[Rd] ":::" operator doesn't work with data object Ecdat:::Crime

  The ":::" operator doesn't work for me with "Ecdat:::Crime" on either macOS 10.15.3 or Windows 10.   A different but related issue is that "plm::Crime" says "Error: 'Crime' is not an exported object from 'namespace:plm'", even though "library(plm); data(Crime); Crime" works.  I

Re: [Bioc-devel] proper way to define an S4 method for 'plot'

We'll discuss this and other issues at the developer forum on Thursday (12pm US Eastern) https://stat.ethz.ch/pipermail/bioc-devel/2020-March/016347.html. The builds are a really big mess at the moment http://bioconductor.org/checkResults/3.11/bioc-LATEST/, with many changes in R-devel causing

[Rd] strange bahaviour of predict.lm

Hello, Below is my code: > A <- matrix(rnorm(10*3),ncol=3) > b <- runif(10) > reg <- lm(b ~ A) > A1 <- matrix(rnorm(5*3),ncol=3) > A1 <- as.data.frame(A1) > b1 <- predict(reg,A1) Warning message: 'newdata' had 5 rows but variables found have 10 rows   And instead of being an array of length 5,

[Rd] new bquote feature splice does not address a common LISP @ use case?

Dear R-devel, There is a new feature in R-devel, which explicitly refers to LISP @ operator for splicing. > The backquote function bquote() has a new argument splice to enable splicing > a computed list of values into an expression, like ,@ in LISP's backquote. Although the most upvoted SO

Re: [Rd] pipe(): input to, and output from, a single process

FWIW if you're on unix, you can use named pipes (fifos) for that: > system("mkfifo my.output") > p = pipe("sed -l s:hello:oops: > my.output", "w") > i = file("my.output", "r", blocking=FALSE, raw=TRUE) > writeLines("hello!\n", p) > flush(p) > readLines(i, 1) [1] "oops!" Cheers, Simon > On

Re: [Bioc-devel] proper way to define an S4 method for 'plot'

At least with 2020-03-16 r77987 (Mac OS) I wasn't able to reproduce this. Btw, there's no real need for an S4 method in this case. An S3 method would work just as well. On Mon, Mar 16, 2020 at 4:12 PM Henrik Bengtsson wrote: > Maybe it's related to: > > * The plot() S3 generic function is now

Re: [Bioc-devel] proper way to define an S4 method for 'plot'

Maybe it's related to: * The plot() S3 generic function is now in package base rather than package graphics, as it is reasonable to have methods that do not use the graphics package. The generic is currently re-exported from the graphics namespace to allow packages importing it from there to

[Bioc-devel] proper way to define an S4 method for 'plot'

I just updated my R and I am getting into trouble with MLInterfaces maintenance. > BiocManager::install("MLInterfaces") *Bioconductor version 3.11 (BiocManager 1.30.10), R Under development (unstable)* * (2020-03-15 r77975)* *Installing package(s) 'MLInterfaces'* *Warning: unable to access

Re: [Rd] pipe(): input to, and output from, a single process

Well, if you want blocking, you can poll with an infinite timeout. This returns if 1) there is output, 2) the process terminates, or 3) you interrupt with CTRL+C / ESC /etc. and then right after the polling, you can read the output. This still works if the process has finished already. Gabor On

Re: [Bioc-devel] Cairo error in Windows server

I have just reinstalled Cairo on our builders and tested the install on both the 64-bit and 32-bit mode. Hopefully this should clear up in tomorrows build report. Please let us know if this continues to be an issue. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer

Re: [Rd] pipe(): input to, and output from, a single process

On 13 March 2020 at 20:26, Greg Minshall wrote: | hi. i'd like to instantiate sed(1), send it some input, and retrieve | its output, all via pipes (rather than an intermediate file). | | my sense from pipe and looking at the sources (sys-unix.c) is that is | not possible. is that true? are

Re: [Rd] pipe(): input to, and output from, a single process

On Fri, 13 Mar 2020 20:26:43 +0300 Greg Minshall wrote: > my sense from pipe and looking at the sources (sys-unix.c) is that is > not possible. is that true? are there any thoughts of providing > such a facility? Pipes (including those created by popen(3), which R pipe() uses internally) are

[Bioc-devel] Cairo error in Windows server

Hello Bioc Community, The CHECK in the windows server throws an error message that is not seen in other platforms and local windows computer: Error: .onLoad failed in loadNamespace() for 'Cairo', details: call: library.dynam("Cairo", pkgname, libname) error: DLL 'Cairo' not found: maybe not

Re: [R-pkg-devel] Warning in dir.create(vd2 <- "vign_test"): 'vign_test' already exists

On 16.03.2020 00:09, Spencer Graves wrote: Hello, All:   Under Windows 10, "R CMD check sos_2.0-1.tar.gz" cloned from "https://github.com/sbgraves237/sos; ends with: * checking rebuild of vignettes outputs ...Warning in dir.create(vd2 <- "vign_test"):  'vign_test' already exists

Re: [R-pkg-devel] An invalid URLs

On 13.03.2020 12:59, Ivan Krylov wrote: On Fri, 13 Mar 2020 11:02:06 +0300 Ivan Krylov wrote: the remote server could deny requests from such automated user agents, only allowing clients that look like browsers Here is what I have been able to observe: If wait for some time, then try to

Re: [R-pkg-devel] packaging biosig for R

On 16.03.2020 10:58, Duncan Murdoch wrote: On 16/03/2020 3:00 a.m., Alois Schlögl wrote: Thanks for your response. For *nix (Linux, MacOSX), this can be achieved. For windows, currently the only way to compile libbiosig is through mingw-cross-compiler environment (MXE) [1]  or in cygwin.

Re: [R-pkg-devel] Examples for functions called by Shiny server

In general: - You need examples for exported functions. - You should test s much of the package as possible, of course. - For shiny you have code on ./inst, but there should only be code for shiny, not additional fdiunctionaliyt that should be striiped out and made availabe via functions

[Bioc-devel] Bioconductor Developers Forum - Thursday 19th March

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 19th March at 09:00 PST/ 12:00 EST / 18:00 CET We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 067 881) As part of this month's call I thought would be

Re: [Rd] pipe(): input to, and output from, a single process

I am not sure if `pipe()` works for this, but if it turns out that it does not, then you can use the processx package, e.g.: > p <- processx::process$new("sed", c("-l", "s/a/x/g"), stdin = "|", stdout = > "|") > p$write_input("foobar\n") > p$read_output() [1] "foobxr\n" The `-l` sed flag is to

Re: [R-pkg-devel] parglm: cannot reproduce error

Sorry for posting twice. I thought that the mail had not been send out but it seems like it has been: https://stat.ethz.ch/pipermail/r-package-devel/2020q1/thread.html Den man. 16. mar. 2020 kl. 12.19 skrev Benjamin Christoffersen : > > Dear Sirs, > > Recently, my parglm package was pulled of

[Rd] pipe(): input to, and output from, a single process

hi. i'd like to instantiate sed(1), send it some input, and retrieve its output, all via pipes (rather than an intermediate file). my sense from pipe and looking at the sources (sys-unix.c) is that is not possible. is that true? are there any thoughts of providing such a facility? cheers,

[R-pkg-devel] parglm: cannot reproduce error

Dear Sirs, Recently, my parglm package was pulled of CRAN because of a segfault on Solaris and an issue on the OpenBLAS additional issues test. I started by trying to reproduce the Solaris issue but failed to reproduce the error with `rhub::checkonsolaris()`. Then I tried to reproduce the

Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

If you can make the changes just to fix the error in release than nitesh is right and it would be better to do that and follow his commands he sent earlier. Get Outlook for Android From: L Rutter Sent: Sunday, March 15, 2020 11:03:42 PM

Re: [R-pkg-devel] packaging biosig for R

On 16/03/2020 3:00 a.m., Alois Schlögl wrote: Thanks for your response. For *nix (Linux, MacOSX), this can be achieved. For windows, currently the only way to compile libbiosig is through mingw-cross-compiler environment (MXE) [1]  or in cygwin. Currently, libbiosig does not compile with with

Re: [R-pkg-devel] packaging biosig for R

Thanks for your response. For *nix (Linux, MacOSX), this can be achieved. For windows, currently the only way to compile libbiosig is through mingw-cross-compiler environment (MXE) [1]  or in cygwin. Currently, libbiosig does not compile with with VC++for various reasons, and libbiosig has some