Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-31 Thread Levi Waldron
On Wed, Feb 1, 2017 at 12:51 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > Levi triggered the problem with install.packages("lazyeval", > repos=biocinstallRepos(), which is an R-only command. Also, there have not > been any changes to the logic of biocLite() in this regard, so the

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-31 Thread Martin Morgan
On 01/31/2017 11:41 AM, Vincent Carey wrote: On Mon, Jan 30, 2017 at 11:14 PM, Martin Morgan > wrote: On 01/30/2017 09:52 AM, Levi Waldron wrote: On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan

Re: [Rd] Unexpected EOF in R-patched_2017-01-30

2017-01-31 Thread Avraham Adler
On Tue, Jan 31, 2017 at 3:30 PM, peter dalgaard wrote: > >> On 31 Jan 2017, at 18:56 , Avraham Adler wrote: >> >> Hello. >> >> When trying to unpack today's version of R-patched, > > From which source? The files from cran.r-project.org seems OK, both

Re: [Rd] Unexpected EOF in R-patched_2017-01-30

2017-01-31 Thread peter dalgaard
> On 31 Jan 2017, at 18:56 , Avraham Adler wrote: > > Hello. > > When trying to unpack today's version of R-patched, >From which source? The files from cran.r-project.org seems OK, both those in >src/base-prerelease and those from ETHZ. Also, is it not "tar -xfz"

[Rd] Unexpected EOF in R-patched_2017-01-30

2017-01-31 Thread Avraham Adler
Hello. When trying to unpack today's version of R-patched, I get the following error: C:\R>tar -xf R-patched_2017-01-30.tar.gz gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now I got the same error for

Re: [Rd] rnbinom Returns Error that says optional argument is missing

2017-01-31 Thread Joris Meys
Hi Thomas, This seems fully expected behaviour. Obviously unspecified arguments are evaluated as missing regardless of a default value. So if you set mu as a default, the function will call C_rnbinom with n, size and prob. As prob is not specified you get the error one would expect. Specifying a

Re: [Rd] RFC: tapply(*, ..., init.value = NA)

2017-01-31 Thread Martin Maechler
> Suharto Anggono Suharto Anggono via R-devel > on Tue, 31 Jan 2017 15:43:53 + writes: > Function 'aggregate.data.frame' in R has taken a different route. With drop=FALSE, the function is also applied to subset corresponding to combination of grouping

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-31 Thread Vincent Carey
On Mon, Jan 30, 2017 at 11:14 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 01/30/2017 09:52 AM, Levi Waldron wrote: > >> On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan >> wrote: >> >>> It seems like this is a local cache of the rstudio file that

Re: [Rd] RFC: tapply(*, ..., init.value = NA)

2017-01-31 Thread Suharto Anggono Suharto Anggono via R-devel
Function 'aggregate.data.frame' in R has taken a different route. With drop=FALSE, the function is also applied to subset corresponding to combination of grouping variables that doesn't appear in the data (example 2 in https://stat.ethz.ch/pipermail/r-devel/2017-January/073678.html). Because

Re: [Bioc-devel] GenomeInfoDb::fetchExtendedChromInfoFromUCSC broken again?

2017-01-31 Thread Martin Morgan
See https://stat.ethz.ch/pipermail/bioc-devel/2017-January/010396.html On 01/31/2017 07:57 AM, Christian Arnold wrote: Hi, it appears that in the newest devel version, fetchExtendedChromInfoFromUCSC is broken (again). I found an earlier post here:

[Bioc-devel] GenomeInfoDb::fetchExtendedChromInfoFromUCSC broken again?

2017-01-31 Thread Christian Arnold
Hi, it appears that in the newest devel version, fetchExtendedChromInfoFromUCSC is broken (again). I found an earlier post here: https://www.mail-archive.com/bioc-devel@r-project.org/msg06193.html, which however states that this has been fixed already in the previous version 1.11.2 of the

Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-31 Thread Cathy Lee Gierke
Thank you. Makes sense. It is *very* helpful to have R CMD check provide that. Cathy Lee Gierke *“Darkness cannot drive out darkness: only light can do that. Hate cannot drive out hate: only love can do that.” * *“The arc of the moral universe is long, but it bends towards justice.”*

Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-31 Thread Martin Maechler
> Dirk Eddelbuettel > on Mon, 30 Jan 2017 20:50:19 -0600 writes: > On 30 January 2017 at 09:58, Kevin Ushey wrote: > | The correct thing to do is indeed import any functions from any R packages > | you use, base or otherwise. The simplest fix, if you