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then it would make sense to use
SEXP-based memory, or even better, to put a thin abstract layer between
the algo itself and memory management so they are decoupled.
Cheers,
H.
On Tue, Jul 1, 2014 at 9:05 AM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Hector, Michael
the sequence lengths when we re-generate it but this will only
happen a few weeks before the BioC 3.0 release (and at that time it
might become TxDb.Athaliana.BioMart.plantsmart22).
Cheers,
H.
Vince
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merged into R at some point.
Cheers,
H.
Radford Neal
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,ScalarLogical(FALSE)));
SET_TAG(CDDR(dfm), install(stringsAsFactors)) ;
SEXP res = PROTECT(eval(dfm,R_GlobalEnv));
UNPROTECT(7);
return res;
}
On Thu, Jun 26, 2014 at 3:49 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi,
On 06/26/2014 02:32 PM, Sandip Nandi wrote
On 06/21/2014 12:56 AM, Prof Brian Ripley wrote:
On 20/06/2014 15:37, Ista Zahn wrote:
Hello,
I've noticed that dget() is much slower in the current and devel R
versions than in previous versions. In 2.15 reading a 1-row
data.frame takes less than half a second:
(which.r -
:42 PM, Hervé Pagès hpa...@fhcrc.org wrote:
On 06/23/2014 03:18 PM, Hervé Pagès wrote:
Hi Christian,
On 06/23/2014 11:54 AM, cstrato wrote:
Dear Romain,
I do not know enough about compilers, but as far as I remember, they
'work' from right to left,
Not necessarily. So you should not rely
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On 06/23/2014 03:18 PM, Hervé Pagès wrote:
Hi Christian,
On 06/23/2014 11:54 AM, cstrato wrote:
Dear Romain,
I do not know enough about compilers, but as far as I remember, they
'work' from right to left,
Not necessarily. So you should not rely on that. This is what the
(somewhat obscure
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for a while now. Won't happen
before a couple of months.
Cheers,
H.
On 06/17/2014 10:37 PM, Hervé Pagès wrote:
Hi Peter,
Yes, as Vince said, the chromosome names are those used by dbSNP. For
whatever reason, dbSNP, which is part of NCBI, felt the need to use
a different naming convention than the rest
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? Also, what about functions that are optimized for
partitionings? Those would be easy to write and would let us greatly
accelerate e.g. sum,CompressedIntegerList. Right now we rely on rowsum()
which is fast but could be much faster.
Michael
On Mon, Jun 2, 2014 at 10:48 AM, Hervé Pagès hpa
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than it needs to
be when the need arises to reorganize/refactor parts of the
infrastructure. Also, the ability to quickly grep the NAMESPACE
files of all BioC packages to see who imports what is very convenient
in this situation.
Cheers,
H.
Hadley
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between packages, and gsubbing for pkga:foo to
pkgb:foo isn't hard
* it's not that much hard to grep for pkg::foo in R/* than it is to
grep NAMESPACE
Hadley
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Hi Peter,
On 05/26/2014 04:37 PM, Peter Hickey wrote:
Thanks for the suggested work-around, Martin. In order to define the method on the group
generic 'Ops' rather than '==' I will need to generalise .MTuples.compare to the 'Arith',
'Compare' and 'Logic' sub-groups listed in ?Ops, won't I?
.
Good. nearest() between a GRanges and a GRangesList is the easy one:
togroup(subject, nearest(query, unlist(subject, use.names=FALSE)))
Is this doing what you need?
Cheers,
H.
-Ryan
On Fri 23 May 2014 11:13:24 AM PDT, Hervé Pagès wrote:
Hi Ryan,
On 05/22/2014 03:38 PM, Ryan C. Thompson
) ## fails
#+END_SRC
Best wishes
Julian
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On 05/20/2014 12:49 PM, Hervé Pagès wrote:
Hi Julian,
At the root of the problem is what rbind() does on DataFrames containing
matrices:
m - matrix(1:4, nrow=2)
df - DataFrame(m=I(m))
df2 - rbind(df, df)
Then:
df2
DataFrame with 8 rows and 1 column
m
matrix
know if you have questions or concerns about this.
Thanks,
H.
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) is
ever released. The memory leak is minor if the sequence passed via
'object' has no masks but can be important if there are masks and
if the masks are made of hundreds of thousands of ranges.
Thanks,
H.
On Fri, May 9, 2014 at 4:07 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org
On 05/12/2014 12:23 PM, Michael Lawrence wrote:
On Mon, May 12, 2014 at 11:41 AM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Michael,
On 05/09/2014 04:39 PM, Michael Lawrence wrote:
What would be the fastest way to do this with a DNAString? Just
?
Thanks,
H.
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in using
GenomeData/GenomeDataList over GRanges/GRangesList.
Thanks,
H.
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, 2014 at 3:32 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi,
I'd like to deprecate the GenomeData and GenomeDataList classes defined
in the BSgenome package. If you've never heard about these containers,
you can stop reading here.
I was able to find only 2
.
metadata(ans) - metadata(x)
names(ans) - names(x)
mcols(ans) - mcols(x)
ans
}
)
###
Kind regards,
Sebastian
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On 05/07/2014 12:52 PM, Simon Urbanek wrote:
On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote:
No big deal. These things can be tricky:
https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html
Sorry I couldn't resist ;-)
Yeah, but that's just yet another trip down
On 05/07/2014 02:01 PM, peter dalgaard wrote:
On 07 May 2014, at 21:52 , Simon Urbanek simon.urba...@r-project.org wrote:
On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote:
No big deal. These things can be tricky:
https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html
On 05/07/2014 02:55 PM, Simon Urbanek wrote:
On May 7, 2014, at 5:41 PM, Hervé Pagès hpa...@fhcrc.org wrote:
On 05/07/2014 02:01 PM, peter dalgaard wrote:
On 07 May 2014, at 21:52 , Simon Urbanek simon.urba...@r-project.org wrote:
On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org
On 05/07/2014 02:45 PM, Simon Urbanek wrote:
On May 7, 2014, at 5:17 PM, Hervé Pagès hpa...@fhcrc.org wrote:
On 05/07/2014 12:52 PM, Simon Urbanek wrote:
On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote:
No big deal. These things can be tricky:
https://stat.ethz.ch/pipermail
On 05/07/2014 02:45 PM, Simon Urbanek wrote:
On May 7, 2014, at 5:17 PM, Hervé Pagès hpa...@fhcrc.org wrote:
On 05/07/2014 12:52 PM, Simon Urbanek wrote:
On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote:
No big deal. These things can be tricky:
https://stat.ethz.ch
behind.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Mon, May 5, 2014 at 10:35 PM, peter dalgaard pda...@gmail.com wrote:
On 06 May 2014, at 01:05 , Hervé Pagès hpa...@fhcrc.org wrote:
BTW, that %in% has precedence over arithmetic operations is surprising,
error-prone, and doesn't cover any
- is.element(els,set)
[1] -1 -1
So following your advice doesn't really help me leave my precedence
problems behind.
H.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, May 6, 2014 at 12:23 PM, Hervé Pagès hpa...@fhcrc.org wrote:
On 05/06/2014 08:54 AM, William Dunlap wrote:
You can also
.
If you ... in the first place. A, but that's not what I did. So
that doesn't help me.
H.
(I avoid creating %xxx% functions because the precedence is
not often what I want.)
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, May 6, 2014 at 1:06 PM, Hervé Pagès hpa...@fhcrc.org wrote
, Hervé Pagès hpa...@fhcrc.org wrote:
On 05/06/2014 01:15 PM, William Dunlap wrote:
In your example els%in%set gave the same result as
is.element(els,set), but because of precedence issues putting a unary
minus in front caused them to be given different inputs - one got -els
and the other got just
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.
to work?
hint: it does not
-Original Message-
From: bioc-devel-boun...@r-project.org
[mailto:bioc-devel-boun...@r-project.org] On Behalf Of Hervé Pagès
Sent: Monday, May 05, 2014 1:28 PM
To: Kasper Daniel Hansen; Michael Lawrence
Cc: Johnston, Jeffrey; ttri...@usc.edu; bioc-devel
this.
Cheers,
H.
to work?
hint: it does not
-Original Message-
From: bioc-devel-boun...@r-project.org
[mailto:bioc-devel-boun...@r-project.org] On Behalf Of Hervé Pagès
Sent: Monday, May 05, 2014 1:28 PM
To: Kasper Daniel Hansen; Michael Lawrence
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On Tue, Apr 29, 2014 at 11:24 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Michael,
I noticed this difference between DataFrame vs data.frame when doing
rbind():
rbind(data.frame(aa=NA), data.frame(aa=1:2))
aa
1 NA
2 1
3
. Then you could choose to suppress this one.
We might be able to do that with options(warning.expression), but I
don't see how...
Duncan Murdohc
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versioning
http://bioconductor.org/developers/how-to/version-numbering/
and the Bioc-style approach to release that we as developers can act
on to enhance reproducibility. What other best pract
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,
some turbulences on the build report are to be expected. I'll keep a
close eye on that and fix the packages affected by this split.
Thanks,
H.
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On Wed, Apr 16, 2014 at 12:59 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Sean
[hope you don't mind if I cc Bioc-devel]
On 04/15/2014 11:47 PM, Maintainer wrote:
Hi The Bioconductor Dev Team,
A new package called BSgenome.Hsapiens.NCBI.GRCh38
Genomics
sbgenomics.com
625 Mt. Auburn St. Suite #208
Cambridge, MA 02138
(617) 866-0446
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with BiocGenerics around, it's hard to avoid this kind of clash.
H.
Best wishes,
Laurent
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Added in IRanges 1.21.41.
H.
On 04/01/2014 06:15 PM, Michael Lawrence wrote:
I like phead/ptail. I was going to write them, so thanks for taking care
of it!
Michael
On Tue, Apr 1, 2014 at 3:24 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 04/01/2014 02:43 PM
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element, but I wanted the line above to
do that.
Michael
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() (they're just fast equivalent to 'mapply(head, x, n)' and
'mapply(tail, x, n))', or...?
Thanks,
H.
Michael
On Tue, Apr 1, 2014 at 12:06 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 04/01/2014 10:17 AM, Ryan wrote:
That won't work if any vector has fewer than
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by
sealed=TRUE, but that did not work either. Any ideas are
gratefully
appreciated!
Thanks a lot,
Ulrich
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by
sealed=TRUE, but that did not work either. Any ideas are
gratefully
appreciated!
Thanks a lot,
Ulrich
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we don't have to remember the family argument?
This way lies madness...
Radford Neal
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beginners, I feel it ought to go in base R.
Before I submit this as a feature request, I thought I'd check here to
see if there was any enthusiasm. Does rep_len sound useful to you?
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Hi Martin,
On 03/21/2014 01:45 PM, Martin Morgan wrote:
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
Hi,
On 03/19/2014 01:10 PM, Michael Lawrence wrote:
You can apparently use 1D extraction for VCF, which is a little
surprising;
I learned it from restrictToSNV.
This is inherited from
On 03/20/2014 05:20 PM, Hervé Pagès wrote:
[...]
Following that logic names(se1) also probably return colnames(se1).
/\
should
H.
H.
On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey
st...@channing.harvard.eduwrote
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On 03/20/2014 01:28 PM, Ted Byers wrote:
On Thu, Mar 20, 2014 at 3:14 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 03/20/2014 03:52 AM, Duncan Murdoch wrote:
On 14-03-20 2:15 AM, Dan Tenenbaum wrote:
- Original Message
On 03/20/2014 03:29 PM, Uwe Ligges wrote:
On 20.03.2014 23:23, Hervé Pagès wrote:
On 03/20/2014 01:28 PM, Ted Byers wrote:
On Thu, Mar 20, 2014 at 3:14 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 03/20/2014 03:52 AM, Duncan Murdoch wrote:
On 14-03-20 2
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) if this problem was addressed upstream.
H.
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Hi Val,
On 03/11/2014 08:57 PM, Valerie Obenchain wrote:
Hi,
On 03/11/14 15:33, Hervé Pagès wrote:
On 03/11/2014 02:52 PM, Hervé Pagès wrote:
On 03/11/2014 09:57 AM, Valerie Obenchain wrote:
Hi Herve,
On 03/10/2014 10:31 PM, Hervé Pagès wrote:
Hi Val,
I think it would help understand
On 03/11/2014 02:52 PM, Hervé Pagès wrote:
On 03/11/2014 09:57 AM, Valerie Obenchain wrote:
Hi Herve,
On 03/10/2014 10:31 PM, Hervé Pagès wrote:
Hi Val,
I think it would help understand the motivations behind this proposal
if you could give an example of a method where the user cannot supply
be by regex
and package name. Still a work in progress.
Valerie
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Fred
, ...) to find out what particular
method was being called (I needed to see the code).
Thanks,
H.
On 02/22/2014 05:59 AM, Michael Lawrence wrote:
Translated it into a patch against R, submitted here:
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15680
On Fri, Feb 21, 2014 at 2:53 PM, Hervé Pagès
‘c’ and signature ‘x = IRanges,
recursive = logical’
Thanks again for working on this.
H.
Michael
On Sat, Feb 22, 2014 at 12:26 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Thanks Michael.
Do you think it would be sensible to offer a similar fix
the
examples below. If the function is not a generic (no S4 methods
are defined for it), the help reverts to documentation on the
function name.
Thanks,
H.
On Fri, Feb 21, 2014 at 11:17 AM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Gabriel,
On 02/20/2014
...)
Cheers,
H.
coverage() is fast and beautiful. Thanks!
/Jesper
On Wed, Feb 19, 2014 at 9:21 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Jesper,
On 02/19/2014 08:44 AM, Michael Lawrence wrote:
On Wed, Feb 19, 2014 at 8:39 AM, Jesper Gådin
On 02/20/2014 02:55 PM, Martin Morgan wrote:
On 02/20/2014 02:32 PM, Hervé Pagès wrote:
Hi Jesper,
On 02/20/2014 02:13 PM, Jesper Gådin wrote:
Very true that it is quite difficult to find the documentation when one
is not aware of its existence :P
Yeah, this has been a source
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E
] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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Fred Hutchinson Cancer Research Center
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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E
, an odd y in devel, with y bump (and z reset to 0) at each
new release. Feedback welcome.
Please let me know if you have questions or concerns about this.
Cheers,
H.
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1100
On 01/22/2014 03:02 PM, Michael Lawrence wrote:
On Wed, Jan 22, 2014 at 1:29 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
Hi Michael,
On 01/12/2014 05:16 AM, Michael Lawrence wrote:
Hi,
It may be time to deprecate the seq*apply family
On 01/22/2014 08:15 PM, Michael Lawrence wrote:
Sounds good. But who is she?
we would, she should, she would, we should... that's it! we should...
that's what I meant :-b
H.
On Wed, Jan 22, 2014 at 3:48 PM, Hervé Pagès hpa...@fhcrc.org
mailto:hpa...@fhcrc.org wrote:
On 01/22/2014 03
] On Behalf Of Hervé Pagès
Sent: Tuesday, 17 December 2013 8:27 p.m.
To: Kasper Daniel Hansen
Cc: Michael Lawrence; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] ordering GenomicRanges without regard for strand
OK. Let's go for unstrand() too. Will add this in the next few days.
H.
On 12/12
.
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
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