From htl10 at users.sourceforge.net  Sat May 16 13:11:52 2015
From: htl10 at users.sourceforge.net (Hin-Tak Leung)
Date: Sat, 16 May 2015 12:11:52 +0100
Subject: [Rd] That 'make check-all' problem with the survival package
Message-ID: <1431774712.43493.BPMail_high_carrier@web172306.mail.ir2.yahoo.com>



------------------------------
On Sat, May 16, 2015 8:04 AM BST Uwe Ligges wrote:

>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.
>

The quickest fix is to add cmprsk to the recommended list , and that's is an R-devel issue.

>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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>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>



[Rd] That 'make check-all' problem with the survival package
Hin-Tak Leung