[GenABEL-dev] Fwd: Your package fails CRAN checks

[Yurii S. Aulchenko]

FYI.

I think we need to address this and submit 1.6-7, which also addresses  
convert.snp.ped bug introduced specifically in 1.6-6

A bit of problem is that current devel version of R fails to build  
under my Mac OS 10.5.8 (tried yesterday). I probably can address this  
by doing checks under virtual machine running OpenSUSE

bw,
Yurii

Begin forwarded message:

> From: Peter Dalgaard <pd.mes at cbs.dk>
> Date: May 16, 2011 1:10:05 PM GMT+02:00
> To: "Chris Fraley (interim)" <fraley at stat.washington.edu>, Yurii  
> Aulchenko <i.aoultchenko at erasmusmc.nl>, Juan R González <jrgonzalez at creal.cat 
> >, Jelle Goeman <j.j.goeman at lumc.nl>
> Subject: Your package fails CRAN checks
>
> Dear maintainers of
>
> BMA GenABEL SNPassoc cherry.
>
> Your packages are currently failing the automatic CRAN checks under  
> r-devel. This is due to a change in the labeling of columns in anova  
> tables, which you have been using to extract p values.
>
> E.g. (from "cherry")
>
> anova(glm(form, data=birthwt, family=binomial), fullfit,  
> test="Chisq")$"P(>|Chi|)"[2]
>
> does no longer work because the column is now labeled "Pr(>Chi)".
>
> Since you probably don't want to break compatibility with R 2.13.x,  
> you can't just change the string. Instead, the straightforward  
> workaround would seem to be
>
> t1 <- glm(form, data=birthwt, family=binomial), fullfit, test="Chisq")
> t2 <- t1$"P(>|Chi|)"
> if (is.null(t2)) t2 <- t1$"Pr(>Chi)"
> t2[2]
>
> Or, at some loss of readability:
>
> t1[2, grep("^P.*Chi",names(t1))]
>
> Apologies for the inconvenience, but please adjust your packages and  
> resubmit to CRAN.
>
>
> -- 
> Peter Dalgaard
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
>
>

-----------------------------------------------------------
Yurii Aulchenko
Erasmus MC Rotterdam
Department of Epidemiology, Ee 2200
Postbus 2040, 3000 CA Rotterdam
The Netherlands

phone: +31107043486
fax: +31107044657