Re: [Bioc-devel] exp. data, updates

2013-07-10 Thread Hervé Pagès
Hi Stephanie, On 07/10/2013 12:51 PM, Stephanie M. Gogarten wrote: I had this issue with GWASTools/GWASdata at one point. There is only one copy of an experiment data package, so if you change it, it will break the current release version of bsseq. Yes there is only one copy of an experiment

Re: [Bioc-devel] exp. data, updates

2013-07-10 Thread Stephanie M. Gogarten
I had this issue with GWASTools/GWASdata at one point. There is only one copy of an experiment data package, so if you change it, it will break the current release version of bsseq. The solution I came up with was to add new objects with different names to the data package, and change my exam

Re: [Bioc-devel] exp. data, updates

2013-07-10 Thread Kasper Daniel Hansen
Thanks, this is very helpful. In general, following our release paradigm, I see no reason to ever want to update bsseqData for Bioconductor 2.12 - since it is a data package chances are small for finding a critical bug. Best, Kasper On Wed, Jul 10, 2013 at 3:17 PM, Hervé Pagès wrote: > It's s

Re: [Bioc-devel] exp. data, updates

2013-07-10 Thread Hervé Pagès
It's simpler than that. Just make the change you need to make. The package will fail to pass the build/check in release so it won't propagate. That means that whatever version of bsseqData is currently in BioC 2.12 will remain forever i.e. you won't be able to update it. Hope that's OK with you.

Re: [Bioc-devel] best practice: verbose messages

2013-07-10 Thread Hervé Pagès
Hi Kasper, On 07/10/2013 10:50 AM, Kasper Daniel Hansen wrote: On Wed, Jul 10, 2013 at 12:38 PM, Dan Tenenbaum wrote: On Wed, Jul 10, 2013 at 9:17 AM, Michael Lawrence wrote: If it's an informational message, like one you might log, use message(). If you're rendering an object as text, li

Re: [Bioc-devel] appending 2 GappedAlignments using "c" takes long

2013-07-10 Thread Hervé Pagès
Hi Nico, On 07/09/2013 08:07 AM, Nicolas Delhomme wrote: Hej Bioc Core! There was some discussion last year about implementing a BamStreamer (à la FastqStreamer), but I haven't seen anything like it in the current devel. I've implemented the following function that should do the job for me -

Re: [Bioc-devel] appending 2 GappedAlignments using "c" takes long

2013-07-10 Thread Martin Morgan
- Nicolas Delhomme wrote: > Hej Bioc Core! > > There was some discussion last year about implementing a BamStreamer (à la > FastqStreamer), but I haven't seen anything like it in the current devel. > I've implemented the following function that should do the job for me - I > have many ver

Re: [Bioc-devel] best practice: verbose messages

2013-07-10 Thread Martin Morgan
- Kasper Daniel Hansen wrote: > On Wed, Jul 10, 2013 at 12:38 PM, Dan Tenenbaum wrote: > > > On Wed, Jul 10, 2013 at 9:17 AM, Michael Lawrence > > wrote: > > > If it's an informational message, like one you might log, use message(). > > If > > > you're rendering an object as text, like in a

Re: [Bioc-devel] exp. data, updates

2013-07-10 Thread Dan Tenenbaum
On Wed, Jul 10, 2013 at 10:51 AM, Kasper Daniel Hansen wrote: > This will help me branch code, but not objects with changed definitions. > Can you store two separate objects, one that's 2.12-compatible and the other newer? After the next release, when we stop building 2.12, this will become unne

Re: [Bioc-devel] best practice: verbose messages

2013-07-10 Thread Dan Tenenbaum
On Wed, Jul 10, 2013 at 10:50 AM, Kasper Daniel Hansen wrote: > > On Wed, Jul 10, 2013 at 12:38 PM, Dan Tenenbaum wrote: >> >> On Wed, Jul 10, 2013 at 9:17 AM, Michael Lawrence >> wrote: >> > If it's an informational message, like one you might log, use message(). >> > If >> > you're rendering a

Re: [Bioc-devel] exp. data, updates

2013-07-10 Thread Kasper Daniel Hansen
This will help me branch code, but not objects with changed definitions. Kasper On Wed, Jul 10, 2013 at 12:44 PM, Dan Tenenbaum wrote: > On Wed, Jul 10, 2013 at 7:05 AM, Kasper Daniel Hansen > wrote: > > I have just changed the class definition for a core class in bsseq. A > > supporting exp

Re: [Bioc-devel] best practice: verbose messages

2013-07-10 Thread Kasper Daniel Hansen
On Wed, Jul 10, 2013 at 12:38 PM, Dan Tenenbaum wrote: > On Wed, Jul 10, 2013 at 9:17 AM, Michael Lawrence > wrote: > > If it's an informational message, like one you might log, use message(). > If > > you're rendering an object as text, like in a show method, use cat(). > > > > Another thing to

Re: [Bioc-devel] exp. data, updates

2013-07-10 Thread Dan Tenenbaum
On Wed, Jul 10, 2013 at 7:05 AM, Kasper Daniel Hansen wrote: > I have just changed the class definition for a core class in bsseq. A > supporting experiment data package, bsseqData, contains two objects of this > core class and now it needs to be updated (specifically because the > example() cont

Re: [Bioc-devel] best practice: verbose messages

2013-07-10 Thread Dan Tenenbaum
On Wed, Jul 10, 2013 at 9:17 AM, Michael Lawrence wrote: > If it's an informational message, like one you might log, use message(). If > you're rendering an object as text, like in a show method, use cat(). > Another thing to consider is that messages can be suppressed with suppressMessages() but

Re: [Bioc-devel] best practice: verbose messages

2013-07-10 Thread Michael Lawrence
If it's an informational message, like one you might log, use message(). If you're rendering an object as text, like in a show method, use cat(). Just my opinion, Michael On Wed, Jul 10, 2013 at 8:24 AM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > Should I use cat() or message

[Bioc-devel] best practice: verbose messages

2013-07-10 Thread Kasper Daniel Hansen
Should I use cat() or message() (or something else) for if(verbose) cat("my message\n") Best, Kasper [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] exp. data, updates

2013-07-10 Thread Kasper Daniel Hansen
I have just changed the class definition for a core class in bsseq. A supporting experiment data package, bsseqData, contains two objects of this core class and now it needs to be updated (specifically because the example() contains a command which prints the object and this printing now fails).