Re: [Rd] enhancement to R CMD check: do imported objects from multiple packages mask each other?

On 27/10/2016 11:58 AM, Hervé Pagès wrote: Hi Duncan, On 10/27/2016 05:17 AM, Duncan Murdoch wrote: [...] > Could you please post it to the bug list as an enhancement request? > Those should be persistent. > > If you have never posted to the bug list you will need to be manually > added to the

[Bioc-devel] Subversion server "hedgehog" reboot Thursday 10/27 4:00 PM Seattle time

Developers, Our sys admins will reboot the Subversion server "hedgehog.fhcrc.org" today at 4:00 PM Seattle time (7:00 PM EST, 11:00 PM UTC). There will be a brief (we hope) interruption in Subversion at that time. This reboot is necessary because of a security update to the Linux kernel. H.

Re: [R-pkg-devel] environment scoping

If I were writing a package for factoring integers I might store a vector of known primes in an environment in my package and have my factoring functions append to the list when they find some more primes. This works because there is only one set of of primes (given we stick with ordinary

Re: [Rd] BUG?: On Linux setTimeLimit() fails to propagate timeout error when it occurs (works on Windows)

On unix, unless event polling is enabled Sys.sleep just waits in a select() call (with a SIGINT handler in place) so the elapsed time isn't checked until after the select call is complete. Rstudio uses event polling, and in particular sets R_wait_usec to 1, which means event and interrupt

Re: [Rd] enhancement to R CMD check: do imported objects from multiple packages mask each other?

Hi Duncan, On 10/27/2016 05:17 AM, Duncan Murdoch wrote: [...] Could you please post it to the bug list as an enhancement request? Those should be persistent. If you have never posted to the bug list you will need to be manually added to the list of people allowed to post. In that case, write

Re: [R-pkg-devel] environment scoping

Hi Glenn, It sounds like you should create an environment for your package. If you store these objects in the global environment, they are exposed to the user and, more importantly, user could modify or delete them. If you use an environment specific to your package, you can be sure you are

[Bioc-devel] Fwd: Question about a package submission

This was accidentally taken off list. I don't have easy access to a devel system at present so cannot investigate. I did not check over the sessionInfo Yes it produces the same error: > c(GRanges(), GRanges()) Error in .Primitive("c")(, ) : could not find symbol "recursive" in environment of

Re: [Bioc-devel] Fwd: Question about a package submission

Since no one else took the bait, I'll try to answer... On 10/25/2016 06:57 PM, Ioannis Vardaxis wrote: Ioannis Vardaxis Stipendiat NTNU Sendt fra min iPhone Videresendt melding: Fra: "bioconductorseat...@gmail.com"

Re: [Bioc-devel] Question about a package submission

Hi Ioannis, Vincent, I'm in the middle of debugging a similar situation myself, which may provide a reproducible example at a package level. I am in the process of setting up AppVeyor CI for my package, and my R CMD check fails because of the same error.

Re: [Rd] enhancement to R CMD check: do imported objects from multiple packages mask each other?

On 27/10/2016 5:26 AM, Steffen Wagner wrote: Dear R-Developement Team, I want to suggest an additiol check to the R CMD check functionality. Consider the situation where the objects of more than one package are imported to the NAMESPACE of a third package, e.g. via import(foo, bar) in

Re: [Bioc-devel] Question about a package submission

Please send a reproducible example with value of sessionInfo() at time of error. On Thu, Oct 27, 2016 at 7:06 AM, Ioannis Vardaxis < ioannis.varda...@math.ntnu.no> wrote: > Hi, > > I am using the R-devel version for writing an R package. I tried to use > the c(Granges,Granges) command to merge

Re: [Bioc-devel] Question about a package submission

Hi, I am using the R-devel version for writing an R package. I tried to use the c(Granges,Granges) command to merge two Granges objects and I get the following error: Error in .Primitive("c")(, ) : could not find symbol "recursive" in environment of the generic function I also get the same

[Rd] enhancement to R CMD check: do imported objects from multiple packages mask each other?

Dear R-Developement Team, I want to suggest an additiol check to the R CMD check functionality. Consider the situation where the objects of more than one package are imported to the NAMESPACE of a third package, e.g. via import(foo, bar) in the NAMESPACE file. There might be situations

Re: [Rd] using with inside loop breaks next

(a)/(c) mostly, I think. The crux is that "next" is unhappy about being evaluated in a different environment than the containing loop. Witness this: > for (i in 1:10) {if (i == 5) evalq(next); print(i)} [1] 1 [1] 2 [1] 3 [1] 4 [1] 6 [1] 7 [1] 8 [1] 9 [1] 10 > for (i in 1:10) {if (i == 5)

Re: [Rd] improve 'package not installed' load errors?

> A side question, which I do not know the answer to, is how users get > themselves into this state. I've fallen over this a few times. It happens when you have multiple R sessions running, and R tries to update Rcpp while it is loaded in the other session. For example, I'm working on one

[Rd] using with inside loop breaks next

If I want to use with inside a loop, it seems that next gets confused. To reproduce: for(lst in list(list(a = 1), list(a = 2), list(a = 3))) { with(lst, if(a == 2) next else print(a)) } I expect 1 and 3 to be printed, but I see [1] 1 Error in eval(expr, envir, enclos) : no loop for