[Bioc-devel] New seqPattern package

2015-01-12 Thread Vanja Haberle
Dear Bioconductor members, I'd like to draw your attention to the new package for visualisation of oligonucleotide patterns and motif occurrences across a set of sorted sequences. The *seqPattern* package is now available in the development branch:

Re: [Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)

2015-01-12 Thread Simon Urbanek
Dan, On Jan 12, 2015, at 7:50 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: R CMD build fails with recent R-devel because it is looking for texi2dvi in /usr/local/bin, but on this system, MacTex has installed it in /usr/bin. No, you're looking at the wrong package - texi2dvi comes from

[Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)

2015-01-12 Thread Dan Tenenbaum
R CMD build fails with recent R-devel because it is looking for texi2dvi in /usr/local/bin, but on this system, MacTex has installed it in /usr/bin. $ R CMD build IRanges * checking for file 'IRanges/DESCRIPTION' ... OK * preparing 'IRanges': * checking DESCRIPTION meta-information ... OK *

Re: [Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)

2015-01-12 Thread Dan Tenenbaum
- Original Message - From: Duncan Murdoch murdoch.dun...@gmail.com To: Dan Tenenbaum dtene...@fredhutch.org, Simon Urbanek simon.urba...@r-project.org Cc: R-devel r-devel@r-project.org Sent: Monday, January 12, 2015 8:40:07 PM Subject: Re: [Rd] R CMD build looking for texi2dvi in

[Rd] [PATCH] Makefile: add support for git svn clones

2015-01-12 Thread Felipe Balbi
git has an interface for cloning SVN repositories into git which some users might decide to use. For those users' surprise, the repository will always fail to build on svnonly target and it will exit early. The problem is simple enough to fix by just checking if a .git directory exists in

Re: [Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)

2015-01-12 Thread Duncan Murdoch
On 12/01/2015 6:26 PM, Dan Tenenbaum wrote: - Original Message - From: Simon Urbanek simon.urba...@r-project.org To: Dan Tenenbaum dtene...@fredhutch.org Cc: R-devel r-devel@r-project.org Sent: Monday, January 12, 2015 5:50:35 PM Subject: Re: [Rd] R CMD build looking for texi2dvi

[Bioc-devel] Replacing deprecated org.Hs.egCHR and friends

2015-01-12 Thread Peter Langfelder
Hi all, can anyone please explain or point me to an explanation of how to replace org.Hs.egCHR and friends that appear to be deprecated in the devel version? The deprecation message isn't very helpful. Thanks! x = org.Hs.egCHR Warning message: In (function () : org.Hs.egCHR is deprecated.

Re: [Rd] New version of Rtools for Windows

2015-01-12 Thread Avraham Adler
On Fri, Jan 9, 2015 at 12:19 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 09/01/2015 10:56 AM, Henric Winell wrote: On 2015-01-08 02:31, Duncan Murdoch wrote: On 07/01/2015 5:20 PM, Jeroen Ooms wrote: On Wed, Jan 7, 2015 at 8:00 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: