[GenABEL-dev] [Genabel-commits] r1429 - pkg/GenABEL/man

[L.C. Karssen]

Dear Maksim, Yakov, others,

About coding style, please see the document on GenABEL coding standards
(work in progress) we created some time ago:
http://genabel.r-forge.r-project.org/codingstyle.html

It would be great to have uniform coding in all of the GenABEL suite.

By the way, suggestions for additions/corrections of the document are
welcome!


Lennart.



On 11/29/2013 10:20 AM, Maksim Struchalin wrote:
> Hi Yakov,
> 
> I made this change because when I run "R CMD check --as-cran ", I got a
> message:
> ______________________________________________
> * checking Rd line widths ... NOTE
> Rd file
> ‘/home/maksim/work/GenABEL_project/genabel/pkg/GenABEL.Rcheck/00_pkg_src/GenABEL/man/PGC.Rd’:
> 
> \examples lines wider than 100 characters:
> #result=PGC(data=chi2.1df,method="group_regress",p=freq,df=1, pol.d=2,
> plot=TRUE, start.corr=FALSE,n_quiantile=3)
> ______________________________________________
> 
> Here are guidlines how to write .Rd files
> (http://developer.r-project.org/Rds.html).
> If I were you, I would replace "result=PGC(d..." by "result<-PGC(d..."
> because using <- instead of = is common R rule for assignments.
> 
> It recommends to keep the line length in .Rd file not more then 65
> characters but I guess this an old rule and now the limit is 100
> characters.
> 
> best,
> Maksim
> 
> On 28/11/2013 16:38, Yury Aulchenko wrote:
>> Yakov,
>>
>> please pay attention to this commit (I know that you were changing the
>> code of the GC procedures recently)
>>
>> YA
>>
>> On Nov 28, 2013, at 05:38 AM, noreply at r-forge.r-project.org wrote:
>>
>>> Author: maksim
>>> Date: 2013-11-28 05:38:54 +0100 (Thu, 28 Nov 2013)
>>> New Revision: 1429
>>>
>>> Modified:
>>>    pkg/GenABEL/man/PGC.Rd
>>> Log:
>>> Deleteted comments because R CMD check --as-cran said that these
>>> lines are wider than 100 characters and they will be truncated in the
>>> PDF manual. This should not have any influence on the code generated
>>> from it.
>>>
>>> Modified: pkg/GenABEL/man/PGC.Rd
>>> ===================================================================
>>> --- pkg/GenABEL/man/PGC.Rd    2013-11-28 04:21:29 UTC (rev 1428)
>>> +++ pkg/GenABEL/man/PGC.Rd    2013-11-28 04:38:54 UTC (rev 1429)
>>> @@ -63,8 +63,6 @@
>>> s <- summary(ge03d2)
>>> freq <- s$Q.2
>>> result=PGC(data=chi2.1df,method="median",p=freq,df=1, pol.d=2,
>>> plot=TRUE, lmax=1.1,start.corr=FALSE)
>>> -#"group_regress" is better to use when we have more than 50K SNPs
>>> -#result=PGC(data=chi2.1df,method="group_regress",p=freq,df=1,
>>> pol.d=2, plot=TRUE, start.corr=FALSE,n_quiantile=3)
>>> }
>>> \author{
>>>    Yakov Tsepilov
>>>
>>> _______________________________________________
>>> Genabel-commits mailing list
>>> Genabel-commits at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
>>>
>> _______________________________________________
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>>
> 
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-- 
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L.C. Karssen
Utrecht
The Netherlands

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

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