What you are doing is great, and that's a pretty clear warning (I would go
ahead and add "DO NOT FORK ME" to the verbiage since I am one of the
dumbasses who submitted a pull request in such a fashion, whereupon the
original author got to set up a Git repo, I re-PR'ed against that, and all
was well
Or maybe it would be sensible to ask GitHub if they can fix this.
If it's a common-ish use case (e.g. for mirrors), it's not something that
should be terribly challenging engineering-wise, and it would prevent a lot
of hooha.
Funfact: GitHub is run and staffed by actual people, most of them prett
> Please tell me what you think.
I think it is awesome, just like the CRAN-github bridge.
It would be cool if you provided CRAN authors with instructions on how to
fork the CRAN-github clones of the source code so that I don't have to
retarget pull requests ;-)
In conclusion, keep up the great w
Except that tests (as vignettes) are mandatory for BioC. So if something blows
up you hear about it right quick :-)
--t
> On Mar 20, 2014, at 7:15 PM, Gábor Csárdi wrote:
>
> On Thu, Mar 20, 2014 at 9:45 PM, William Dunlap wrote:
>
>>> In particular, updating a package with many reverse depe
Heh, you just described BioC
--t
> On Mar 20, 2014, at 7:15 PM, Gábor Csárdi wrote:
>
> On Thu, Mar 20, 2014 at 9:45 PM, William Dunlap wrote:
>
>>> In particular, updating a package with many reverse dependencies is a
>>> frustrating process, for everybody. As a maintainer with ~150 reverse
> There is nothing like backups with due attention to detail.
Agreed, although given the complexity of dependencies among packages, this
might entail several GB of snapshots per paper (if not several TB for some
papers) in various cases. Anyone who is reasonably prolific then gets the
exciting pr
That doesn't make sense.
If an API changes (e.g. in Matrix) and a program written against the old
API can no longer run, that is a very different issue than if the same
numbers (data) give different results. The latter is what I am guessing
you address. The former is what I believe most people a
short of running everything in a VM, I'd have to guess you're hosed... I
don't understand how an operating system with internals as opaque as
Windows (NT/2000/beyond, not just the old DOS-based garbage) could ever be
considered secure for intensive computation, but that seems beside the
point. Yo
Murdoch wrote:
> On 01/05/2013 1:34 PM, Tim Triche, Jr. wrote:
>
>> +1 to having runnable code emitted
>>
>
> It does emit runnable code, which is why Herve's complaint was nonsense.
> It doesn't emit code of which every substring is runnable.
>
> Duncan
+1 to having runnable code emitted
patch seems to work nicely, hopefully R-core will agree to apply it to HEAD
On Wed, May 1, 2013 at 9:45 AM, Paul Johnson wrote:
> Whoa.
>
> Don't let my valuable suggestion get lost.
>
> I want "} else {". Yihue wants "} else {". And I have not heard anyb
seen QuasR (and/or gmapR, Rsubread, etc.)? one can run BowTie, gsnap, etc.
from R
this certainly makes it easier for me to remember how I did some ChIP-seq
or BS-seq or RNA-seq processing a year ago, when it turns out I need to add
a sample or samples and carry on with an existing analysis pipeli
I think it may have been John D. Cook who first observed that p-values are
linearly correlated with the amount of time remaining on a grant.
Perhaps a suitable transform would reveal an ordinal relationship with
stars.
On Tue, Feb 12, 2013 at 7:03 AM, Ravi Varadhan wrote:
> They are "reaching
, Feb 9, 2013 at 12:44 PM, Tim Triche, Jr. wrote:
> Changing the default for show.signif.stars should be sufficient to ensure
> that, if people are going to get themselves into trouble, they will have to
> do it on purpose. It's just a visual cue; removing it will not remove the
>
Changing the default for show.signif.stars should be sufficient to ensure
that, if people are going to get themselves into trouble, they will have to
do it on purpose. It's just a visual cue; removing it will not remove the
underlying issue, namely blind acceptance of unlikely null models and
dist
from a package I'm writing
##setClass('Occupancy',contains="DataFrame",
## representation(states="StatesORNULL"))
##
R> foo <- occupancy(pooledMethSegs)
R> plotOccupancy(foo)
Error in slot(object, "states") :
no slot of name "states" for this object of class "Occupancy"
R> sl
a n00b question:
if I call importFrom(IRanges, ranges) in my NAMESPACE file, that works
great.
but if I call
R> importFrom(IRanges, ranges)
## Error: could not find function "importFrom"
well, that doesn't work great. The closest thing I can find in base is
base:::importIntoEnv
which helpfu
Here is a JIT suggestion: add the message to errors/coredump reports
"If you would like to submit a patch for this error, please contact r-devel@
r-project.org for further instructions.
If you cannot, or would prefer not to, fix this error yourself, please
consider donating $20 to the Fix My Bug
It's in VGAM, remember? Not a bug.
On Fri, Jun 1, 2012 at 10:38 AM, Joan Maspons wrote:
> Hi,
> I filled a bug [1] and I tried to build a package without success. If there
> are no news in a while I'll try some to convince some package developers to
> add this distribution
>
> [1] https://bugs
it's already in the VGAM package
http://www.stat.auckland.ac.nz/~yee/VGAM/
On Tue, May 22, 2012 at 7:59 AM, Joshua Ulrich wrote:
> On Tue, May 22, 2012 at 8:27 AM, Joan Maspons
> wrote:
> > Hello,
> >
> > 2012/5/22 Christophe Dutang
> >
> >> Dear Joan,
> >>
>
> >> If you want to contribute
there's also Rgraphviz, although with 30,000+ edges it may not survive
*this* graph :-)
On Tue, Mar 27, 2012 at 4:11 AM, Whit Armstrong wrote:
> if you don't mind going outside of R to create it, then check out
> Graphviz: http://www.graphviz.org/Gallery.php
>
> you may have to reformat your dat
use the gsl package for Kummer's hypergeometric and others.
you might find implementing the distributions in C or C++ worthwhile for
speed.
thanks for doing this, by the way.
On Sat, Mar 17, 2012 at 11:38 AM, Joan Maspons wrote:
> Hello,
>
>
> El 16 de març de 2012 20:34, Christophe Dutang h
quot;
without having Windows users get left out in the cold (unless they add flags
to their function calls).
Thank you for your suggestions, I will look into this further.
--
Tim Triche, Jr.
USC Biostatistics
[[alternative HTML version deleted]]
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R-devel@r-project.org mailing list
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Hi all,
Would it be possible to have the new 'parallel' library export a dummy
function, something akin to
if(Windows) mclapply <- lapply
to paper over the lack of fork() support on said platform? This may not be
the world's greatest idea, but it would make it easier for me to maintain my
packa
they have
> such issues?
>
> Tim do you have concrete examples of the issues you talked with other
> developers?
>
> Thank you.
>
> Renaud
>
> On 17/08/2011 12:45, Tim Triche, Jr. wrote:
>
> yes -- doMC (and doSMP) are kind of bogus and I just use
> multico
(re-sending after confirming list subscription; apologies if this ends up
being sent to the list twice)
Is the expected behavior from cat(), as used below, a hanging space before
\n at the end of the emitted line?
firstheader = gsub("\\s+$", "", paste(c("Hybridization REF", s, s),
collapse = "\t
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