Re: [Rd] running R with users home dirs on a shared filesystems

Another thing to avoid are having multiple processes simultaneously access single sqlite3 database stored on NFS mount. From sqlite manual: “Your best defense is to not use SQLite for files on a network filesystem” So, if you configuring RStudio Server, ma

Re: [Rd] Best practices in developing package: From a single file

> >> I am wondering what are the best practices for developing an R > >> package. I am aware of Hadley Wickham's best practice > >> documentation/book (http://r-pkgs.had.co.nz/).  I recall a couple of > >> years ago there were some tools for generating a package out of a > >> single file, such

Re: [Rd] tempdir() may be deleted during long-running R session

> Martin, > > Thanks for your work on this. > > One thing that seems to be missing from the conversation is that recreating > the temp directory will prevent future failures when R wants to write a > temp file, but the files will, of course, not be there. Any code written > assuming the co

Re: [Rd] tempdir() may be deleted during long-running R session

Chiming in late on this thread... > > | Are there any packages which > > | would break if a call to 'tempdir' automatically recreated this > > | directory? (Or would it be too much of a performance hit to have > > | 'tempdir' check and even just issue a warning when the director

Re: [Rd] should `data` respect default.stringsAsFactors()?

ctory. This > will be > run in preference to loading foo.txt (or foo.csv, etc) and can contain, like, > > dd <- read.table(foo.txt,.) > dd$cook <- factor(dd$cook, levels=c("rare","medium","well-done")) > > etc. > > -pd

Re: [Rd] should `data` respect default.stringsAsFactors()?

Joshua, > On Thu, Feb 18, 2016 at 6:03 PM, Cook, Malcolm wrote: > > Hi Peter, > > > > Sorry if I was not clear. Perhaps an example will make my point: > > > >> data(iris) > >> class(iris$Species) > > [1] "factor" > >&

Re: [Rd] should `data` respect default.stringsAsFactors()?

r should change (the behavior of data, or the documentation). , ~ Malcolm > -Original Message- > From: peter dalgaard [mailto:pda...@gmail.com] > Sent: Thursday, February 18, 2016 3:32 PM > To: Cook, Malcolm > Cc: r-de...@stat.math.ethz.ch > Subject: Re: [Rd] should `

[Rd] should `data` respect default.stringsAsFactors()?

Hiya, Probably been debated elsewhere I note that R's `data` function does not respect default.stringsAsFactors By my lights, it should, especially as it is documented to call read.table, which DOES respect. Oh, but: http://r.789695.n4.nabble.com/stringsAsFactors-FALSE-tp921891p921893.h

Re: [Rd] Error generated by .Internal(nchar) disappears when debugging

OK – definitely a red herring – thanks for following up… From: Joris Meys [mailto:jorism...@gmail.com] Sent: Wednesday, October 07, 2015 4:09 PM To: Cook, Malcolm Cc: Duncan Murdoch ; Matt Dowle ; r-de...@stat.math.ethz.ch Subject: Re: [Rd] Error generated by .Internal(nchar) disappears when

Re: [Rd] Error generated by .Internal(nchar) disappears when debugging

What other packages do you have loaded? Perhaps a BioConductor one that loads S4Vectors that announces upon load: Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' Maybe a red herring... ~Malcolm > -Original Message- > From: R-devel [mailto:

[Rd] BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround

Hello , I am not sure what the best solution is, but, in my hands using Org-mode version 8.3.2-elpa org-20150929 the reg-expt used to "cleanup extra prompts left in output" is over-aggressive and will trim session :output at lines consisting exclusively of blanks and periods such as produced w

[Rd] ShortRead::FastqStreamer and parallelization

Hi, I understand ShortRead::FastqStreamer will read chunks in parallel depending on the value of ShortRead:::.set_omp_threads I see this discussed here: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004355.html and nowhere else. It probably should be documented in ShortRead. Possibly th

Re: [Rd] problem using rJava with parallel::mclapply

Karl, I have the following notes to self that may be pertinent: options(java.parameters= ## Must preceed `library(XLConnect)` in order to prevent "Java ## requested System.exit(130), closing R." which happens when ## rJava quits R upon trapping INT (control-c), as is do

Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite

Malcolm .-Original Message- .From: Lapointe, David [mailto:david.lapoi...@umassmed.edu] .Sent: Wednesday, March 06, 2013 7:46 AM .To: Cook, Malcolm; 'Paul Gilbert' .Cc: 'r-devel@r-project.org'; 'bioconduc...@r-project.org'; 'r-discuss...@listserv.s

Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite

.To: Cook, Malcolm .Cc: 'r-devel@r-project.org'; 'bioconduc...@r-project.org'; 'r-discuss...@listserv.stowers.org' .Subject: Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite . .(More on the or

Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite

.> So, even if I wanted to go where dragons lurked, it would not be .> possible to cobble a version of biocLite that installed specific .> versions of software. .> .> Thus, I might rather consider an approach that at 'publish' time .> tarzips up a copy of the R package dependencies based on a

Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite

d when users should expect the installed library to change. Perhaps there are improvements to this Best, Malcolm .-Original Message- .From: Mike Marchywka [mailto:marchy...@hotmail.com] .Sent: Tuesday, March 05, 2013 5:24 AM .To: amac...@virginia.edu; Cook, Malcolm .C

Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite

.>>> * where do the dragons lurk .>>> .>> .>> webs of interconnected dynamically loaded libraries, identical versions of .>> R compiled with different BLAS/LAPACK options, etc. Go with the VM if you .>> really, truly, want this level of exact reproducibility. .> .> Sounds like the best bet

[Rd] enabling reproducible research & R package management & install.package.version & BiocLite

Hi, In support of reproducible research at my Institute, I seek an approach to re-creating the R environments in which an analysis has been conducted. By which I mean, the exact version of R and the exact version of all packages used in a particular R session. I am seeking comments/criticism o

[Rd] Error: 'mcMap' is not an exported object from 'namespace:parallel'

> library(parallel) > mcMap(identity,1:5) Error: could not find function "mcMap" > parallel:::mcMap(identity,1:5) [[1]] [1] 1 [[2]] [1] 2 [[3]] [1] 3 [[4]] [1] 4 [[5]] [1] 5 > parallel::mcMap(identity,1:5) Error: 'mcMap' is not an exported object from 'namespace:parallel' > sessionInfo() R ve

Re: [Rd] library(tcltk) v. SIGPIPE BUG (?!?)

Excellent, thanks for the workaround, that gets _me_ by, for now. ~Malcolm > -Original Message- > From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com] > Sent: Tuesday, December 11, 2012 2:40 PM > To: Cook, Malcolm > Cc: r-discuss...@listserv.stowers.org; r-deve

[Rd] library(tcltk) v. SIGPIPE BUG (?!?)

Hi R-devel, tcltk devel, and sqldf devel, The transcript below shows how loading the tcl/tk library in under R causes subprocesses to ignore SIGPIPE. I am including the developer of the (wonderful) sqldf package since it requires tcltk and you might like to make this dependence optional to the

Re: [Rd] bug with mapply() on an S4 object

Yes, yes, excellent and great , I am tracking this development with great interest. Am I correct that the implications for BioConductor is the tearing out of the Xapply from generics and the expecations that List and descendents would now "just work" with {t,mc,mcl,...}apply? That would be a g

Re: [Rd] test suites for packages

svUnit - is Runit compatible and provides some IDE integration and report generation and easy syntax for defining tests. I find it works a treat, and fits very nicely with my R coding/packaging style (which also uses inlinedocs for easy package creation). --Malcolm Cook On 5/17/12 9:10 AM, "Wh

Re: [Rd] loading multiple CSV files into a single data frame

Victor, I understand you as follows The first two columns of the desired combined dataframe are the last two levels of the pathname to the csv file. The columns in all the data.csv files are the same, namely, there is only one column, and it is named PERF. If so, the following

Re: [Rd] using R as SHELL in gnu make

Sent: Tuesday, September 20, 2011 8:32 AM To: Cook, Malcolm; 'help-m...@gnu.org'; 'r-devel@r-project.org' Subject: RE: using R as SHELL in gnu make Other than the RServe part, I do this all the time. It works well. Perhaps we can put together some notes off-line and then

[Rd] using R as SHELL in gnu make

I am intrigued by the possibility of using R as the SHELL in a (Gnu) makefile (instead of /bin/sh). (c.f. http://www.gnu.org/software/make/manual/make.html#Choosing-the-Shell) Well, rather, I would like the makefile's SHELL to be a command which communicated with an R process. The makefile ta