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,

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

On this topic, one way of staying abreast of conflicts as you introduce them during the evolution of a project through use of the `conflicted` library toward the top of your project, usage modelled as follows: ``` ## Force use of package prefixes for ALL conflicting function names ## lacking

Re: [Bioc-devel] IGV - a new package in preparation

Hi, > -Original Message- > From: Bioc-devel On Behalf Of > Michael Lawrence > Sent: Friday, March 09, 2018 1:49 PM > To: Paul Shannon > Cc: Gabe Becker ; bioc-devel@r-project.org > Subject: Re:

Re: [Bioc-devel] IGV - a new package in preparation

Hello, Jumping in the conversation perhaps late. If it helps the effort, below are some IGV related R functions I've used in the past to good effect communicating with IGV running on local/remote host and issuing GOTO and Save Snapshot commands. They use utils::write.socket One things that

Re: [Bioc-devel] as.list of a GRanges

Hi, Can I ask, is this change under discussion in current release or so far in Bioconductor devel only (my assumption)? > On 02/15/2018 08:37 AM, Michael Lawrence wrote: > > So is as.list() no longer supported for GRanges objects? I have found it > > useful in places. > > Very few places.

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

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

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

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

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

hange (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 <m...@stowers.org> > Cc: r-de...@stat.math.ethz.ch > Subject:

[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:

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

> -Original Message- > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of > Hervé Pagès > Sent: Monday, October 26, 2015 12:39 PM > To: Thomas Girke ; Arora, Sonali > ; bioc-devel@r-project.org > Subject: Re:

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

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 <m...@stowers.org> Cc: Duncan Murdoch <murdoch.dun...@gmail.com>; Matt Dowle <mattjdo...@gmail.com>; r-de...

[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

[Bioc-devel] 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

Re: [Bioc-devel] Adding a lengths() method to List class

Yay m- thx From: Michael Lawrence [mailto:lawrence.mich...@gene.com] Sent: Tuesday, September 29, 2015 11:16 AM To: Cook, Malcolm <m...@stowers.org> Cc: Michael Lawrence <lawrence.mich...@gene.com>; Peter Hickey <peter.hic...@gmail.com>; bioc-devel@r-project.org Subject: Re: [

Re: [Bioc-devel] Adding a lengths() method to List class

Dumb question (?) follows in line: > That is the plan. Note that we already have elementLengths() that serves the > same purpose. It was the direct inspiration for lengths(). Why have both? > > On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey > wrote: > > > The

[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

Re: [Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

Hi, https://github.com/vjcitn/biocMultiAssay/blob/master/vignettes/SEresolver.Rnw shows some modifications to [ that allow subsetting of SE by gene or pathway name Without reading the code, do you intend that SE[i,j] will , if i is provided as vector of string, will subset those rows where

Re: [Bioc-devel] Bug tracker for Bioconductor?

Great. It sounds like promoting this in http://www.bioconductor.org/developers/package-guidelines/ might be the path of least pain/most gain. The BioConductor project _could_ at some point as a service choose to host a single bug/issue tracking system which individual package developers could

Re: [Bioc-devel] Bug tracker for Bioconductor?

Martin, I'm sure you're watching this thread. Can we take it as some feedback from other developers that you requested way back in https://stat.ethz.ch/pipermail/bioc- devel/2011-October/002854.html when I wished for similar I don't really have anything constructive to

Re: [Bioc-devel] Bug tracker for Bioconductor?

Martin, I'm sure you're watching this thread. Can we take it as some feedback from other developers that you requested way back in https://stat.ethz.ch/pipermail/bioc-devel/2011-October/002854.html when I wished for similar In any case, +1, Malcolm -Original Message-

Re: [Bioc-devel] Bug tracker for Bioconductor?

your question “do we really need...”, I’d vote +2 !Malcolm From: Michael Lawrence [mailto:lawrence.mich...@gene.com] Sent: Friday, May 23, 2014 1:31 PM To: Cook, Malcolm Cc: Keith Hughitt; Nicolas Delhomme; Martin Morgan; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Bug tracker

Re: [Bioc-devel] [BioC] granges() method for GenomicRanges objects akin to ranges()...

Wondering, Is it too off the beaten track to expect `mcols-`(x,NULL) to work? hint: it does not -Original Message- From: bioc-devel-boun...@r-project.org [mailto:bioc-devel-boun...@r-project.org] On Behalf Of Hervé Pagès Sent: Monday, May 05, 2014 1:28 PM To: Kasper Daniel

Re: [Bioc-devel] [BioC] granges() method for GenomicRanges objects akin to ranges()...

On 05/05/2014 01:00 PM, Cook, Malcolm wrote: Wondering, Is it too off the beaten track to expect `mcols-`(x,NULL) args(`mcols-`) function (x, ..., value) Arguments after the ellipsis must be named: `mcols-`(x, value=NULL) Herve - Great - of course - so - does

[Bioc-devel] rJava .jpackage(RDAVIDWebService) segfaults in restored R session

Hi, I'm having trouble making a minimal reproducible example, but, pretty reliably I get the following segfault calling DAVIDWebService in a restored R session: david-DAVIDWebService$new(email=m...@stowers.org) *** caught segfault *** address 0x7f5b1bd0e000, cause 'invalid permissions'

Re: [Bioc-devel] BigWigViews

Hi, I just went through this approach in yeast, regions = gene promoters assays = H3K3ME1, H3K3ME2, H3K3ME3 ChipSeq experimental conditions: 7 recombinant knock-outs and knock-ins of different domains of different genes. two replicates So, what I first

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

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.stowers.org' .Subject: RE: [BioC] [Rd] enabling reproducible

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 -- maybe tools

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

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 .Cc: r-devel@r-project.org; bioconduc...@r

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

.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 original question further below.) . .On 13-03

[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

Re: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914)

14, 2013 6:54 AM .To: Cook, Malcolm .Cc: bioc-devel@r-project.org; zhuj...@mail.nih.gov .Subject: RE: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914) . .Dear Malcolm, . .We have reverted minor differences in the reports for submitted

Re: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914)

Fix confirmed. Thanks very much. .-Original Message- .From: datas...@ebi.ac.uk [mailto:datas...@ebi.ac.uk] .Sent: Thursday, February 14, 2013 10:04 AM .To: Cook, Malcolm .Cc: bioc-devel@r-project.org; zhuj...@mail.nih.gov .Subject: RE: [Bioc-devel] SRAdb listSRAfile returns empty

[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 version

Re: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq'

...@r-project.org] On Behalf Of Cook, Malcolm .Sent: Wednesday, February 13, 2013 5:18 PM .To: 'bioc-devel@r-project.org'; 'zhuj...@mail.nih.gov' .Subject: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' . .Hi Jack, . .Do you happen to know if EBI is refreshing

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

.Hi Tengfei, . .Yes that looks like an oversight. Thanks for reporting that! I will .extend makeTxDbPackage so that it's more accommodating of these newer .transcriptDbs. If you want to help me out, you could call saveDb() on .your gmax189 object and send me the .sqlite file that you save

[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] 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-devel@r-project.org

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

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,

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

, 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 bring it back to the list. Paul

[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