[Bioc-devel] Bioconductor 3.3 release schedule

The Bioconductor 3.3 release schedule is now available: http://bioconductor.org/developers/release-schedule/ One important deadline is April 6, after which we will not accept any new packages into the release. Also, all packages must pass R CMD build and R CMD check without error by April 1,

Re: [Bioc-devel] github mirror

On Fri, Feb 19, 2016 at 12:52 PM, Dan Tenenbaum wrote: > https://github.com/Bioconductor/mirror.git I cloned out the update_remotes.sh script. Executing that results in a fatal error because the "bioc" remote has already been defined. So I edited that script to

Re: [Bioc-devel] github mirror

BTW, I did the following: git clone https://github.com/kasperdanielhansen/minfi.git cd minfi ~/dev/github/mirrors/update_remotes.sh # this is where I have cloned https://github.com/Bioconductor/mirror.git git branch -a dtenenba@loquat minfi (master)$ git branch -a devel * master release-3.0

[Bioc-devel] [Bio-dev]: how to iterate and index set of bed files ?

Dear all: I am developing my package for my projects, and I have done couple of utility function that used for parsing bed files in R. My goal is to parse and analyze multiple bed files in parallel, in ideal case, we have three sample that comes from chip-seq experiments where each has different

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" > >> write.table(iris,'data/myiris.tab') > >>

[Rd] Reading from an existing connection in compiled code

Dear all, I'd like to be able to read from an arbitrary R connection (in the sense of ?connections), which would be passed to an R function by the user and then down into some C code via .Call. The R API, in file R_ext/Connections.h, specifies a function, R_ReadConnection, which takes a pointer

Re: [Rd] R, AIX 64-bit builds - trying to understand root cause for message: "Error: Line starting 'Package: tools ...' is malformed!"

Hi Simon, I have been busy with work, but I finally got around to repackaging libiconv for AIX - in a way that both adds GNU libiconv support (libiconv.so.2 member) and is both 32 and 64 bit without breaking support for IBM iconv applications. I concur that iconv is a pain as IBM and GNU

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

Aha... Hadn't noticed that stringsAsFactors only works via as.is in read.table. Yes, the doc should probably be fixed. The code probably not -- packages loading different data sets depending on user options is an even worse idea than havíng the option in the first place... (I don't mean having