Re: [Rd] Tips for debugging: R CMD check examples
On 06/29/2010 11:56 PM, Hadley Wickham wrote: Does anyone have any suggestions for debugging the execution of examples by R CMD check? The examples work fine when I run them from a live R prompt, but I get errors when they are run by R CMD check. Not a real tip, but when it occurs I immediately check for namespace issues (which often turn out to be the origin). Things I do are - verify all packages involved have namespaces; - load all packages (i.e. put explicitly on the search path) to detect masking issues; - check all imports and exports and if relevant turn package imports into individual function imports to have a more fine-grained view. Agreed this is a very indirect way, but at times faster than trying to interpret the error message. Best, Tobias __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Tips for debugging: R CMD check examples
On Wed, Jun 30, 2010 at 3:26 AM, Hadley Wickham had...@rice.edu wrote: Hi all, Does anyone have any suggestions for debugging the execution of examples by R CMD check? The examples work fine when I run them from a live R prompt, but I get errors when they are run by R CMD check. 'R CMD check pkg' will produce a pkg.Rcheck/pkg-Ex.R file that collects the examples into a single file (and also does other things). You could try running that file interactively to see if the error is reproduced. -Deepayan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Tips for debugging: R CMD check examples
Hi, Hadley: 1. Is your memory clear when you run the examples successfully? I.e., start with rm(list=objects()), then try the examples that work interactively but fail in R CMD check. 2. Also, does R CMD check give any warnings, e.g., undefined global, in addition to the error message? If yes, fixing those might also fix the error message. The suggestions of Deepayan and Sarker are excellent, but the two things I suggests are more targeted and might work, so I'd try them first. Hope this helps. Spencer On 6/30/2010 1:05 AM, Deepayan Sarkar wrote: On Wed, Jun 30, 2010 at 3:26 AM, Hadley Wickhamhad...@rice.edu wrote: Hi all, Does anyone have any suggestions for debugging the execution of examples by R CMD check? The examples work fine when I run them from a live R prompt, but I get errors when they are run by R CMD check. 'R CMD check pkg' will produce a pkg.Rcheck/pkg-Ex.R file that collects the examples into a single file (and also does other things). You could try running that file interactively to see if the error is reproduced. -Deepayan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Spencer Graves, PE, PhD President and Chief Operating Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Tips for debugging: R CMD check examples
R CMD check produces a foo-Ex.R file where foo is the package name. You could start by sourcing that file in R --vanilla and see where it fails and also use standard debugging tools in R from there (i.e. drop into a debugger on error). I knew about the foo-Ex.R file, but unfortunately running that produced no errors. I ended up resorting to inserting print statements every few lines to narrow down the exact location of the problem, which revealed that my code assumed options(keep.source = TRUE) but during R CMD check, options(keep.source = FALSE). Hopefully this type of problem will be easier to sort out with the new pure R R CMD check in 2.11. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Tips for debugging: R CMD check examples
Not a real tip, but when it occurs I immediately check for namespace issues (which often turn out to be the origin). Things I do are I agree that namespace issues are often a problem, and are never easy to diagnose - I often find that I've forgotten to export a method definition so other code silently falls back on the default method and leads to head scratching bugs. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Tips for debugging: R CMD check examples
On Wed, 30 Jun 2010, hadley wickham wrote: R CMD check produces a foo-Ex.R file where foo is the package name. You could start by sourcing that file in R --vanilla and see where it fails and also use standard debugging tools in R from there (i.e. drop into a debugger on error). I knew about the foo-Ex.R file, but unfortunately running that produced no errors. How did you 'run' it? I suspect you source()d it, not at all the same thing. I have yet to encounter a problem which R --vanilla foo-Ex.R or perhaps env LANGUAGE=en R --vanilla --encoding=latin1 foo-Ex.R did not reproduce. I ended up resorting to inserting print statements every few lines to narrow down the exact location of the problem, which revealed that my code assumed options(keep.source = TRUE) but during R CMD check, options(keep.source = FALSE). Rather, the default (along with many others) differs in interactive use and batch running. If you had used a command like those a few lines about you would have had 'keep.source = FALSE' set. Hopefully this type of problem will be easier to sort out with the new pure R R CMD check in 2.11. Maybe (if you meant the one in R-devel, 2.12.0-to-be). But the examples are run in a sub-process just as before, so your very rare mis-assumption still needs an understanding of how R code is run. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ -- Brian D. Ripley, rip...@stats.ox.ac.uk 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
Re: [Rd] Tips for debugging: R CMD check examples
How did you 'run' it? I suspect you source()d it, not at all the same thing. I have yet to encounter a problem which R --vanilla foo-Ex.R or perhaps env LANGUAGE=en R --vanilla --encoding=latin1 foo-Ex.R did not reproduce. Thanks, that was exactly what I was looking for. I hadn't tried running it in batch mode. Rather, the default (along with many others) differs in interactive use and batch running. If you had used a command like those a few lines about you would have had 'keep.source = FALSE' set. I think the root of the problem is the way that source is written - it uses a global option in an internal branch, which is difficult to notice unless you read the source code. It seems like a good principle that global options should only affect program behaviour by modifying the function arguments. Hopefully this type of problem will be easier to sort out with the new pure R R CMD check in 2.11. Maybe (if you meant the one in R-devel, 2.12.0-to-be). But the examples are run in a sub-process just as before, so your very rare mis-assumption still needs an understanding of how R code is run. Ooops, yes, I meant 2.12.0-to-be. I was thinking it would make the problem easier for me to understand because I'm more inclined to read R code rather than perl code. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Tips for debugging: R CMD check examples
Hi all, Does anyone have any suggestions for debugging the execution of examples by R CMD check? The examples work fine when I run them from a live R prompt, but I get errors when they are run by R CMD check. Thanks, Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
