From ligges at statistik.tu-dortmund.de  Sat May 16 09:04:52 2015
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Sat, 16 May 2015 09:04:52 +0200
Subject: [Rd] That 'make check-all' problem with the survival package
In-Reply-To: <1431753767.50109.YahooMailBasic@web172306.mail.ir2.yahoo.com>
References: <1431753767.50109.YahooMailBasic@web172306.mail.ir2.yahoo.com>
Message-ID: <5556EC14.9020005@statistik.tu-dortmund.de>

Not sure why this goes to R-devel. You just could have asked the 
maintainer. Terry Therneau is aware of it and promised he will fix it.

Best,
Uwe Ligges

On 16.05.2015 07:22, Hin-Tak Leung wrote:
> 'make check-all' for current R has been showing this error in the middle
> for a few months now - any thought on fixing this? I think cmprsk
> should be either included in the recommended bundle, or
> the survival vignette to not depend on it. Having 'make check-all' showing
> glaring ERROR's for a few months seems to defeat the purpose of
> doing any checking at all via 'make check-all'.
>
> FWIW, I did look at when/how the issue was introduced, but it appeared
> that svn://svn.r-forge.r-project.org/svnroot/survival is no longer being
> updated, and git://github.com/cran/survival.git only shows release jumps.
> Anyway, if first appears with survival 2.38-1 in February, and as the previous
> 2.37-7 was 13 months older, this info is of no use to anybody.
> I didn't write earlier as I thought the issue would go away at some point;
> but obviously this isn't the case after 3 months.
>
> -----------------------------------------------
>   ERROR
> Errors in running code in vignettes:
> when running code in ?compete.Rnw?
>    ...
>> temp$fstat <- as.numeric(event)
>
>> temp$msex <- with(temp, 1 * (sex == "M"))
>
>> fgfit1 <- with(temp, crr(etime, fstat, cov1 = cbind(age,
> +     msex, mspike), failcode = 2, cencode = 1, variance = TRUE))
>
>    When sourcing ?compete.R?:
> Error: could not find function "crr"
> Execution halted
>
> * checking re-building of vignette outputs ... NOTE
> Error in re-building vignettes:
>    ...
> Warning in coxph(Surv(futime, death) ~ group:age2 + sex + strata(group),  :
>    X matrix deemed to be singular; variable 23 24 25
> Loading required package: cmprsk
> Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>    there is no package called ?cmprsk?
>
> Error: processing vignette 'compete.Rnw' failed with diagnostics:
>   chunk 15 (label = finegray)
> Error in eval(expr, envir, enclos) : could not find function "crr"
> Execution halted
>
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>



[Rd] That 'make check-all' problem with the survival package
Uwe Ligges