[Bioc-devel] (persistent) issue with rgl dependency on Windows server

Hi Dan, After submitting the newest version of flowcatchR (with the updated NEWS), I noticed that an issue with the rgl package dependency is (again/still) there. Is this a recurring bug in the build system? Will it affect somehow what happens with the upcoming release? Thanks in advance

Re: [Rd] reverse object creation

Dear Bo, I think that you are looking for dput() Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the

[Rd] reverse object creation

Dear all, this is my first message to this mailing list - please advise if it is not the right place for the subject I've been using R very intensively the last 3-4 years and one of the most tedious tasks is modification of lookup or conversion tables So far, I have not found functions that

Re: [Rd] rank(, ties.method="last")

> I ran into a problem where I actually need rank(, ties.method="last"). It > would > be great to have this feature in base and it's also simple to get (see below). > Thanks & cheers, > Marius > rank2 <- function (x, na.last = TRUE, ties.method = c("average", > "first", "last", # new "last" >

[Rd] A where() functions that does what exists() does but return the environment when object lives?

Hi, exists("foo", inherits=TRUE) check whether an object named "foo" exists, and get("foo", inherits=TRUE) retrieves it. I'm looking for a similar function to exists() that returns the environment where the object "foo" exists, iff at all. If not found, NULL is returned. Does that exist?

[Bioc-devel] Minor (impossible to trigger?) bug in assay, SummarizedExperiment0, character-method

See https://github.com/Bioconductor-mirror/SummarizedExperiment/blob/744eea36e9f8ee4daea00baa7a1d9eea68d957ca/R/SummarizedExperiment0-class.R#L210 I think it should be 'i = assayNames(x)[1]'. I say it is impossible to trigger because I don't think this method is ever called since if 'i' is

Re: [Rd] R 3.2.2 64 bit compilation error on AIX

> Vinh Nguyen > on Thu, 8 Oct 2015 20:21:32 -0700 writes: > Ahh, sorry for not googling the error message. Found > [this](http://r.789695.n4.nabble.com/Error-compiling-R-2-10-1-on-AIX-td1017862.html) > post that suggests modifying

[Bioc-devel] Bug Report - for goseq - for RefSeq Genes track - RefSeq identifiers or Entrez Gene ID ?

Hi everyone, I am using goseq to perform Gene Ontology analysis of RNA-seq data and I think I found the following bug. Since my RNA-seq data was aligned using Refseq table - so I need to supply id as "refGene" which are actually EntrezId's from goseq::supportedGeneIDs() The bug is - that

[Rd] Improvement of R_orderVector() via orderVector1()

Hi, I think R_orderVector() can be improved by calling orderVector1() if possible. In a problem we had, this gave us a run time improvement factor of 4 so my hope is that this can be included. Below is the suggested change, I'm just not 100% sure if the test "CDR(arglist) == R_NilValue" is

Re: [Rd] reverse object creation

Dear Bo, Please keep the mailing list in cc. Your function only works properly with a data.frame in which all variables are characters. dput() will preserve the structure of the object and works with all R objects. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek /

Re: [Rd] R 3.2.2 64 bit compilation error on AIX

On Oct 8, 2015 11:36 PM, "Martin Maechler" wrote: > > > Vinh Nguyen > > on Thu, 8 Oct 2015 20:21:32 -0700 writes: > > > Ahh, sorry for not googling the error message. Found > > [this](

Re: [Rd] reverse object creation

Bo, More philosophically, the dput output is more idiomatically appropriate for R. Data.frames are emphatically column-major data structures in R, by (very good) design. Best, ~G On Oct 9, 2015 3:55 AM, "Thierry Onkelinx" wrote: > Dear Bo, > > Please keep the mailing

Re: [Bioc-devel] (persistent) issue with rgl dependency on Windows server

- Original Message - > From: "Federico Marini" > To: bioc-devel@r-project.org > Cc: "Dan Tenenbaum" > Sent: Friday, October 9, 2015 1:47:32 AM > Subject: (persistent) issue with rgl dependency on Windows server > > Hi Dan, > > After

Re: [Bioc-devel] (persistent) issue with rgl dependency on Windows server

On 09.10.15 17:34, Dan Tenenbaum wrote: - Original Message - From: "Federico Marini" To: bioc-devel@r-project.org Cc: "Dan Tenenbaum" Sent: Friday, October 9, 2015 1:47:32 AM Subject: (persistent) issue with rgl dependency on Windows