[R-pkg-devel] Run-away R CMD check ?
For Rcpp and friends, I frequently run 'R CMD check' in "batch mode" over a large set of packages. That works fine, apart from taking long :) I am using the exact same script (which is home-grown and could do with a revision, but is public at [1] -- basically just a big loop over a set of packages), and the exact same ~/.R/check.Renviron. Yet on the (bigger, better, newerm ...) machine at work I have three packages which get into a loop and never finish R CMD check. Any idea why / how and what to do? Besides skipping these three packages which I'll do next? The only commonality is that all three use testthat, but so do many other packages that test fine. Dirk [1] https://github.com/RcppCore/rcpp-logs/blob/master/scripts/runRcppDepends.r -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Run-away R CMD check ?
On 12/12/2015 9:30 AM, Dirk Eddelbuettel wrote: For Rcpp and friends, I frequently run 'R CMD check' in "batch mode" over a large set of packages. That works fine, apart from taking long :) I am using the exact same script (which is home-grown and could do with a revision, but is public at [1] -- basically just a big loop over a set of packages), and the exact same ~/.R/check.Renviron. Yet on the (bigger, better, newerm ...) machine at work I have three packages which get into a loop and never finish R CMD check. Any idea why / how and what to do? Besides skipping these three packages which I'll do next? The only commonality is that all three use testthat, but so do many other packages that test fine. Dirk [1] https://github.com/RcppCore/rcpp-logs/blob/master/scripts/runRcppDepends.r I'd put a time limit on the process so it fails eventually, and then see what the log shows just before the failure. That is, I would if I could remember how to do that. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Run-away R CMD check ?
On 12 December 2015 at 11:00, Duncan Murdoch wrote: | On 12/12/2015 9:30 AM, Dirk Eddelbuettel wrote: | > | > For Rcpp and friends, I frequently run 'R CMD check' in "batch mode" over a | > large set of packages. That works fine, apart from taking long :) | > | > I am using the exact same script (which is home-grown and could do with a | > revision, but is public at [1] -- basically just a big loop over a set of | > packages), and the exact same ~/.R/check.Renviron. | > | > Yet on the (bigger, better, newerm ...) machine at work I have three packages | > which get into a loop and never finish R CMD check. | > | > Any idea why / how and what to do? Besides skipping these three packages | > which I'll do next? | > | > The only commonality is that all three use testthat, but so do many other | > packages that test fine. | > | > Dirk | > | > [1] https://github.com/RcppCore/rcpp-logs/blob/master/scripts/runRcppDepends.r | > | | I'd put a time limit on the process so it fails eventually, and then see | what the log shows just before the failure. That is, I would if I could | remember how to do that. Yes. I thought about watcher processes too. But I haven't come up with something simple enough to implement. So for now I will just skip those three bad boys. Two of them, as I recall, are merely unreasonable and finish after a while. The other way ran all night. I'd love to know how CRAN deals with that, or understand better why it doesn't bite me on the server at home. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Run-away R CMD check ?
On 12/12/2015 11:00 AM, Duncan Murdoch wrote: On 12/12/2015 9:30 AM, Dirk Eddelbuettel wrote: For Rcpp and friends, I frequently run 'R CMD check' in "batch mode" over a large set of packages. That works fine, apart from taking long :) I am using the exact same script (which is home-grown and could do with a revision, but is public at [1] -- basically just a big loop over a set of packages), and the exact same ~/.R/check.Renviron. Yet on the (bigger, better, newerm ...) machine at work I have three packages which get into a loop and never finish R CMD check. Any idea why / how and what to do? Besides skipping these three packages which I'll do next? Two possibilities occur to me. 1/ Since I am just looking for a way to eliminate "No repository set..." and see you had the same concern once, if you actually solved that you may be getting into the "...cyclic dependency check" which notes in the code suggest may give an endless loop. I've skipped several details I don't understand. 2/ You can get a lock condition with make -j 2. For example, I have a test that can clobber a test db that another test is using, so I have to be carefully not to run these in parallel. This is easy to check, if you try without parallel make and don't have a problem then it is likely the issue. Paul Gilbert The only commonality is that all three use testthat, but so do many other packages that test fine. Dirk [1] https://github.com/RcppCore/rcpp-logs/blob/master/scripts/runRcppDepends.r I'd put a time limit on the process so it fails eventually, and then see what the log shows just before the failure. That is, I would if I could remember how to do that. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Run-away R CMD check ?
On 12 December 2015 at 11:36, Paul Gilbert wrote: | | | On 12/12/2015 11:00 AM, Duncan Murdoch wrote: | > On 12/12/2015 9:30 AM, Dirk Eddelbuettel wrote: | >> | >> For Rcpp and friends, I frequently run 'R CMD check' in "batch mode" | >> over a | >> large set of packages. That works fine, apart from taking long :) | >> | >> I am using the exact same script (which is home-grown and could do with a | >> revision, but is public at [1] -- basically just a big loop over a set of | >> packages), and the exact same ~/.R/check.Renviron. | >> | >> Yet on the (bigger, better, newerm ...) machine at work I have three | >> packages | >> which get into a loop and never finish R CMD check. | >> | >> Any idea why / how and what to do? Besides skipping these three packages | >> which I'll do next? | | Two possibilities occur to me. | 1/ Since I am just looking for a way to eliminate "No repository set..." | and see you had the same concern once, if you actually solved that you | may be getting into the "...cyclic dependency check" which notes in the | code suggest may give an endless loop. I've skipped several details I | don't understand. No, it's not that. These build fine; they 'merely' go on too long when running the tests. | 2/ You can get a lock condition with make -j 2. For example, I have a | test that can clobber a test db that another test is using, so I have to | be carefully not to run these in parallel. This is easy to check, if you | try without parallel make and don't have a problem then it is likely the | issue. That is a really good suggestion. I have so little ram on the older server here at home that don't usually set a parallel make. At work I do, and that may well be the difference. Will test and report back. Thanks! Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Run-away R CMD check ?
On 12.12.2015 17:34, Dirk Eddelbuettel wrote: On 12 December 2015 at 11:00, Duncan Murdoch wrote: | On 12/12/2015 9:30 AM, Dirk Eddelbuettel wrote: | > | > For Rcpp and friends, I frequently run 'R CMD check' in "batch mode" over a | > large set of packages. That works fine, apart from taking long :) | > | > I am using the exact same script (which is home-grown and could do with a | > revision, but is public at [1] -- basically just a big loop over a set of | > packages), and the exact same ~/.R/check.Renviron. | > | > Yet on the (bigger, better, newerm ...) machine at work I have three packages | > which get into a loop and never finish R CMD check. | > | > Any idea why / how and what to do? Besides skipping these three packages | > which I'll do next? | > | > The only commonality is that all three use testthat, but so do many other | > packages that test fine. | > | > Dirk | > | > [1] https://github.com/RcppCore/rcpp-logs/blob/master/scripts/runRcppDepends.r | > | | I'd put a time limit on the process so it fails eventually, and then see | what the log shows just before the failure. That is, I would if I could | remember how to do that. Yes. I thought about watcher processes too. But I haven't come up with something simple enough to implement. So for now I will just skip those three bad boys. Two of them, as I recall, are merely unreasonable and finish after a while. The other way ran all night. I'd love to know how CRAN deals with that, or understand better why it doesn't bite me on the server at home. CRAN has different approaches. Under Windows, I typically have an R process that controls the check process and writes out the process id and timestamp and then starts R CMD check. Another watcher simply kills the process of a given process ID including all childs if they are beyond some timeout threshold. Best, Uwe __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Run-away R CMD check ?
On 12 December 2015 at 18:57, Uwe Ligges wrote: | CRAN has different approaches. | | Under Windows, I typically have an R process that controls the check | process and writes out the process id and timestamp and then starts R | CMD check. Another watcher simply kills the process of a given process | ID including all childs if they are beyond some timeout threshold. I was leaning towards something like that. We'll see what I end up doing... Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] saving user preferences per workspace
Hello,
I wish to offer users of my BrailleR package the ability to save their
preferences, which may change by the workspace.
I've toyed with the ideas:
1.saving a file in the corresponding folder; or,
2. creating an object containing all the settings in the workspace
In either scenario, the settings get picked up next time the user loads the
package in the right workspace. Both have worked.
My problem is that I think my functions to create or modify the file or object
breach CRAN policies. I am certainly getting a NOTE for using assign(..., pos=1)
I had thought to try using the parent environment instead of explicitly using
'pos=1' but sometimes my functions are operating at the grandchild level with
respect to pos=1 and therefore fail.
I think my previous solution of writing a file in the current folder was only
getting past the CRAN checks because I was doing it with a condition of running
R in interactive mode. if(interactive()){...}
But I think it is a breach of the policies to write a file to the user's hard
drive, and sneaking around with a solution that CRAN checks can't cope with
(yet) really doesn't work for me.
Any ideas, especially pointers to other packages that do manage this task would
help me greatly.
Thanks for any help/advice,
Jonathan
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