Re: [Bioc-devel] tip: memory profiling using lineprof

2014-02-09 Thread Martin Morgan
On 02/09/2014 02:38 PM, Kasper Daniel Hansen wrote: Memory usage is a common bottleneck. For people interested in profiling their memory usage I want to recommend the lineprof package by Hadley Wickham which I have had great success with so far. There is some details in his 'Advanced R programm

[Bioc-devel] Help in designing class based on SummarizedExperiment

2014-02-09 Thread Peter Hickey
Hi all, Apologies up front for the rather long post. I'm designing a class to store what I call co-methylation m-tuples. These are based on a very simple tab-delimited file format. For example, here are 1-tuples (m = 1): chr pos1M U chr157691 0 1 chr159276

[Bioc-devel] tip: memory profiling using lineprof

2014-02-09 Thread Kasper Daniel Hansen
Memory usage is a common bottleneck. For people interested in profiling their memory usage I want to recommend the lineprof package by Hadley Wickham which I have had great success with so far. There is some details in his 'Advanced R programming' at http://adv-r.had.co.nz/memory.html I see thi

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

2014-02-09 Thread Kasper Daniel Hansen
Seems to work for me; I have now populated my github repo. Thanks for the help, Kasper On Sun, Feb 9, 2014 at 2:35 AM, Dan Tenenbaum wrote: > This should be fixed now. > Thanks. > Dan > > > - Original Message - > > From: "Kasper Daniel Hansen" > > To: "Dan Tenenbaum" > > Cc: bioc-dev