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
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
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
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.
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
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 -
- 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
- 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
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
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
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
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
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
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
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
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
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).
17 matches
Mail list logo