Re: [Bioc-devel] Package not being built on Windows or Mac

As I recall, there were issues building RCytoscape (and packages that depend on it) on Mac and Windows. Mostly because this requires a running instance of Cytoscape for each platform (and double that for release + devel). That used too much infrastructure so we disabled building on those

Re: [R-pkg-devel] How do you discover and learn about R packages?

Yes, great input! I appreciate Dirk also bringing up CRANberries earlier; it is such a valuable resource. I know that users are glad to access it via Twitter and its separate website. Thanks so much, Julia On Mon, Mar 20, 2017 at 3:27 PM Mark van der Loo wrote: >

Re: [R-pkg-devel] How do you discover and learn about R packages?

Julia, Just took the poll. I think cranberries would deserve mention there as well. It is the only continuous feed that reports in new pkgs and updates (that I know of). Best, Mark On Mon, Mar 20, 2017, 14:57 Julia Silge wrote: > I am contributing to a session at userR

Re: [Bioc-devel] Package not being built on Windows or Mac

It's probably because you depend on RCytoscape, which isn't supported on Windows or MacOS. And maybe this has something to do with XMLRPC? Jim On Mon, Mar 20, 2017 at 4:59 PM, Robert M. Flight wrote: > As per the exhortation to check the build status on Devel prior to

[Bioc-devel] Package not being built on Windows or Mac

As per the exhortation to check the build status on Devel prior to next version of Bioconductor release, I just noticed that my package categoryCompare has a "not supported" on Windows and Mac. Looking at release history, this seems to I have changed at Bioc v 3.4, and I'm curious why that would

[Bioc-devel] tximport fails to build on Windows

Anyone have any ideas for how to debug this? I get an error from the tximport vignette on tokay2, but I can't figure out what could be the issue: ... 1 Quitting from lines 185-189 (tximport.Rmd) Error: processing vignette 'tximport.Rmd' failed with diagnostics: cannot open the connection

[Bioc-devel] Bioconductor 3.5 release

Hi all, The release of Bioconductor 3.5 will be Tuesday, April 25. Please see the schedule for details: http://www.bioconductor.org/developers/release-schedule/ Over the next month we'll announce the key deadlines on bioc-devel. Lori sent the first one last week and it's important for anyone

Re: [Bioc-devel] Perl version issue with building Rhtslib

Hi Dinakar -- your patch didn't make it through the mailing list; can you forward it to me directly? Thanks, Martin On 03/17/2017 12:45 PM, Dinakar Kulkarni wrote: Hello, The following error was generated while attempting to install the "Rhtslib" package in R v3.3.2: /usr/bin/perl: symbol

[R-pkg-devel] How do you discover and learn about R packages?

I am contributing to a session at userR 2017 this coming July that will focus on discovering and learning about R packages. This is an increasingly important issue for R users as we all decide which of the 10,000+ packages to invest time in understanding and then use in our work. To prepare for

Re: [Rd] outer not applying a constant function

> Or is this a bad idea? I don't like the proposal. I have seen code like the following (in fact, I have written such code, where I had forgotten a function was not vectorized) where the error would have been discovered much later if outer() didn't catch it. > outer(1:3, 11:13, sum) Error

Re: [Rd] Experimental CXX_STD problem in R 3.4

On Sun, Mar 19, 2017 at 9:09 PM, Martyn Plummer wrote: > I have just added some code to ensure that the compilation fails with an > informative error message if a specific C++ standard is requested but the > corresponding compiler has not been defined. Please test this. I can

Re: [Bioc-devel] developing R package for new release

On Fri, Mar 17, 2017 at 3:45 PM, Nicholas Clark wrote: > I’m planning on adding some new features to my package (GRmetrics) before > this upcoming release and I have a few development questions. > > > 1) Which version of R should I be using? I looked at this page ( >

Re: [Rd] Experimental CXX_STD problem in R 3.4

On Sun, Mar 19, 2017 at 9:09 PM, Martyn Plummer wrote: > I have just added some code to ensure that the compilation fails with an > informative error message if a specific C++ standard is requested but the > corresponding compiler has not been defined. Please test this. Are

Re: [Rd] Fwd: Possible memory problems with mallloc when called with .C()

> void dnk_c(double *sortedFsample, unsigned long int n, unsigned long int k, double *dKol) All arguments to C functions called by .C() must be pointers. Also, R integers are C ints, not unsigned long ints. Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Mar 20, 2017 at 5:55 AM, Hristo

[R-pkg-devel] NOTE with unusual but theoretically allowed person roles

While checking a package as cran with R 3.3.2 (Windows 8 and Ubuntu 16.04), I am getting a NOTE about person roles which are unusual but theoretically allowed. In the DESCRIPTION file I set: Authors@R: c( person("First", "Person", email = "m...@mail.com", role = c("aut", "cre")),

[Bioc-devel] developing R package for new release

I’m planning on adding some new features to my package (GRmetrics) before this upcoming release and I have a few development questions. 1) Which version of R should I be using? I looked at this page (http://bioconductor.org/developers/how-to/useDevel/ ), but I was still confused as to whether

Re: [Rd] outer not applying a constant function

> Gebhardt, Albrecht > on Sun, 19 Mar 2017 09:14:56 + writes: > Hi, > the function outer can not apply a constant function as in the last line of the following example: >> xg <- 1:4 >> yg <- 1:4 >> fxyg <- outer(xg, yg,

[Rd] IO error when writing to disk

Hello, Here a small improvement for R. When you use the function write.table, if the disk is full for example, the function doesn't return an error and the file is written but truncated. It can be a source of mistakes because you can then copy the output file and think everything is ok. How to

[Rd] Fwd: Possible memory problems with mallloc when called with .C()

Hello, I'm trying to calculate a certain distance estimator for my thesis. I have a program in C that works fine when I call it with .C() in R, but since I'm dealing with big matrices like 3x2 it was getting a stack overflow. Now I have the same program but more efficeintly coded using