R help - May 2009 - Checking a (new) package - examples require other package functions

I am creating an R package.  I ran R CMD check on the package, and everything
passed until it tried to run the examples.  Then, the result was:

* checking examples ... ERROR
Running examples in REEMtree-Ex.R failed.
The error most likely occurred in:
> ### * AutoCorrelationLRtest
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: AutoCorrelationLRtest
> ### Title: Test for autocorrelation in the residuals of a RE-EM tree
> ### Aliases: AutoCorrelationLRtest
> ### Keywords: htest tree models
> 
> ### ** Examples
> 
> # Estimation without autocorrelation
> simpleEMresult<-RandomEffectsTree(Y~D+t+X, data=simpleREEMdata,
random=~1|ID, simpleREEMdata$ID)
Error: couldn't find function "RandomEffectsTree"
Execution halted


The function "RandomEffectsTree" is defined in the R code for the
package.  How can I refer to other functions from the package in examples?  (I
have the "Writing R-extensions" PDF, so it would be enough to point me
to the right page, if the answer is in there and I just missed it.)

Thanks!

Rebecca

Did you try putting

library("your-package-name", char=TRUE)

at the start of the examples?

-- Tony Plate


Rebecca Sela wrote:
> I am creating an R package.  I ran R CMD check on the package, and
everything passed until it tried to run the examples.  Then, the result was:
> 
> * checking examples ... ERROR
> Running examples in REEMtree-Ex.R failed.
> The error most likely occurred in:
> 
>> ### * AutoCorrelationLRtest
>>
>> flush(stderr()); flush(stdout())
>>
>> ### Name: AutoCorrelationLRtest
>> ### Title: Test for autocorrelation in the residuals of a RE-EM tree
>> ### Aliases: AutoCorrelationLRtest
>> ### Keywords: htest tree models
>>
>> ### ** Examples
>>
>> # Estimation without autocorrelation
>> simpleEMresult<-RandomEffectsTree(Y~D+t+X, data=simpleREEMdata,
random=~1|ID, simpleREEMdata$ID)
> Error: couldn't find function "RandomEffectsTree"
> Execution halted
> 
> 
> The function "RandomEffectsTree" is defined in the R code for the
package.  How can I refer to other functions from the package in examples?  (I
have the "Writing R-extensions" PDF, so it would be enough to point me
to the right page, if the answer is in there and I just missed it.)
> 
> Thanks!
> 
> Rebecca
> 
> ______________________________________________
> 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.
>

On 13/05/2009 2:38 PM, Rebecca Sela wrote:
> I am creating an R package.  I ran R CMD check on the package, and
everything passed until it tried to run the examples.  Then, the result was:
> 
> * checking examples ... ERROR
> Running examples in REEMtree-Ex.R failed.
> The error most likely occurred in:
> 
>> ### * AutoCorrelationLRtest
>>
>> flush(stderr()); flush(stdout())
>>
>> ### Name: AutoCorrelationLRtest
>> ### Title: Test for autocorrelation in the residuals of a RE-EM tree
>> ### Aliases: AutoCorrelationLRtest
>> ### Keywords: htest tree models
>>
>> ### ** Examples
>>
>> # Estimation without autocorrelation
>> simpleEMresult<-RandomEffectsTree(Y~D+t+X, data=simpleREEMdata,
random=~1|ID, simpleREEMdata$ID)
> Error: couldn't find function "RandomEffectsTree"
> Execution halted
> 
> 
> The function "RandomEffectsTree" is defined in the R code for the
package.  How can I refer to other functions from the package in examples?  (I
have the "Writing R-extensions" PDF, so it would be enough to point me
to the right page, if the answer is in there and I just missed it.)
You should not need to do anything special to make package functions 
visible, as long as they would be visible to a normal user.  (Functions 
not exported in the NAMESPACE file won't be visible in the examples.)

Are you sure you have a function with that exact name?  It could be a 
typo somewhere, e.g. RandomEffectTree or RandomeffectsTree.

Duncan Murdoch

After adding the right functions to the NAMESPACE file, I am now getting a
different error:

Error: package/namespace load failed for 'REEMtree'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'",
libraryPkgName(package)),
       call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted

I have attached the NAMESPACE file in case that is where the problem is.  

Thanks again for your help!

Rebecca


----- Original Message -----
From: "Duncan Murdoch" <murdoch at stats.uwo.ca>
To: "Rebecca Sela" <rsela at stern.nyu.edu>
Cc: "r-help" <r-help at r-project.org>
Sent: Thursday, May 14, 2009 6:57:21 AM GMT -05:00 US/Canada Eastern
Subject: Re: [R] Checking a (new) package - examples require other package
functions

On 13/05/2009 2:38 PM, Rebecca Sela wrote:
> I am creating an R package.  I ran R CMD check on the package, and
everything passed until it tried to run the examples.  Then, the result was:
> 
> * checking examples ... ERROR
> Running examples in REEMtree-Ex.R failed.
> The error most likely occurred in:
> 
>> ### * AutoCorrelationLRtest
>>
>> flush(stderr()); flush(stdout())
>>
>> ### Name: AutoCorrelationLRtest
>> ### Title: Test for autocorrelation in the residuals of a RE-EM tree
>> ### Aliases: AutoCorrelationLRtest
>> ### Keywords: htest tree models
>>
>> ### ** Examples
>>
>> # Estimation without autocorrelation
>> simpleEMresult<-RandomEffectsTree(Y~D+t+X, data=simpleREEMdata,
random=~1|ID, simpleREEMdata$ID)
> Error: couldn't find function "RandomEffectsTree"
> Execution halted
> 
> 
> The function "RandomEffectsTree" is defined in the R code for the
package.  How can I refer to other functions from the package in examples?  (I
have the "Writing R-extensions" PDF, so it would be enough to point me
to the right page, if the answer is in there and I just missed it.)
You should not need to do anything special to make package functions 
visible, as long as they would be visible to a normal user.  (Functions 
not exported in the NAMESPACE file won't be visible in the examples.)

Are you sure you have a function with that exact name?  It could be a 
typo somewhere, e.g. RandomEffectTree or RandomeffectsTree.

Duncan Murdoch