Re: [Bioc-devel] cigarToRleList fails

On 02/21/2014 02:01 PM, Michael Lawrence wrote: This function seems to solve the problem: helpwith <- function(expr) { env <- IRanges:::top_prenv(expr) expr <- substitute(expr) fun <- eval(expr[[1L]], env) fun.name <- deparse(expr[[1L]]) if (!isGeneric(fun.name

Re: [Bioc-devel] cigarToRleList fails

On Fri, Feb 21, 2014 at 2:03 PM, Gabriel Becker wrote: > Michael, > > Why not just load the help page for the function if it's not a generic > instead of throwing an error? > > Also, it's possible that it skipping missing arguments and going straight > to any is a bug in help, rather than the desi

Re: [Bioc-devel] cigarToRleList fails

Michael, Why not just load the help page for the function if it's not a generic instead of throwing an error? Also, it's possible that it skipping missing arguments and going straight to any is a bug in help, rather than the designed behavior. Perhaps we should check? ~G On Fri, Feb 21, 2014 a

Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available

- Original Message - > From: "Dan Tenenbaum" > To: "Kasper Daniel Hansen" > Cc: bioc-devel@r-project.org, "Sean Davis" > Sent: Friday, February 21, 2014 1:48:05 PM > Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available > > > > - Original Message - > > From

Re: [Bioc-devel] cigarToRleList fails

This function seems to solve the problem: helpwith <- function(expr) { env <- IRanges:::top_prenv(expr) expr <- substitute(expr) fun <- eval(expr[[1L]], env) fun.name <- deparse(expr[[1L]]) if (!isGeneric(fun.name, env)) { stop("'expr' must be a call to a generic") } args <- form

Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available

- Original Message - > From: "Kasper Daniel Hansen" > To: "Dan Tenenbaum" > Cc: "Sean Davis" , bioc-devel@r-project.org > Sent: Friday, February 21, 2014 1:26:10 PM > Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available > > > Just tried to add a completely empty git

Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available

Just tried to add a completely empty github repository. Then I got an error message saying something like "the repos needs a master branch" (sorry, I did not copy and paste), when I tried to create the github-svn bridge. I then added a temporary file to the github branch and things worked. You ma

Re: [Bioc-devel] Revising biocViews

Hi, It may be a minor note, but all of the sequencing technologies included in the list are “High Throughput” technologies. Perhaps it would help to add a category for Sequencing->Sanger (i.e. chain terminator) sequencing. This technology is still widely used to confirm putative variants or c

Re: [Bioc-devel] cigarToRleList fails

Hi Gabriel, On 02/20/2014 05:03 PM, Gabriel Becker wrote: Herve, The help is correct (though possibly a bit pedantic), there is no method for that signature. But the dispatch mechanism is able to find one because 'import(path_to_gff)' *does* work. So the help maybe is correct but that doesn'

Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available

Thanks everyone, it was worth a question. Perhaps I will figure out how to use submodules. Kasper On Fri, Feb 21, 2014 at 11:45 AM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Sean Davis" > > To: "Kasper Daniel Hansen" > > Cc: bioc-devel@r-project.org, "Dan Tenenbaum"

Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available

- Original Message - > From: "Sean Davis" > To: "Kasper Daniel Hansen" > Cc: bioc-devel@r-project.org, "Dan Tenenbaum" > Sent: Friday, February 21, 2014 7:08:21 AM > Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available > > > > I doubt this is possible given the at

Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available

I doubt this is possible given the atomic nature of a git repository. You might look at using a second git repository and including the minfi package as a git submodule of that second repository. Then, you can keep things in sync, but the minfi repository remains atomic. Sean On Feb 21, 2014 9:4

Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available

Question: is it possible to synchronize a subset of a github repos? For minfi, I would like my github to be minfi-devel /minfi OTHER SCRIPTS where OTHER SCRIPTS could be notes or test scripts I use for internal development. I then only want to synchronize the minfi-devel/minfi directory w