Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

You need to figure out where R is installed, probably in c:\program files\R-3.4\bin If you go to that directory (you can do it with this command in a command window): cd c:\progra~1\R-3.4\bin Then start R like this: .\R.exe --vanilla Dan - Original Message - > From: "Jurat

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

Don't do this in RStudio, do it at the command line/terminal. Type in R --vanilla. You won't get the same interface as RStudio but you can see if the problem persists. Dan - Original Message - > From: "Jurat Shayidin" > To: "Kasper Daniel Hansen"

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

Dear Kasper : Thanks for your explanation. However, I opened the shell from Rstudio and type the command R --vanilla, seems it works fine, but still not sure about efficiency of using R -vanilla. I am not confident about using R commands, so is there any quick example that I can practice and

Re: [Rd] Frames in compiled functions

That's about it. The plan is to modify the interpreter to do the same so the inconsistency will go away. Code that is affected by this is making assumptions that it should not. Best, luke On Fri, 11 Nov 2016, Winston Chang wrote: It looks like the byte compiler is optimizing local() to an

Re: [Rd] Frames in compiled functions

It looks like the byte compiler is optimizing local() to an immediately-invoked function, instead of using eval() and substitute(). I don't know if that's exactly how it's implemented internally, but that's what it looks like here: compiler::enableJIT(0) fun <- function(x) {

[Rd] Frames in compiled functions

I noticed some problems that cropped in the latest versions of R-devel (2016-11-08 r71639 in my case) for one of my packages. I _think_ I have narrowed it down to the changes to what gets byte-compiled by default. The following example run illustrates the problem I'm having:

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

sorry for this simple question. why use R vanilla ? not familiar enough with this term. On Fri, Nov 11, 2016 at 5:51 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 11/11/2016 11:42 AM, Jurat Shayidin wrote: > >> I'll keep this in mind. Thanks for reminding. Could you please

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

On 11/11/2016 11:42 AM, Jurat Shayidin wrote: I'll keep this in mind. Thanks for reminding. Could you please elaborate your answer on my doubt ? Thanks On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: Please respond on the mailing list, so that others in

Re: [Bioc-devel] can't install CRAN Packages after installed devel version of R and Bioc 3.4

Thanks for reminding, I'll keep this in mind. I figured out that after clean R session, problem is solved. But how can I avoid this sort of issue and facilitate the building package ? How can make R session vanilla ? Any recommendation for configuration before start building packages ? Could you

[Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

I'll keep this in mind. Thanks for reminding. Could you please elaborate your answer on my doubt ? Thanks On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > Please respond on the mailing list, so that others in similar situations > can benefit / contribute.

Re: [Bioc-devel] can't install CRAN Packages after installed devel version of R and Bioc 3.4

On 11/11/2016 09:44 AM, Jurat Shayidin wrote: Dear BiocDevel: I ran into the issue after installed devel version of R and Bioc 3.4. Because my packages depends on some packages from CRAN repository, now I failed to installed paclages from CRAN. I don't have problem when I used released version

[Bioc-devel] can't install CRAN Packages after installed devel version of R and Bioc 3.4

Dear BiocDevel: I ran into the issue after installed devel version of R and Bioc 3.4. Because my packages depends on some packages from CRAN repository, now I failed to installed paclages from CRAN. I don't have problem when I used released version of R. Because new packages must coordinate with

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

On Fri, Nov 11, 2016 at 12:46 PM, Gergely Daróczi wrote: [...] >> I've changed the above to *print* the gc() result every 1000th >> iteration, and after 100'000 iterations, there is still no >> memory increase from the point of view of R itself. Yes, R does not know about

[Rd] .S3methods: issue in content of info data.frame

Hi, I was trying to get a list of S3 method for a given generic, along with the package in which they are defined, and I came across what looks like an issue in the data.frame returned in attribute 'info'. The column 'from' mostly gets the value "registered S3method for ..." except for visible

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

On Fri, Nov 11, 2016 at 12:08 PM, Martin Maechler wrote: >> Gergely Daróczi >> on Thu, 10 Nov 2016 16:48:12 +0100 writes: > > > Dear All, > > I'm developing an R application running inside of a Java daemon on > >

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

> Gergely Daróczi > on Thu, 10 Nov 2016 16:48:12 +0100 writes: > Dear All, > I'm developing an R application running inside of a Java daemon on > multiple threads, and interacting with the parent daemon via stdin and > stdout. > Everything