[Rd] A package that traces base functions

I'm working on a package that implements a REPL.  A typical interaction with the package might look like: > launch_REPL()REPL> 1 + 1[1] 2REPL> QDo you wish to save results? [y/n]REPL> > ygoodbye ...> This is very similar to what happens when in `browser()`: the REPL evaluates arbitrary R user

Re: [Rd] Web site for MacOSX R-devel precompiled version

[Moving to R-SIG-Mac where it belongs] The machine building 10.6 binaries has died and since it was responsible for merging the 10.9 and 10.6 binaries to the website it means neither were published. 10.9 binaries are now up. > On Sep 29, 2016, at 2:09 PM, Simon Urbanek

[Bioc-devel] TxDbs for Bioconductor 3.4

The TxDbs for Bioconductor 3.4 are built and available in the devel branch. One new package has been added (version 3.4): TxDb.Ptroglodytes.UCSC.rheMac8.refGene These packages are live tracks and have been updated (bumped to version 3.4): TxDb.Celegans.UCSC.ce11.refGene

[Rd] winbuilder down

Dear all, winbuilder is down. Given current inspection results and circumstances, I expect a downtime of *at least* 24 hours. This applies to on-demand check services, CRAN check service results and CRAN binary builds for Windows. Best, Uwe Ligges

Re: [Rd] Web site for MacOSX R-devel precompiled version

> On Sep 29, 2016, at 8:42 AM, Marc Girondot via R-devel > wrote: > > From several years, I used this site http://r.research.att.com to get a > precompiled version of macosx R-devol but the most recent version is frozen > at the 18/8 build (r 71112). > > Is there an

[Rd] Problems with sub() due to inability to set encoding of ASCII strings

I'm encountering a problem using sub() on strings in R 3.3.1 in Windows, using both RGui and RStudio. The problem happens when the starting string is ASCII, but the replacement string is UTF-8. If we create an ASCII string x1, its encoding is marked as "unknown", and doing a sub() on that string

Re: [Bioc-devel] Change in the function getHPa( ) of the hpar package

Thanks very much! It's nice to see that you've added gene symbols to the new hpaNormalTissue dataset. Best wishes, Andrea From: Laurent Gatto Sent: 29 September 2016 16:01:57 To: Rodriguez Martinez, Andrea Cc: bioc-devel@r-project.org Subject:

Re: [Bioc-devel] Change in the function getHPa( ) of the hpar package

Dear Andrea, There won't be any additional changes to the hpar package before the upcoming release. A new version of the HPA data is expected by the end of the year, but that should not lead to any changes to the interface. Best wishes, Laurent On 29 September 2016 15:24, Rodriguez Martinez,

Re: [Bioc-devel] Change in the function getHPa( ) of the hpar package

Ok! Thanks very much! Andrea From: Shepherd, Lori Sent: 29 September 2016 15:53:15 To: Rodriguez Martinez, Andrea; bioc-devel@r-project.org Subject: Re: Change in the function getHPa( ) of the hpar package Hi, Please do not

Re: [Bioc-devel] Change in the function getHPa( ) of the hpar package

Hi, Please do not write your own function. We encourage utilizing existing functionality. As long as you are using the development version of hpar, that will be the version that is used in the upcoming release. Over the next few weeks I would recommend checking that you are using/testing

Re: [Rd] Web site for MacOSX R-devel precompiled version

I've had a TODO on the list for a while to produce a daily R-devel binary build for macOS since I have some spare macOS compute cycles available. If there's sufficient interest I can copy the build setup and start generating them. I'm also a registered Apple developer so can make signed binaries

[Bioc-devel] Change in the function getHPa( ) of the hpar package

Hi, I've just noticed that the function getHPa package has recently changed in the devel branch of the package, as follows: # Old function (in the current release branch) getHpa(id, hpadata = "NormalTissue") #New function (in the current devel branch) getHpa(id, hpadata =

Re: [Bioc-devel] Package submission

It was a problem with the single package builder. We are making the necessary adjustments and rerunning any packages that did not receive build reports; You should receive results later this morning. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

Re: [Bioc-devel] Package submission

We have the same issue: got a "starting to build message" yesterday night but never got a result. It worked yesterday, so I am guessing something is up with the single package builder. Best, Kasper On Thu, Sep 29, 2016 at 4:00 AM, Lidia Chrabąszcz < chrabaszcz.li...@gmail.com> wrote: > Hi all,

Re: [Bioc-devel] unit test results not showing up for BridgeDbR?

Oh, duh! OK, thanks! Egon On Thu, Sep 29, 2016 at 2:44 PM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Looks like you forgot to bump the version. > > These are the last commits: > > > r121440 |

Re: [Bioc-devel] unit test results not showing up for BridgeDbR?

Looks like you forgot to bump the version. These are the last commits: r121440 | e.willighagen | 2016-09-27 04:58:02 -0700 (Tue, 27 Sep 2016) | 1 line Changed paths: M /trunk/madman/Rpacks/BridgeDbR/DESCRIPTION I've

[Rd] Web site for MacOSX R-devel precompiled version

From several years, I used this site http://r.research.att.com to get a precompiled version of macosx R-devol but the most recent version is frozen at the 18/8 build (r 71112). Is there an alternative (except than compile myself !) ? Thanks, Marc

[Bioc-devel] unit test results not showing up for BridgeDbR?

Hi all, I have pushed a newer version of BridgeDbR to the repository, which includes tests with 'testthat', but when looking at the package homepage [0], it does not seem the test results are being picked up... I looked at the documentation, and did not find anything that could explain it (e.g.

Re: [Bioc-devel] Git mirrors

On 09/29/2016 05:27 AM, Alejandra Gonzalez-Beltran wrote: Hi, I was wondering if the documentation about Git Mirrors [1] is up to date, and in particular, what is described as scenario 2, as I noticed that the gitsvn [2] site is down. Is still required to disable the Git-Svn bridge or given

Re: [Rd] Undocumented 'use.names' argument to c()

> Martin Maechler > on Mon, 26 Sep 2016 18:26:25 +0200 writes: > Suharto Anggono Suharto Anggono > on Mon, 26 Sep 2016 14:51:11 + writes: >> By "an argument named 'use.names' is included for concatenation",

[Bioc-devel] Git mirrors

Hi, I was wondering if the documentation about Git Mirrors [1] is up to date, and in particular, what is described as scenario 2, as I noticed that the gitsvn [2] site is down. Is still required to disable the Git-Svn bridge or given that it has been deprecated [3], disabling it is no longer

[Bioc-devel] Package submission

Hi all, I have submitted a new package, it has already been build on all platforms. I made changes to my repository and I want to start a new build. I have incremented the version twice and received a comment "Received a valid push; starting a build." but 12 hours later I still haven't got a