Re: [Rd] R-2.6.0 package check problems
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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.6.0 package check problems
Robin Hankin wrote: thanks everyone. My problems were solved by following Peter D's (offline) suggestion... 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. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.6.0 package check problems
On Tue, 9 Oct 2007, Peter Dalgaard wrote: Robin Hankin wrote: thanks everyone. My problems were solved by following Peter D's (offline) suggestion... 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. 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R-2.6.0 package check problems
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 day03 svn rev43063 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.6.0 package check problems
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 day03 svn rev43063 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.6.0 package check problems
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[EMAIL PROTECTED] 01062 Dresden http://tu-dresden.de/hydrobiologie/ GERMANY __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
