Re: [Rd] Understanding the sequence of events when calling the R dpois function

2018-06-04 Thread Clark Fitzgerald
Hi Jason, Duncan Temple Lang answered a similar question for me last year and wrote up the method here: http://dsi.ucdavis.edu/Notes/R/FindingNativeCodeInR.html Basically the C level debugger can be very helpful for figuring out what's happening. Best, Clark On Fri, Jun 1, 2018 at 4:47 AM,

[Bioc-devel] .o file information request from window system

2018-06-04 Thread Irene Zeng
Hi, Lori, Thank you for your help on Saturday. We have pushed the version 16.0 mlm4omics, there is no warnings or errors, except for this note from the window system: Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File

Re: [Rd] user macros with multi-line arguments in Rd (was Re: Rd parser throws error for user macros invoked with empty argument)

2018-06-04 Thread Tomas Kalibera
Now in R-devel, Best, Tomas On 06/01/2018 11:33 AM, Tomas Kalibera wrote: Thanks for the report, I am testing a patch that will allow multi-line arguments to user macros. Best Tomas On 05/25/2018 04:45 PM, Georgi Boshnakov wrote: While on the topic of Rd macro arguments, it seems that  if a

Re: [Rd] Byte-compilation failure on different architectures / low-memory systems

2018-06-04 Thread Tomas Kalibera
Hi Dirk, thanks for the report. Access to the test system is not necessary, the memory requirements of the byte-code compiler are usually platform-independent and specifically with this package I can reproduce they are very high. We'll have a look what we can do, certainly there should at

Re: [Rd] Byte-compilation failure on different architectures / low-memory systems

2018-06-04 Thread Hugh Parsonage
I believe a reproducible example is to simply have a very large object defined literally (i.e. through structure() etc) in ./R/ . For example, fBasics has a couple of files test-jbLM.R and test-jbTable.R which are about 500 KB. For a given amount of RAM, I believe any sufficiently large file will

[Rd] Byte-compilation failure on different architectures / low-memory systems

2018-06-04 Thread Dirk Eddelbuettel
As you may know, I look after the R package for Debian. My fellow Debianers make me follow a specific protocol -- a so-called "transition" in which all dependent packages on an identified potential breakge are rebuilt under the new (potentially breaking) change. We started adding an r-api-3.4

Re: [R-pkg-devel] r-patched error

2018-06-04 Thread Duncan Murdoch
On 04/06/2018 8:56 AM, David Hugh-Jones wrote: Thank you very much for this thoughtful advice! I am guessing that getNamespace("huxtable") would be another more self-documenting way to do this. I will make the change. Yes! I didn't see that one. Duncan Murdoch

Re: [Rd] aic() component in GLM-family objects

2018-06-04 Thread Martin Maechler
> Ben Bolker > on Sun, 3 Jun 2018 17:33:18 -0400 writes: > Is it generally known/has it been previously discussed here that the > $aic() component in GLM-family objects (e.g. results of binomial(), > poisson(), etc.) does not as implemented actually return the AIC, but

Re: [R-pkg-devel] r-patched error

2018-06-04 Thread David Hugh-Jones
Thank you very much for this thoughtful advice! I am guessing that getNamespace("huxtable") would be another more self-documenting way to do this. I will make the change. David On Mon, 4 Jun 2018 at 13:26, Duncan Murdoch wrote: > > I'd worry a little bit about your "make_getter_setters"

Re: [Rd] encoding argument of source() in 3.5.0

2018-06-04 Thread NELSON, Michael
On R 3.5.0 (Mac) The issue appears when using the default (libcurl) method and specifying the encoding Note that using method='internal' causes a segfault if used in conjunction with encoding. (and works when encoding is not set) urlR <- "http://home.versanet.de/~s-berman/source2.R; #

Re: [Bioc-devel] Git error when pushing to bioconductor

2018-06-04 Thread Turaga, Nitesh
Hi Divy, It might be possible that you did not resolve all the conflicts you have. Generally, a `git status` will show you all the conflict files which are needed to be cleaned up by the merge. When you do a clean conflict resolution, you will be able to push cleanly to git.bioconductor.org.

Re: [R-pkg-devel] r-patched error

2018-06-04 Thread Duncan Murdoch
On 04/06/2018 7:34 AM, David Hugh-Jones wrote: Hi all, Latest release of my package has an error when checked on r-patched-linux and r-devel-linux. Relevant output is shown below (from https://cran.r-project.org/web/checks/check_results_huxtable.html). It suggests that there's no method for

[R-pkg-devel] r-patched error

2018-06-04 Thread David Hugh-Jones
Hi all, Latest release of my package has an error when checked on r-patched-linux and r-devel-linux. Relevant output is shown below (from https://cran.r-project.org/web/checks/check_results_huxtable.html). It suggests that there's no method for `align<-` and `bold` for huxtable objects. In fact

Re: [Rd] encoding argument of source() in 3.5.0

2018-06-04 Thread Stephen Berman
On Mon, 4 Jun 2018 10:44:11 +0200 Martin Maechler wrote: >> peter dalgaard >> on Sun, 3 Jun 2018 23:51:24 +0200 writes: > > > Looks like this actually comes from readLines(), nothing > > to do with source() as such: In current R-devel (still): > > >> f <-

Re: [Rd] encoding argument of source() in 3.5.0

2018-06-04 Thread peter dalgaard
It's not Windows-specific, though. My example was on a Mac... I hope we can sort this out before 3.5.1. -pd > On 4 Jun 2018, at 10:44 , Martin Maechler wrote: > > So it seems as if the bug is in the file() [or url()] C code .. > But then we also have to consider Windows .. where I think most

Re: [Rd] encoding argument of source() in 3.5.0

2018-06-04 Thread Martin Maechler
> peter dalgaard > on Sun, 3 Jun 2018 23:51:24 +0200 writes: > Looks like this actually comes from readLines(), nothing > to do with source() as such: In current R-devel (still): >> f <- file("http://home.versanet.de/~s-berman/source2.R;, encoding="UTF-8") >>