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
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?- 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> > 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 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
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. -- Thomas Petzoldt Technische Universitaet Dresden Institut fuer Hydrobiologie thomas.petzoldt at tu-dresden.de 01062 Dresden http://tu-dresden.de/hydrobiologie/ GERMANY
On 5 Oct 2007, at 15:47, 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? > >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