[Rd] creating a long list puts R in a state where many things stop working

Hi, After I create a long list e.g. with x <- vector(mode="list", length=3e9) many bad things start to happen e.g. some things stop working with a spurious error message: gc() # Error in gc() : # long vectors not supported yet: /home/hpages/src/R-3.3.2/src/main/memory.c:1137

Re: [Bioc-devel] Files removed from svn are not disappearing from Git mirror

Hi James, On 11/14/2016 06:38 PM, James Collins wrote: I have attempted to remove several .tar.gz files from the LOBSTAHS package directory using a series of cherry-picked commits. (I had successfully removed these .tar files a few months ago, but somehow they just reappeared in the directory

[Bioc-devel] Files removed from svn are not disappearing from Git mirror

I have attempted to remove several .tar.gz files from the LOBSTAHS package directory using a series of cherry-picked commits. (I had successfully removed these .tar files a few months ago, but somehow they just reappeared in the directory after I invoked git svn rebase during a recent attempt to

Re: [Rd] Missing objects using dump.frames for post-mortem debugging of crashed batch jobs. Bug or gap in documentation?

Martin, thanks for the good news and sorry for wasting your (and others time) by not doing my homework and query bugzilla first (lesson learned! ). I have tested the new implementation from R-devel and observe a semantic difference when playing with the parameters: # Test script 1 g <-

Re: [Bioc-devel] recent changes in ggplot2 break some packages

Hi Ramon, Diego, Thanks for bringing this to our attention. This week we'll update R to 3.3.2 on the machines building release and that will trigger re-installation of all the packages on these machines. For the devel builds, the issue will also go away when we update R, which we'll do in 4 or 5

Re: [Rd] getGraphicsEvent() alternative for cairo graphics device?

Thanks Frederick. Mark, if you have any examples to share, they would also be gratefully received. Paul On 14/11/16 14:53, frede...@ofb.net wrote: Hi Paul, OK I tried not to make the examples too fancy. Please let me know what you think. They should probably be amended to support the

Re: [Bioc-devel] recent changes in ggplot2 break some packages

Hi Diego, On Mon, 14-11-2016, at 12:25, Diego Diez wrote: > Hi Ramon, > > My experience with this issue is that it requires reinstalling the > depending packages from source (but not ggplot2 itself). Makes sense (in my machines, I just reinstalled both, for the sake of

[Rd] Potential integer overflow in 'do_mapply'

Function 'do_mapply' in mapply.c has the following fragment. for (int i = 0; i < longest; i++) { Variable 'longest' is declared as R_xlen_t. Its value can be larger than the maximum int. In the fragment, when 'longest' is larger than the maximum int, when 'i' reaches the maximum int, i++

[Rd] Read.dcf with no newline ending: gzfile drops last line

I don't know if this is a bug per se, but an undesired behavior in read.dcf. read.dcf takes a file argument and passes it to gzfile if it's a character: if (is.character(file)) { file <- gzfile(file) on.exit(close(file)) } This gzfile connection is passed to readLines

Re: [Bioc-devel] programming note: return() is a function call

Fixed in ensembldb thanks Martin! > On 14 Nov 2016, at 11:37, Martin Morgan wrote: > > An interested R-help thread (starting at > https://stat.ethz.ch/pipermail/r-help/2016-November/443123.html) points out > that return() is treated as a function by the R

Re: [Bioc-devel] recent changes in ggplot2 break some packages

Hi Ramon, My experience with this issue is that it requires reinstalling the depending packages from source (but not ggplot2 itself). Alternatively, this should be fixed (I think) once all dependent packages are rebuilt with the newest ggplot2 installed. See this related post in the ggtree

[Bioc-devel] recent changes in ggplot2 break some packages

Dear All, At least some packages (partial list in links below) are failing checks in both release and devel; the error logs for Linux, Windows, and Mac all show "Error: processing vignette 'OncoSimulR.Rmd' failed with diagnostics: [GeomTextRepel/PositionQuasirandom/etc] was built with an

[Bioc-devel] unexpected error : BiocInstaller - unable to access the index for reporitory

Hi BiocDevel: I got an error when tried to install several packages from Bioconductor (rtracklayer, SummarizedExperiments), so I removed BiocInstaller and reinstall again now error is gone. But, I got warning which previously happened when I failed to install rtracklayer packages. Because this

[Bioc-devel] programming note: return() is a function call

An interested R-help thread (starting at https://stat.ethz.ch/pipermail/r-help/2016-November/443123.html) points out that return() is treated as a function by the R parser. This has some surprising consequences when it is used without parentheses, for instance f0 = function(i) return (i

Re: [Rd] Missing objects using dump.frames for post-mortem debugging of crashed batch jobs. Bug or gap in documentation?

> nospam@altfeld-im de > on Sun, 13 Nov 2016 13:11:38 +0100 writes: > Dear R friends, to allow post-mortem debugging In my > Rscript based batch jobs I use >tryCatch( , error = function(e) { > dump.frames(to.file = TRUE) }) > to write

Re: [Rd] Memory leak with tons of closed connections

> Gábor Csárdi > on Sun, 13 Nov 2016 20:49:57 + writes: > Using dup() before fdopen() (and calling fclose() on the connection > when it is closed) indeed fixes the memory leak. > Thank you, Gábor! Yes I can confirm that this fixes the memory leak. I'm