[R-pkg-devel] Downloading software as part of package installation

2018-09-03 Thread David B. Dahl
I would like advise and help in interpreting a part of the CRAN Repository Policy. It states, "Downloads of additional software or data as part of package installation or startup should only use secure download mechanisms (e.g., ‘https’ or ‘ftps’)." >From this, I take that it is permissible for

Re: [Rd] True length - length(unclass(x)) - without having to call unclass()?

2018-09-03 Thread Tomas Kalibera
On 09/03/2018 03:59 PM, Dénes Tóth wrote: Hi Tomas, On 09/03/2018 11:49 AM, Tomas Kalibera wrote: Please don't do this to get the underlying vector length (or to achieve anything else). Setting/deleting attributes of an R object without checking the reference count violates R semantics, which

Re: [Rd] True length - length(unclass(x)) - without having to call unclass()?

2018-09-03 Thread Dénes Tóth
Hi Tomas, On 09/03/2018 11:49 AM, Tomas Kalibera wrote: Please don't do this to get the underlying vector length (or to achieve anything else). Setting/deleting attributes of an R object without checking the reference count violates R semantics, which in turn can have unpredictable results on

Re: [Rd] compairing doubles

2018-09-03 Thread Martin Maechler
> Rui Barradas > on Mon, 3 Sep 2018 09:58:34 +0100 writes: > Hello, Watch out for operator precedence. indeed! (but not only) > all.equal(0.3, 0.1*3) > #[1] TRUE > > > `%~~%` <- function (e1, e2) all.equal(e1, e2) > > 0.3 %~~% 0.1*3 > #Error in 0.3 %~~% 0.1 * 3 : argumento

Re: [Rd] Get Logical processor count correctly whether NUMA is enabled or disabled

2018-09-03 Thread Srinivasan, Arunkumar
Tomas, Luke, thank you very much once again for patching both issues swiftly. This’ll be incredibly valuable to us once we move to 3.6.0. From: Tomas Kalibera Sent: 03 September 2018 13:07 To: r-devel@r-project.org Cc: Srinivasan, Arunkumar Subject: Re: [Rd] Get Logical processor count

Re: [Rd] True length - length(unclass(x)) - without having to call unclass()?

2018-09-03 Thread Radford Neal
Regarding the discussion of getting length(unclass(x)) without an unclassed version of x being created... There are already no copies done for length(unclass(x)) in pqR (current version of 2017-06-09 at pqR-project.org, as well as the soon-to-be-release new version). This is part of a more

Re: [Bioc-devel] ProteomicsAnnotationHubData duplicated commits

2018-09-03 Thread Rainer Johannes
Hi Laurent, I had the same problem with my ensembldb and FamAgg packages (guess the duplicated commits were introduced by my old git-svn setup). The solution for me was to iteratively do a git rebase (`git rebase -i ` with of the last commit before any duplicates) removing all duplicated

Re: [Rd] Get Logical processor count correctly whether NUMA is enabled or disabled

2018-09-03 Thread Tomas Kalibera
A summary for reference: the new detectCores() for Windows in R-devel seems to be working both for logical and physical cores on systems with >64 logical processors  (thanks to Arun for testing!). If the feature is important for anyone particularly using an older version of Windows and/or on

[Rd] Bug report: problems with saving plots on a Windows PC with 4k monitor - wrong picture size

2018-09-03 Thread Yu Lee
Steps to reproduce the problem: win.metafile("myplot.wmf",height=3,width=5) plot(1:9) dev.off() Details: When I try to save plots as WMF or EMF pictures specifying small picture size, e.g.., 3x5 inches, I get a wrong size of the WMF/EMF picture. The plot itself resides in the left upper

[Bioc-devel] Change the citation of my Bioconductor R package "BUScorrect"

2018-09-03 Thread Xiangyu Luo
Dear All, The citation information of my "BUScorrect" R package is shown as an R package version (e.g., xxx, xxx, R package version 0.99.10.), but I want it to be my original paper (e.g., xxx, xxx, JournalName). I tried to manually insert the "CITATION" file in the "inst" folder, as described in

[Bioc-devel] ProteomicsAnnotationHubData duplicated commits

2018-09-03 Thread Laurent Gatto
Dear Bioc admins, I am trying to push the latest changes from my github master branch to Bioconductor's upstreas/master (called devel below), but can't due to duplicated commits: lg390@elyacin [12:56:09] [~/dev/ProteomicsAnnotationHubData] [devel] -> % git push Counting objects: 622, done.

Re: [Rd] True length - length(unclass(x)) - without having to call unclass()?

2018-09-03 Thread Tomas Kalibera
Please don't do this to get the underlying vector length (or to achieve anything else). Setting/deleting attributes of an R object without checking the reference count violates R semantics, which in turn can have unpredictable results on R programs (essentially undebuggable segfaults now or

Re: [Rd] compairing doubles

2018-09-03 Thread Rui Barradas
Hello, Watch out for operator precedence. all.equal(0.3, 0.1*3) #[1] TRUE `%~~%` <- function (e1, e2) all.equal(e1, e2) 0.3 %~~% 0.1*3 #Error in 0.3 %~~% 0.1 * 3 : argumento não-numérico para operador binário 0.3 %~~% (0.1*3) #[1] TRUE Now with isTRUE. The problem changes a bit.

Re: [Rd] compairing doubles

2018-09-03 Thread Juan Telleria Ruiz de Aguirre
Maybe a new Operator could be defined for a fast and easy double Comparison: `~~` `~~` <- function (e1, e2) all.equal(e1, e2) And document it properly. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Bioc-devel] Git failing to push upstream to Bioc devel

2018-09-03 Thread Turaga, Nitesh
Hi Koen, It seems you have not followed the support documentation to sync the Github and Bioconductor repositories first. http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ If you follow the steps, you’d get this. /tmp ❯❯❯ git clone https://github.com/statOmics/stageR