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

[Yakov Tsepilov]

Dear Maksim, Lenart,

Thanks a lot for your notifications - I will change the code style
regarding standards a little bit later.

With kind regards, Yakov Tsepilov.



2013/11/29 L.C. Karssen <lennart at karssen.org>

> 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
> >>>
> >> _______________________________________________
> >> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20131129/62e1f204/attachment-0001.html>