Skip to content

R-2.6.0 package check problems

6 messages · Uwe Ligges, Thomas Petzoldt, robin hankin +2 more

Original
robin hankin
# 
Hello


One of my packages, untb_1.3-2, passes R CMD check under
MacOSX (and apparently the systems used in the package check
summary page on CRAN) but fails with the following message on
R-2.6.0.tgz compiled last night on my (home) linux box.  I hasten
to add that I have never seen this error before on home-compiled
pre-releases of R-2.6.0.

Can anyone help me understand what is going on?


localhost:~/scratch%R CMD check untb_1.3-2.tgz

[snip]

creating untb-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'untb-Ex.R' failed.
The error most likely occurred in:

 > ### * butterflies
 >
 > flush(stderr()); flush(stdout())
 >
 > ### Name: butterflies
 > ### Title: abundance data for butterflies
 > ### Aliases: butterflies butterfly
 > ### Keywords: datasets
 >
 > ### ** Examples
 >
 > data(butterflies)
 > plot(butterflies, uncertainty=TRUE)
Error in log(theta) :
   could not find symbol "base" in environment of the generic function
Calls: plot ... optimal.theta -> optimize -> <Anonymous> -> f -> log
Execution halted







localhost:~/scratch%R
 > sessionInfo()
R version 2.6.0 (2007-10-03)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=e 
n_US;LC_
MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_M 
EASUREME
NT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15
 > R.version
                _
platform       i686-pc-linux-gnu
arch           i686
os             linux-gnu
system         i686, linux-gnu
status
major          2
minor          6.0
year           2007
month          10
day            03
svn rev        43063
language       R
version.string R version 2.6.0 (2007-10-03)
 >
 >







--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
  tel  023-8059-7743
Uwe Ligges
#
Robin Hankin wrote:
- I only see version 1.3-0 of your package passing the checks on CRAN.
- Do you have set R_LIBS inappropriate for your new R version or are you 
using some other binary packages compiled with a former version of R?

Uwe
Thomas Petzoldt
#
Robin Hankin wrote:
> Hello
 >
 >
 > One of my packages, untb_1.3-2, passes R CMD check under
 > MacOSX (and apparently the systems used in the package check
 > summary page on CRAN) but fails with the following message on
 > R-2.6.0.tgz compiled last night on my (home) linux box.  I hasten
 > to add that I have never seen this error before on home-compiled
 > pre-releases of R-2.6.0.
 >
 > Can anyone help me understand what is going on?

Hi Robin,

congratulations to your published article about untb ;-)

One possible explanation is that your examples use random numbers which 
may be different ones during the CRAN check. I had this problem with 
another package where a "rare random number event" lead to 
non-convergence of optim during the package check. You may use 
set.seed() as a first aid and then try to stabilize your algorithms.

BTW: untb_1.3-2.tar.gz passed the check just now on my system: R 2.7.0 
Under development (unstable), svn rev 43092 (5. Oct), i386-pc-mingw32


Thomas P.
3 days later
robin hankin
#
On 5 Oct 2007, at 15:47, Robin Hankin wrote:

            

      
      
      
    

        
thanks everyone.   My problems were solved by following Peter D's
(offline) suggestion to update all the dependencies: he noted that
log() became generic in R-2.6.0; untb depends on Brobdingnag,
the newest version of which tests for log() being generic [using
isGeneric("log")] and executes different code
depending on the answer.

crisis over!







--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
  tel  023-8059-7743

  
  


  


      

    

    

      
      

        


  

        

      Peter Dalgaard
    

    

      
      #
    

  


  

      
Robin Hankin wrote:

            

      
      
      
    

        
That (offline) must have been unintentional. I usually try to keep
discussions on the list, unless there is very good reason not to.

In this particular case I was clearly speculating (the reply starts with
"Hmm"!) and thus expecting that someone would know more than me and
might chime In.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
      #
    

  


  

      
On Tue, 9 Oct 2007, Peter Dalgaard wrote:

        

            

      
      
      
    

        
Given the number of times I have said it, I did assume that packages would 
have been re-installed for 2.6.0.  So let me say it once again ...

      **** Several packages do not work if installed under R < 2.6.0. ****