <CAHX9t6+9zDDQcREwz4kTzoZYW_WJOoLRnsBk9r_bZ3wQCuTsOw@mail.gmail.com>
Message-ID: <52B82654.80105@mail.ru>

Yes. Just run the 'GenABEL-general/scripts/makedistrib_GenABEL.sh' 
script from any dir. It will make a 'GenABEL_version_for_submission' 
directory, download and build everything there. The GenABEL distributive 
will be in 'GenABEL_version_for_submission/GenABEL_DISTRIBUTIVE_IS_HERE' 
dir. After the script is done, plz, check out the file 
GenABEL_version_for_submission/GenABEL.Rcheck/00check.log for possible 
WARNINGs NOTEs.

thanks,
Maksim

On 23/12/2013 18:47, Yurii Aulchenko wrote:
> I can run Mac tests
>
> Should I use the makedistrib... on SVN to do it?
>
> Yurii
>
> On Monday, December 23, 2013, Maksim Struchalin wrote:
>
>     Hi Yurii,
>
>     I have considered the comments on GenABEL from CRAN after the last
>     submission:
>
>     1) Fixed warnings from 'clang' compiler
>     2) Compressed the GenABEL tutorial down to 2.3Mb.
>     3) Changed the tutorial.
>     4) About itearator: By now, I can write an R function as CRAN
>     suggested but it will take some time. I propose use GenABEL's
>     iterator for this submission as it was before and make all the
>     changes later.
>
>     I did not test GenABEL on Mac and win. Could someone do it? If
>     these tests will pass ok, I can submit the GenABEL.
>
>     best,
>     Maksim
>
>
>
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
>
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter 
> <http://twitter.com/YuriiAulchenko> ] [ Blog 
> <http://yurii-aulchenko.blogspot.nl/> ]
>

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From yurii.aulchenko at gmail.com  Mon Dec 23 19:22:23 2013
From: yurii.aulchenko at gmail.com (Yury Aulchenko)
Date: Mon, 23 Dec 2013 19:22:23 +0100
Subject: [GenABEL-dev] new GenA submision
In-Reply-To: <52B82654.80105@mail.ru>
References: <52B81ADB.907@mail.ru>
 <CAHX9t6+9zDDQcREwz4kTzoZYW_WJOoLRnsBk9r_bZ3wQCuTsOw@mail.gmail.com>
 <52B82654.80105@mail.ru>
Message-ID: <E0F5DA37-1050-4D56-B779-63452476CA3E@gmail.com>

Done. I got

* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ?GenABEL_1.8-0.tar.gz?

The distributive of GenABEL is in GenABEL_version_for_submission/GenABEL_DISTRIBUTIVE_IS_HERE directory. Check out that there were no errors/warnings during running this script.
GenABEL building DONE!

The NOTE was

* checking foreign function calls ... NOTE
Foreign function call with ?~@~XPACKAGE?~@~Y argument in a different package:
  .Call("iterator", ..., PACKAGE = "DatABEL")
See the chapter ?~@~XSystem and foreign language interfaces?~@~Y of the
?~@~XWriting R Extensions?~@~Y manual.



On Dec 23, 2013, at 13:02 PM, Maksim Struchalin <m.v.struchalin at mail.ru> wrote:

> Yes. Just run the 'GenABEL-general/scripts/makedistrib_GenABEL.sh' script from any dir. It will make a 'GenABEL_version_for_submission' directory, download and build everything there. The GenABEL distributive will be in 'GenABEL_version_for_submission/GenABEL_DISTRIBUTIVE_IS_HERE' dir. After the script is done, plz, check out the file GenABEL_version_for_submission/GenABEL.Rcheck/00check.log for possible WARNINGs NOTEs.
> 
> thanks,
> Maksim
> 
> On 23/12/2013 18:47, Yurii Aulchenko wrote:
>> I can run Mac tests
>> 
>> Should I use the makedistrib... on SVN to do it?
>> 
>> Yurii
>> 
>> On Monday, December 23, 2013, Maksim Struchalin wrote:
>> Hi Yurii,
>> 
>> I have considered the comments on GenABEL from CRAN after the last submission:
>> 
>> 1) Fixed warnings from 'clang' compiler
>> 2) Compressed the GenABEL tutorial down to 2.3Mb.
>> 3) Changed the tutorial.
>> 4) About itearator: By now, I can write an R function as CRAN suggested but it will take some time. I propose use GenABEL's iterator for this submission as it was before and make all the changes later.
>> 
>> I did not test GenABEL on Mac and win. Could someone do it? If these tests will pass ok, I can submit the GenABEL.
>> 
>> best,
>> Maksim
>> 
>> 
>> -- 
>> -----------------------------------------------------
>> Yurii S. Aulchenko
>> 
>> [ LinkedIn ] [ Twitter ] [ Blog ]
>> 
> 

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From m.v.struchalin at mail.ru  Thu Dec 26 09:15:37 2013
From: m.v.struchalin at mail.ru (Maksim Struchalin)
Date: Thu, 26 Dec 2013 15:15:37 +0700
Subject: [GenABEL-dev] GenABEL.data and GenABEl packages on CRAN
Message-ID: <52BBE5A9.7070004@mail.ru>

Dear CRAN maintainer,

Please find two packages uploaded on ftp://cran.r-project.org/incoming/: 
GenABEL.data_1.0.0.tar.gz and GenABEL_1.8-0.tar.gz. This is the second 
attempt to upload these packages after the two week ago try when the 
packages did not comply with the CRAN policy. The current uploaded 
versions should comply with CRAN policy.

best regards,
Maksim

From yurii.aulchenko at gmail.com  Fri Dec 27 14:59:47 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 27 Dec 2013 14:59:47 +0100
Subject: [GenABEL-dev] GenABEL 1.8-0
Message-ID: <CAHX9t6J_KB4uz6EGom3-w50zaDBbrHypejNMj3S5UtbdmveJ2A@mail.gmail.com>

Good news just before the New Year: GenABEL 1.8-0 and GenABEL.data got
accepted to CRAN! - thanks to a lot of work by Maksim! From previous
experience, we may get some further comments from Win and Mac maintainers
(but may be not; also, we did checks for at least Mac).

Anyways, I hope soon we could announce this much updated version.  Maksim,
would you like to come up with a draft of news/advertisement item for the
genabel.org (in style with what we did before for the new versions)?

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  Fri Dec 27 22:07:28 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 27 Dec 2013 22:07:28 +0100
Subject: [GenABEL-dev] Jenkins upgraded
Message-ID: <52BDEC10.2020800@karssen.org>

Dear list,

I've moved Jenkins to a separate virtual machine (still on my home
server) as discussed earlier. This makes it easier to update software to
the latest versions (the previous VM was running on Ubuntu 12.04 LTS,
which is more conservative).
In the coming days I will try to incorporate clang checks and maybe R
CMD check runs as well.
The url has not changed: http://jenkins.genabel.org.

Let me know if you have any questions or suggestions. I hope everyone
keeps an eye on Jenkins so we can keep on improving our code in terms of
stability, maintainability and ease of deployment!


Enjoy the holidays,

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

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From lennart at karssen.org  Sat Dec 28 12:39:39 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Sat, 28 Dec 2013 12:39:39 +0100
Subject: [GenABEL-dev] GenABEL 1.8-0
In-Reply-To: <CAHX9t6J_KB4uz6EGom3-w50zaDBbrHypejNMj3S5UtbdmveJ2A@mail.gmail.com>
References: <CAHX9t6J_KB4uz6EGom3-w50zaDBbrHypejNMj3S5UtbdmveJ2A@mail.gmail.com>
Message-ID: <52BEB87B.2080707@karssen.org>

Indeed good news! Let's hope it gets accepted without problems.
Thanks for the work so far, Maksim! By the way, I've made some small
changes to the makedistrib_GenABEL.sh script. With these changes I'm
trying to get the script to run (and give meaningful errors) on Jenkins.
Let me know if they break anything on your machine.


Best regards,

Lennart.


On 27-12-13 14:59, Yurii Aulchenko wrote:
> Good news just before the New Year: GenABEL 1.8-0 and GenABEL.data got
> accepted to CRAN! - thanks to a lot of work by Maksim! From previous
> experience, we may get some further comments from Win and Mac
> maintainers (but may be not; also, we did checks for at least Mac). 
> 
> Anyways, I hope soon we could announce this much updated version.
>  Maksim, would you like to come up with a draft of news/advertisement
> item for the genabel.org <http://genabel.org> (in style with what we did
> before for the new versions)?
> 
> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From lennart at karssen.org  Sat Dec 28 12:46:39 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Sat, 28 Dec 2013 12:46:39 +0100
Subject: [GenABEL-dev] Trying to get ProbABEL packaged in Debian
In-Reply-To: <52A5BA14.2010508@karssen.org>
References: <52A5BA14.2010508@karssen.org>
Message-ID: <52BEBA1F.801@karssen.org>

Dear list,

Here's an update of my 'getting ProbABEL into Debian' project.
On 2013-12-17 the package was uploaded for inclusion into the Debian
repositories by Andreas Tille, my Debian-med mentor. After that it is a
matter of waiting for one of the ftpmasters to do a final check.
Unfortunately I got a rejection e-mail today:
 > Howdy maintainer,
 >
 > Thanks for your work so far,
 >
 > Could you please document the LGPL license from the files in
 > src\include? It'd be great to give this another run-through to
 > catch any other licenses as well. I stoped processing there.
 >
 > Let me know when it's back in NEW so that I can process it again.

I'll try to address this issue (the files in src/include are actually
copied from R; not sure how many of these we actually need) in the
coming days and will try to resubmit again. To me it doesn't look like a
big problem.


I'll keep you updated,

Lennart.

On 09-12-13 13:39, L.C. Karssen wrote:
> Dear list,
>
> Last week I applied for membership of the Debian-med team [1], this can
> be seen as a subproject (a so-called blend) of Debian which focusses on
> getting software for the fields of medicine and life sciences packaged
> into the default Debian repositories.
>
> The people in Debian-med are very helpful and I'm now in the process of
> getting ProbABEL v0.4.1 packaged according to the Debian guidelines.
> Luckily I had my Ubuntu PPA package to start from, so a lot of the
> learning had already been done. They have already packaged GenABEL
> (r-cran-genabel) [2,3], so that's a good starting point for those who
> want to package other R-base packages in the GenABEL suite.
>
> I hope to get ProbABEL accepted soon, hopefully in time so that it makes
> it into Ubuntu 14.04, which will be an LTS (long term support) release
> (Debian Import Freeze is Feb 6th 2014 [4]).
>
>
> I'll keep the list updated on progress.
>
> Lennart.
>
>
> [1] https://wiki.debian.org/DebianMed
> [2] http://packages.debian.org/search?keywords=r-cran-genabel
> [3] http://packages.qa.debian.org/r/r-cran-genabel.html
> [4] https://wiki.ubuntu.com/TrustyTahr/ReleaseSchedule
>
>
>
> _______________________________________________
> 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
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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From lennart at karssen.org  Mon Dec 30 13:53:03 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Mon, 30 Dec 2013 13:53:03 +0100
Subject: [GenABEL-dev] Trying to get ProbABEL packaged in Debian
In-Reply-To: <52BEBA1F.801@karssen.org>
References: <52A5BA14.2010508@karssen.org> <52BEBA1F.801@karssen.org>
Message-ID: <52C16CAF.7080403@karssen.org>

Dear list,

I'm happy to inform you that ProbABEL v0.4.1 has been accepted in Debian
Unstable [1]. This means that ProbABEL will be available in the next
Debian release and also in upcoming releases of Ubuntu [2], Linux mint
and other Debian derivatives.
Note that the examples have been split of in a second package called
probabel-examples.

Many thanks to the people of the Debian Med team, especially Andreas
Tille, who mentored me through the packaging process.

To announce this to our wider community I'll draft a post for
www.genabel.org later today. In the mean time, I'll work on releasing
v0.4.2 (and package that for Debian as well).


Best regards,

Lennart.

[1] http://packages.qa.debian.org/p/probabel.html
[2] https://wiki.ubuntu.com/UbuntuDevelopment/NewPackages

On 28-12-13 12:46, L.C. Karssen wrote:
> Dear list,
> 
> Here's an update of my 'getting ProbABEL into Debian' project.
> On 2013-12-17 the package was uploaded for inclusion into the Debian
> repositories by Andreas Tille, my Debian-med mentor. After that it is a
> matter of waiting for one of the ftpmasters to do a final check.
> Unfortunately I got a rejection e-mail today:
>  > Howdy maintainer,
>  >
>  > Thanks for your work so far,
>  >
>  > Could you please document the LGPL license from the files in
>  > src\include? It'd be great to give this another run-through to
>  > catch any other licenses as well. I stoped processing there.
>  >
>  > Let me know when it's back in NEW so that I can process it again.
> 
> I'll try to address this issue (the files in src/include are actually
> copied from R; not sure how many of these we actually need) in the
> coming days and will try to resubmit again. To me it doesn't look like a
> big problem.
> 
> 
> I'll keep you updated,
> 
> Lennart.
> 
> On 09-12-13 13:39, L.C. Karssen wrote:
>> Dear list,
>>
>> Last week I applied for membership of the Debian-med team [1], this can
>> be seen as a subproject (a so-called blend) of Debian which focusses on
>> getting software for the fields of medicine and life sciences packaged
>> into the default Debian repositories.
>>
>> The people in Debian-med are very helpful and I'm now in the process of
>> getting ProbABEL v0.4.1 packaged according to the Debian guidelines.
>> Luckily I had my Ubuntu PPA package to start from, so a lot of the
>> learning had already been done. They have already packaged GenABEL
>> (r-cran-genabel) [2,3], so that's a good starting point for those who
>> want to package other R-base packages in the GenABEL suite.
>>
>> I hope to get ProbABEL accepted soon, hopefully in time so that it makes
>> it into Ubuntu 14.04, which will be an LTS (long term support) release
>> (Debian Import Freeze is Feb 6th 2014 [4]).
>>
>>
>> I'll keep the list updated on progress.
>>
>> Lennart.
>>
>>
>> [1] https://wiki.debian.org/DebianMed
>> [2] http://packages.debian.org/search?keywords=r-cran-genabel
>> [3] http://packages.qa.debian.org/r/r-cran-genabel.html
>> [4] https://wiki.ubuntu.com/TrustyTahr/ReleaseSchedule
>>
>>
>>
>> _______________________________________________
>> 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
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
> 
> 
> 
> _______________________________________________
> 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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