Re: [Bioc-devel] Use of Matrix inside SummarizedExperiment

Hi Pete, On 01/25/2016 12:32 PM, Peter Hickey wrote: The Matrix virtual class in the Matrix package seems to mostly work as an assays element in a SummarizedExperiment. This is especially useful for data that can be efficiently represented as a sparse matrix, e.g., using the dgCMatrix class.

[Bioc-devel] Fwd: Git-Svn bridge will be removed permanently on January 29, 2016

Reminder, this will happen this coming Friday, January 29th. Dan - Forwarded Message - From: "Dan Tenenbaum" To: "bioc-devel" Sent: Monday, December 28, 2015 11:08:29 AM Subject: [Bioc-devel] Git-Svn bridge will be removed permanently

Re: [Bioc-devel] C library or C package API for regular expressions

Hi Martin Dne 25.1.2016 v 13:08 Morgan, Martin napsal(a): There is discussion at http://stackoverflow.com/questions/23556205/using-boost-regex-with-rcpp pointing to http://gallery.rcpp.org/articles/boost-regular-expressions/ There is a Bioconductor example in that bundles the regex library

Re: [Bioc-devel] C library or C package API for regular expressions

The static library is available for linking once flowCore is installed. But headers comes from BH package. So you need to add BH to 'linkingTo' field of DESCRIPTION file and point to flowCore's compiled static library through 'PKG_LIBS' in your Makevars file. Use 'flowCore:::LdFlags()' to

Re: [Bioc-devel] C library or C package API for regular expressions

R requires PCRE to build, therefore perhaps it is available for use within packages? Dan - Original Message - > From: "Jiří Hon" > To: "bioc-devel" > Sent: Saturday, January 23, 2016 1:56:52 AM > Subject: [Bioc-devel] C library or

Re: [Bioc-devel] C library or C package API for regular expressions

Hi Jiri, On 01/25/2016 09:40 AM, Jiří Hon wrote: Hi Martin Dne 25.1.2016 v 13:08 Morgan, Martin napsal(a): There is discussion at http://stackoverflow.com/questions/23556205/using-boost-regex-with-rcpp pointing to http://gallery.rcpp.org/articles/boost-regular-expressions/ There is a

Re: [Bioc-devel] seqlevelsStyle() warning-message by message-warning, and NCBI/Ensembl seq styles

Hi Robert, I've made the following changes to the seqlevelsStyle() getter and setter: 1) No more warning when the getter returns more than 1 compatible style. 2) When more than 1 style is supplied, the setter uses the 1st one only with a warning. That should address the issues you

Re: [Bioc-devel] C library or C package API for regular expressions

Hi Charles, thank you a lot for your helpful hint. There is still a thing that I'm not sure about - Boost manual says that Boost.Regex is not header only [1]. So as BH package contains only headers, I will have to bundle the Boost.Regex library into the package code anyway. Am I right? Jiri