<div dir="ltr">Dear Maksim, Lenart,<div><br></div><div>Thanks a lot for your notifications - I will change the code style regarding standards a little bit later. </div><div class="gmail_extra"><div><br>With kind regards, Yakov Tsepilov.<br>
</div>
<br><br><div class="gmail_quote">2013/11/29 L.C. Karssen <span dir="ltr"><<a href="mailto:lennart@karssen.org" target="_blank">lennart@karssen.org</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Maksim, Yakov, others,<br>
<br>
About coding style, please see the document on GenABEL coding standards<br>
(work in progress) we created some time ago:<br>
<a href="http://genabel.r-forge.r-project.org/codingstyle.html" target="_blank">http://genabel.r-forge.r-project.org/codingstyle.html</a><br>
<br>
It would be great to have uniform coding in all of the GenABEL suite.<br>
<br>
By the way, suggestions for additions/corrections of the document are<br>
welcome!<br>
<br>
<br>
Lennart.<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
<br>
On 11/29/2013 10:20 AM, Maksim Struchalin wrote:<br>
> Hi Yakov,<br>
><br>
> I made this change because when I run "R CMD check --as-cran ", I got a<br>
> message:<br>
> ______________________________________________<br>
> * checking Rd line widths ... NOTE<br>
> Rd file<br>
> ‘/home/maksim/work/GenABEL_project/genabel/pkg/GenABEL.Rcheck/00_pkg_src/GenABEL/man/PGC.Rd’:<br>
><br>
> \examples lines wider than 100 characters:<br>
> #result=PGC(data=chi2.1df,method="group_regress",p=freq,df=1, pol.d=2,<br>
> plot=TRUE, start.corr=FALSE,n_quiantile=3)<br>
> ______________________________________________<br>
><br>
> Here are guidlines how to write .Rd files<br>
> (<a href="http://developer.r-project.org/Rds.html" target="_blank">http://developer.r-project.org/Rds.html</a>).<br>
> If I were you, I would replace "result=PGC(d..." by "result<-PGC(d..."<br>
> because using <- instead of = is common R rule for assignments.<br>
><br>
> It recommends to keep the line length in .Rd file not more then 65<br>
> characters but I guess this an old rule and now the limit is 100<br>
> characters.<br>
><br>
> best,<br>
> Maksim<br>
><br>
> On 28/11/2013 16:38, Yury Aulchenko wrote:<br>
>> Yakov,<br>
>><br>
>> please pay attention to this commit (I know that you were changing the<br>
>> code of the GC procedures recently)<br>
>><br>
>> YA<br>
>><br>
>> On Nov 28, 2013, at 05:38 AM, <a href="mailto:noreply@r-forge.r-project.org">noreply@r-forge.r-project.org</a> wrote:<br>
>><br>
>>> Author: maksim<br>
>>> Date: 2013-11-28 05:38:54 +0100 (Thu, 28 Nov 2013)<br>
>>> New Revision: 1429<br>
>>><br>
>>> Modified:<br>
>>> pkg/GenABEL/man/PGC.Rd<br>
>>> Log:<br>
>>> Deleteted comments because R CMD check --as-cran said that these<br>
>>> lines are wider than 100 characters and they will be truncated in the<br>
>>> PDF manual. This should not have any influence on the code generated<br>
>>> from it.<br>
>>><br>
>>> Modified: pkg/GenABEL/man/PGC.Rd<br>
>>> ===================================================================<br>
>>> --- pkg/GenABEL/man/PGC.Rd 2013-11-28 04:21:29 UTC (rev 1428)<br>
>>> +++ pkg/GenABEL/man/PGC.Rd 2013-11-28 04:38:54 UTC (rev 1429)<br>
>>> @@ -63,8 +63,6 @@<br>
>>> s <- summary(ge03d2)<br>
>>> freq <- s$Q.2<br>
>>> result=PGC(data=chi2.1df,method="median",p=freq,df=1, pol.d=2,<br>
>>> plot=TRUE, lmax=1.1,start.corr=FALSE)<br>
>>> -#"group_regress" is better to use when we have more than 50K SNPs<br>
>>> -#result=PGC(data=chi2.1df,method="group_regress",p=freq,df=1,<br>
>>> pol.d=2, plot=TRUE, start.corr=FALSE,n_quiantile=3)<br>
>>> }<br>
>>> \author{<br>
>>> Yakov Tsepilov<br>
>>><br>
>>> _______________________________________________<br>
>>> Genabel-commits mailing list<br>
>>> <a href="mailto:Genabel-commits@lists.r-forge.r-project.org">Genabel-commits@lists.r-forge.r-project.org</a><br>
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>>><br>
>> _______________________________________________<br>
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</div></div><span class="HOEnZb"><font color="#888888">--<br>
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*<br>
L.C. Karssen<br>
Utrecht<br>
The Netherlands<br>
<br>
<a href="mailto:lennart@karssen.org">lennart@karssen.org</a><br>
<a href="http://blog.karssen.org" target="_blank">http://blog.karssen.org</a><br>
GPG key ID: A88F554A<br>
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