[GenABEL-dev] [Genabel-commits] r1137 - tutorials/GenABEL_general

[L.C. Karssen]

Dear Yurii,

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

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

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

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

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

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

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

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


Keep up the good work,

Lennart.

> 
> best wishes,
> YA
> 
> On Wed, Mar 13, 2013 at 6:35 PM, <noreply at r-forge.r-project.org
> <mailto:noreply at r-forge.r-project.org>> wrote:
> 
>     Author: yurii
>     Date: 2013-03-13 18:35:20 +0100 (Wed, 13 Mar 2013)
>     New Revision: 1137
> 
>     Added:
>        tutorials/GenABEL_general/GWA.Rnw
>        tutorials/GenABEL_general/GWAprotocol.Rnw
>        tutorials/GenABEL_general/GWAsimple.Rnw
>        tutorials/GenABEL_general/GenABEL-tutorial.Rnw
>        tutorials/GenABEL_general/ImputedDataAnalysis.Rnw
>        tutorials/GenABEL_general/Makefile
>        tutorials/GenABEL_general/QC.Rnw
>        tutorials/GenABEL_general/Sweave.sty
>        tutorials/GenABEL_general/answers.Rnw
>        tutorials/GenABEL_general/answers2.Rnw
>        tutorials/GenABEL_general/assoc.Rnw
>        tutorials/GenABEL_general/bibliography.bib
>        tutorials/GenABEL_general/dataimport.Rnw
>        tutorials/GenABEL_general/dbasing.Rnw
>        tutorials/GenABEL_general/fetchData.Rnw
>        tutorials/GenABEL_general/genetics.bst
>        tutorials/GenABEL_general/impute.Rnw
>        tutorials/GenABEL_general/internals.Rnw
>        tutorials/GenABEL_general/intro.Rnw
>        tutorials/GenABEL_general/introR.Rnw
>        tutorials/GenABEL_general/meta.Rnw
>        tutorials/GenABEL_general/myxhtml.cfg
>        tutorials/GenABEL_general/preface.Rnw
>        tutorials/GenABEL_general/probabel.Rnw
>        tutorials/GenABEL_general/reg.Rnw
>        tutorials/GenABEL_general/siman.Rnw
>        tutorials/GenABEL_general/strat.Rnw
>        tutorials/GenABEL_general/strat0.Rnw
>        tutorials/GenABEL_general/workgwaaclass.Rnw
>     Log:
>     first version of GenABEL-general tutorial
> 
> 
> 
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> genabel-devel at lists.r-forge.r-project.org
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> 

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

lennart at karssen.org
http://blog.karssen.org

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