Re: [Bioc-devel] inconsistent results from applyPileups and pileLettersAt

support site, > https://support.bioconductor.org. > > Jim > > > > On Fri, May 27, 2016 at 11:05 AM, Jesper Gådin <jesper.ga...@gmail.com> > wrote: > >> Hello everyone, >> >> I find inconsistent results from applyPileups and pileLettersAt. I hav

[Bioc-devel] inconsistent results from applyPileups and pileLettersAt

Hello everyone, I find inconsistent results from applyPileups and pileLettersAt. I have a placed a full example on github, so you can try the code with data that will reproduce what I am suspecting is a "bug". #Repo with reproducible example https://github.com/pappewaio/ExampleData #Here a

Re: [Rd] configure statement for R-devel with updated zlib in user account

Hi Paul, This might be what you are looking for. https://stat.ethz.ch/pipermail/r-devel/2015-April/070951.html Jesper On Fri, Feb 12, 2016 at 6:13 PM, Paul Johnson wrote: > I'm aware R-devel no longer includes zlib. This works find on > up-to-date Linux systems. > > On

Re: [Bioc-devel] Problem with the git mirror when committing to SVN

tinue/--skip increases. Last time it lead to me missing correctly > editing one of the files which broke my package in svn. > > Diego > > On Fri, Sep 18, 2015 at 5:13 PM, Jesper Gådin <jesper.ga...@gmail.com> > wrote: > > Hi Diego, > > > > I had the sam

[Rd] PCRE, and setting C-, LD- and CPP-FLAGS for a local r-devel installation (Part 2)

Hi! I'm sorry I could not reply on the original message ( https://stat.ethz.ch/pipermail/r-devel/2015-April/070943.html), while I wasn't a subscriber of the r-devel mail-list. But I got the ./configure to work in the end. See below for the solution. ./configure

[Rd] PCRE, and setting C-, LD- and CPP-FLAGS for a local r-devel installation

Hello, Got some at the time surprising errors some days ago when building a local r-devel installation on a cluster, with apparent outdated or missing dev versions of some files. After reading the r-devel news ( https://developer.r-project.org/blosxom.cgi/R-devel/NEWS), it turned out that Use of

Re: [Bioc-devel] SummarizedExperiment subset of 4 dimensions

) by putting dimensions on a list. That way, generic code can at least assume consistent dimensionality, even if the values are complex. I don't really have any use cases though; just seems possibly beneficial in the abstract. On Wed, Apr 1, 2015 at 1:19 AM, Jesper Gådin jesper.ga...@gmail.com wrote

[Bioc-devel] SummarizedExperiment subset of 4 dimensions

Hi! The SummarizedExperiment class is an extremely powerful container for biological data(thank you!), and all my thinking nowadays is just circling around how to stuff it as effectively as possible. Have been using 3 dimension for a long time, which has been very successful. Now I also have a

[Bioc-devel] Error in .doLoadActions(where, attach) :

Hi all, Tried to R CMD build and check the AllelicImbalance package, but got a strange NOTE during R CMD check (see below). Have checked previous versions of AllelicImbalance to try to find when the NOTE/Error got introduced, but the R CMD check on the old build files gives the same response. And

Re: [Bioc-devel] cigarToRleList fails

. Michael On Mon, Feb 17, 2014 at 1:10 AM, Jesper Gådin jesper.ga...@gmail.comwrote: Hi, Have come across a cigar-vector that is problematic to process. #load package library(GenomicAlignments) #load data (see attached file) load(2014-02-17-cigarExample.rdata) #run function

[Bioc-devel] cigarToRleList fails

Hi, Have come across a cigar-vector that is problematic to process. #load package library(GenomicAlignments) #load data (see attached file) load(2014-02-17-cigarExample.rdata) #run function cigarToRleList cigarRle - cigarToRleList(cigarExample) Error in .Call2(Rle_constructor, values,

Re: [Bioc-devel] Add OrgDb class to slot, warning during build

, Dec 28, 2012 at 8:31 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Fri, Dec 28, 2012 at 11:01 AM, Jesper Gådin jesper.ga...@gmail.com wrote: After some fighting I have now the bleeding edge of R and the bioconductor packages, and my own package was installed without any errors. Perfect