[R] could not find function "Varcov" after upgrade of R?

Sat Sep 12 20:07:14 CEST 2009

David Freedman wrote:
> Thanks for the reminder - actually I think I've become sloppy about the 'T'
> (and the order of loading the Hmisc and Design packages), but that doesn't
> seem to be the problem.  Also, all of my packages have been updated

Note that Frank Harrell already answered that there is a Hmisc - Design 
issue which will be fixed early next week.

You had the unfortune to be too up to date and got the bug that was 
introduced very recently (and most people who answered had not so recent 
packages).

Uwe Ligges

> david
> 
> Carlos Alzola wrote:
>> Did you type library(Hmisc,T) before loading Design?
>>
>> Carlos
>>
>> --------------------------------------------------
>> From: "David Freedman" <3.14david at gmail.com>
>> Sent: Saturday, September 12, 2009 8:26 AM
>> To: <r-help at r-project.org>
>> Subject: Re: [R] could not find function "Varcov" after upgrade of R?
>>
>>> I've had the same problem with predict.Design, and have sent an email to 
>>> the
>>> maintainer of the Design package at Vanderbilt University.  I wasn't even
>>> able to run the examples given on the help page of predict.Design - I
>>> received the same error about Varcov that you did.
>>>
>>> I *think* it's a problem with the package, rather than R 2.9.2, and I
>>> hope
>>> the problem will soon be fixed.  I was able to use predict.Design with 
>>> 2.9.2
>>> until I updated the Design package a few days ago.
>>>
>>> david freedman
>>>
>>>
>>> zhu yao wrote:
>>>> I uses the Design library.
>>>>
>>>> take this example:
>>>>
>>>> library(Design)
>>>> n <- 1000
>>>> set.seed(731)
>>>> age <- 50 + 12*rnorm(n)
>>>> label(age) <- "Age"
>>>> sex <- factor(sample(c('Male','Female'), n,
>>>>               rep=TRUE, prob=c(.6, .4)))
>>>> cens <- 15*runif(n)
>>>> h <- .02*exp(.04*(age-50)+.8*(sex=='Female'))
>>>> dt <- -log(runif(n))/h
>>>> label(dt) <- 'Follow-up Time'
>>>> e <- ifelse(dt <= cens,1,0)
>>>> dt <- pmin(dt, cens)
>>>> units(dt) <- "Year"
>>>> dd <- datadist(age, sex)
>>>> options(datadist='dd')
>>>> Srv <- Surv(dt,e)
>>>>
>>>> f <- cph(Srv ~ rcs(age,4) + sex, x=TRUE, y=TRUE)
>>>> cox.zph(f, "rank")             # tests of PH
>>>> anova(f)
>>>> # Error in anova.Design(f) : could not find function "Varcov"
>>>>
>>>>
>>>>
>>>> Yao Zhu
>>>> Department of Urology
>>>> Fudan University Shanghai Cancer Center
>>>> No. 270 Dongan Road, Shanghai, China
>>>>
>>>>
>>>> 2009/9/12 Ronggui Huang <ronggui.huang at gmail.com>
>>>>
>>>>> I cannot reproduce the problem you mentioned.
>>>>>
>>>>>>  ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
>>>>>>  trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
>>>>>>   group <- gl(2,10,20, labels=c("Ctl","Trt"))
>>>>>>   weight <- c(ctl, trt)
>>>>>>   anova(lm.D9 <- lm(weight ~ group))
>>>>>> sessionInfo()
>>>>> R version 2.9.2 (2009-08-24)
>>>>> i386-pc-mingw32
>>>>>
>>>>> locale:
>>>>> LC_COLLATE=Chinese (Simplified)_People's Republic of
>>>>> China.936;LC_CTYPE=Chinese (Simplified)_People's Republic of
>>>>> China.936;LC_MONETARY=Chinese (Simplified)_People's Republic of
>>>>> China.936;LC_NUMERIC=C;LC_TIME=Chinese (Simplified)_People's Republic
>>>>> of China.936
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>
>>>>> 2009/9/12 zhu yao <mailzhuyao at gmail.com>:
>>>>>> After upgrading R to 2.9.2, I can't use the anova() fuction.
>>>>>> It says "could not find function "Varcov" ".
>>>>>> What's wrong with my computer? Help needed, thanks!
>>>>>>
>>>>>> Yao Zhu
>>>>>> Department of Urology
>>>>>> Fudan University Shanghai Cancer Center
>>>>>> No. 270 Dongan Road, Shanghai, China
>>>>>>
>>>>>>        [[alternative HTML version deleted]]
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-help at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> HUANG Ronggui, Wincent
>>>>> Doctoral Candidate
>>>>> Dept of Public and Social Administration
>>>>> City University of Hong Kong
>>>>> Home page: http://asrr.r-forge.r-project.org/rghuang.html
>>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>>
>>> -- 
>>> View this message in context: 
>>> http://www.nabble.com/could-not-find-function-%22Varcov%22-after-upgrade-of-R--tp25412881p25414017.html
>>> Sent from the R help mailing list archive at Nabble.com.
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide 
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>