/ignore/taxonclass2.R:157
/testthat/R/utils.r:13
/textreuse/R/TextReuseCorpus.R:137
/textreuse/R/minhash.R:46
/textreuse/R/similarity.R:111
/tidyr/R/id.R:17
On Tue, Feb 9, 2016 at 3:37 AM, Martin Maechler
<maech...@stat.math.ethz.ch> wrote:
Hervé Pagès <hpa...@fredhutch.org>
on Mon, 8
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lia
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her than subsetting break as well in this case).
# No error
y <- makeSE(5)
y
# Error
y[1, ]
Perhaps there should be a check in the constructor that all assay
elements have < 5 dimensions?
Cheers,
Pete
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;a", B=1:2), USE.NAMES=FALSE)
[1] FALSE TRUE
If the behavior of sapply() cannot be changed, at least the man page
could clarify what happens when 'USE.NAMES' is FALSE, which is
different for each function.
Thanks,
H.
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unlist'
Is this a problem with moscato2? I don’t get this if I build locally…
best
Thomas
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rg> on behalf of Michael Love
<michaelisaiahl...@gmail.com>
Sent: Monday, February 1, 2016 3:35 PM
To: Dan Tenenbaum
Cc: bioc-devel; Hervé Pagès
Subject: Re: [Bioc-devel] TIMEOUTs on Morelia
I was able to construct a minimal example where it seems the bug originates
from Summariz
ny matrix-like object as
long as the resulting SummarizedExperiment object is valid.
These 2 changes are in SummarizedExperiment 1.1.17.
Thanks for the suggestions,
H.
Cheers,
Pete
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Di
at now if you have a UCSC-style GRanges object like this one:
gr <- GRanges(c("chr1", "chr2"), IRanges(c(10, 20), c(30, 40)))
seqlevelsStyle(gr)
[1] "UCSC"
that you want to use with the BSgenome object, the following simple
operation will not work anymore:
seq
ch I’m not aware of.
Thanks for help or any alternative solutions!
jo
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On 01/13/2016 07:28 PM, Hervé Pagès wrote:
Hi Ben, Martin,
On 01/13/2016 08:19 AM, Morgan, Martin wrote:
[...]
So this is a bug in S4Vectors, but fixed in Bioc-devel where new
package development should be occurring.
I'll leave it to Herve or others to decide whether S4Vectors in
release
This breaks some Bioconductor packages that are calling as.data.frame()
on the result of this subscripting (as.data.frame.table and
as.data.frame.matrix behave very differently).
Could this change be mentioned in the NEWS file?
Thanks,
H.
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Gene to have an easy starting point for the
analysis of human data.
cheers,
robert.
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ince human gene annotations are at the core of many BioC pipelines, i'd
like to suggest for the forthcoming release cycles, that the BioC core
team packages Gencode annotations anchored at Entrez IDs, at least what
is called the "basic set", similarly to what is done with
TxDb.Hsapie
TwoBitFile.
Martin
From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Rainer
Johannes [johannes.rai...@eurac.edu]
Sent: Saturday, January 09, 2016 11:01 AM
To: Hervé Pagès
Cc: Michael Lawrence; Martin Morgan
Subject: Re: [Bioc-devel] Problem with seqnames of TwoBitFile
;-,TwoBitFile for that particular
use case. Just wanted to mention that the ability to rename the
sequences in a TwoBitFile, FastaFile, or other file-based object that
supports seqinfo() would be useful in general.
H.
On Fri, Jan 8, 2016 at 11:04 AM, Hervé Pagès <hpa...@fredhutch.org> wro
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ry(GenomicRanges)
gr = GRanges("chr", IRanges(1, 5))
mcols(gr) = data.frame(name="range1")
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This is fixed in S4Vectors release (0.8.6) and devel (0.9.16).
Cheers,
H.
On 01/04/2016 11:52 AM, Hervé Pagès wrote:
Hi Malcolm,
Thanks for reporting this. Will fix.
H.
On 01/04/2016 10:53 AM, Malcolm Perry wrote:
Hello,
A recent question on the support site (
https
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quot;))
[1] FALSE
Here's the surprising behavior:
x <- 1L
xx <- as(x, "numeric")
class(xx)
## [1] "integer"
It occurs because the call to `as(x, "numeric")` dispatches the coerce
S4 method for the signature `c("integer", "numeric")`, whose bo
quot;))
[1] FALSE
Here's the surprising behavior:
x <- 1L
xx <- as(x, "numeric")
class(xx)
## [1] "integer"
It occurs because the call to `as(x, "numeric")` dispatches the coerce
S4 method for the signature `c("integer", "numeric")`, whose bo
to map GRCh38 seqlevels to
hg38 seqlevels.
H.
Michael
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On 12/15/2015 03:13 PM, Michael Lawrence wrote:
On Tue, Dec 15, 2015 at 2:15 PM, Hervé Pagès <hpa...@fredhutch.org> wrote:
SummarizedExperiment has long been supporting unidimensional subsetting
which was subsetting by row. However the length of any SE object was
always considered to be 1
istinfo/bioc-devel
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---
On Fri, Dec 11, 2015 at 3:38 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
Hi Krithika,
NSBS() is the internal helper defined in the S4Vectors package tha
yaml2.1.13 2014-06-12 CRAN (R 3.2.0)
zlibbioc1.16.0 2015-10-14 Bioconductor
Thanks,
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TIFICATION=C
attached base packages:
[1] stats4parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicRanges_1.22.1 GenomeInfoDb_1.6.1 IRanges_2.4.4
[4] S4Vectors_0.8.3 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] zlibbio
l message from your computer. Thank you.
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Hi Malcolm,
On 12/01/2015 12:29 PM, Cook, Malcolm wrote:
-Original Message-
> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of
> Hervé Pagès
> Sent: Monday, October 26, 2015 12:39 PM
> To: Thomas Girke <thomas.gi...@ucr.edu>; Aror
.
thanks,
Stephanie
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On 11/20/2015 03:21 PM, Hervé Pagès wrote:
Hi Jim,
I think we should choose the biomaRt model, that is, duplicated are
allowed but silently ignored.
Note that this is also the SQL model. When you do
SELECT * FROM ... WHERE key IN c('key1', 'key2
dups
were removed?
2. If the answer to #1 is yes, then to be consistent, I will just commit
the patch I have made to both devel and release.
Best,
Jim
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Bioinformatics and Computational Biology
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Developers,
On 11/16/2015 11:39 PM, Hervé Pagès wrote:
Hi Aaron,
On 11/16/2015 09:39 AM, Hervé Pagès wrote:
[...]
Anyway, you convinced me that we should not try to follow too closely
the names model for how we treat metadata columns. If nobody objects,
I'll change the behavior
cts,
I'll change the behavior of the various "replaceROWS" methods in the
S4Vectors stack and make sure that they all transfer the metadata
columns from 'value' to 'x'.
Cheers,
H.
Cheers,
Aaron
Hervé Pagès wrote:
Hi Aaron,
On 11/15/2015 10:59 AM, Aaron Lun wrote:
Hello all,
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Hi Aaron,
On 11/16/2015 09:39 AM, Hervé Pagès wrote:
Hi Aaron,
On 11/15/2015 12:37 PM, Aaron Lun wrote:
Hi Herve,
I would have expected GRanges behaviour, where the metadata is affected
by the replacement. For example, with GRanges objects, I often use the
metadata to store statistics
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behavior between order() and sort(). The
problem is that order() and sort() use a different default
for the 'na.last' argument (TRUE and NA, respectively). Is
there any reason for that? Any chance this could be revisited?
Thanks,
H.
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the
time. I was thinking it might be possible to make this quite fast by
looping over the GRanges object at the C-level and breaking out of the
loop if gr[i+1] <= gr[i] or gr[i+1] < gr[i], as appropriate. Does this
sound reasonable?
Cheers,
Pete
On 3 November 2015 at 14:06, Michael Law
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E-mail: hpa...@fredh
does (thru the default method for
normalizeSingleBracketReplacementValue).
Thanks,
H.
Michael
On Wed, Oct 21, 2015 at 11:14 AM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
Hi Michael,
On 10/21/2015 07:09 AM, Michael Lawrence wrote:
News t
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None of the reasons you listed as causing an implicit attach seems to
apply here.
Thanks,
Marcin
On Mon, Oct 19, 2015 at 5:56 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
Hi Marcin,
On 10/19/2015 05:11 AM, Marcin Cieślik wrote:
Dea
check in for discordant pairs in readGAlignmentPairs, but not in
GAlignmentPairs itself; could be mistaken though...
Martin
From: Michael Lawrence [lawrence.mich...@gene.com
<mailto:lawrence.mich...@gene.com>]
Sent: Saturday, October 17, 2015 9:
om ‘package:parallel’:
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Fred H
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On 10/16/2015 10:52 AM, Dan Tenenbaum wrote:
- Original Message -
From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "Levi Waldron"
<levi.wald...@hunter.cuny.edu>
Cc: "bioc-devel" <bioc
strand of the location is unknown, or irrelevant, or when the "feature"
at that location belongs to both strands. A pair with discordant strand
belongs to both strands. Also there is a lot of code around that
assumes strand() never returns NAs.
H.
On Fri, Oct 16, 2015 at 9:15 AM, Hervé
is clearly a misnomer and a source of confusion.
H.
On Wed, Sep 30, 2015 at 9:37 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
On 09/30/2015 05:28 PM, Michael Lawrence wrote:
It wasn't a conscious choice, but it would slow things down a
iling list
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E-mail: hpa...@fre
do not
necessarily represent the views of the Babraham Institute. Full conditions at:
www.babraham.ac.uk<http://www.babraham.ac.uk/terms>
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Progr
to the build system
is too big to make it 1 week before a release.
H.
Dan
- Original Message -
From: "Hervé Pagès" <hpa...@fredhutch.org>
To: "Dan Tenenbaum" <dtene...@fredhutch.org>
Cc: "bioc-devel" <bioc-devel@r-project.org>
Sent: Monda
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ling list
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t(a=runif(2500), L=LETTERS))
object.size(env3) # 56 bytes
This makes it pretty useless on reference class instances and other
objects that use environments internally for caching or other purposes.
What about changing this and make it return something more meaningful?
Cheers,
H.
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He
Hi Hervé,
This still looks broken in the current bioc-devel. Just wanted to
follow up in case it got missed. Thanks again.
Leonard
On Thu, Jun 11, 2015 at 11:59 AM, Leonard Goldstein <golds...@gene.com> wrote:
Thanks Hervé.
Best wishes,
Leonard
On Thu, Jun 11, 2015 at 10:58 AM,
On 09/29/2015 03:18 PM, Hervé Pagès wrote:
Hi Gabe,
On 09/29/2015 02:51 PM, Gabriel Becker wrote:
Herve,
The problem then would be that for A a refClass whose fields take up N
bytes (in the sense that you mean), if we do
B <- A
A and B would look like the BOTH take up N bytes, for a to
ust a collection
of pointers to stuff that is shared thru the global CHARSXP cache and
AFAIK object.size() takes this stuff into account.
H.
~G
On Tue, Sep 29, 2015 at 2:42 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
Hi,
Currently object.size() is
let the user choose which column
to return at the moment so that's why it was decided (a long time ago)
to return exon internal ids *and* names (better more than less).
H.
Marc
On Tue, Sep 22, 2015 at 5:29 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wro
13] RCurl_1.95-4.7 biomaRt_2.25.3
[15] RSQLite_1.0.0 Biostrings_2.37.8
[17] Rsamtools_1.21.17 XML_3.98-1.3
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P
rtunately
this won't happen for BioC 3.2...
H.
so here the modification of txdb gets carried through to the original
object.
Best,
Kasper
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On 09/21/2015 02:48 PM, Duncan Murdoch wrote:
On 21/09/2015 4:50 PM, Hervé Pagès wrote:
Hi,at
Note that one significant change to read.dcf() that happened since R
3.0.2 is the addition of support for arbitrary long lines (commit
63281), which never worked:
dcf <- paste(c("aa
On 09/21/2015 10:39 AM, Hervé Pagès wrote:
On 09/21/2015 02:06 AM, Christian Arnold wrote:
Hi Jim, Kasper, and Hervé,
thanks a lot for the quick answer. For some reason, I was under the
impression that I have to use exactly the original prototype from the
generics, but I didn't fully realize
R 2.15.3, I do not see the error.
Would be great to get this resolved. Thank you for your help.
-- Vinh
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On 09/21/2015 01:50 PM, Hervé Pagès wrote:
Hi,
Note that one significant change to read.dcf() that happened since R
3.0.2 is the addition of support for arbitrary long lines (commit
63281), which never worked:
dcf <- paste(c("aa: ", rep(letters, length.out=1000
uot; counts
function, but I thought if a generics already exists, I should use it
because this is exactly what my function does also...
Thanks,
Christian
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and whenever there is at least one range
with +/-.
Michael
On Mon, Apr 27, 2015 at 2:23 PM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
> On 04/27/2015 02:15 PM, Michael Lawrence wrote:
>
>> It would be nice to ha
] Error 1
ERROR: compilation failed for package ‘S4Vectors’
Did I miss something?
Thanks,
Charles
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,
target='V102', weight = 'weight',
tag = NULL, hard_parse = F)
system('head -3 ../out.vw')
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)
system('head -3 ../out.vw')
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Fred
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for the addressee.
You must not disclose, forward, print or use it without the
permission of the sender.
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Fred
Hi Peter,
Starting with S4Vectors 0.7.12, labeledLine() belongs to S4Vectors so
using the triple colon should not be necessary (and doing so will
actually trigger a note from R CMD check). Can you provide more
details on why you need this?
Thanks,
H.
On 08/09/2015 09:16 PM, Peter Hickey
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Done in BiocGenerics 0.15.4.
H.
On 07/29/2015 11:00 AM, Hervé Pagès wrote:
Hi Steve,
On 07/29/2015 10:40 AM, Steve Lianoglou wrote:
Hi folks,
I'm looking to define a `subset` method on an S4 class of mine, but
can't find where to import the generic from.
That's because subset
/cleaner if we make subset() an explicit
generic by adding setGeneric(subset) to BiocGenerics. Which I'm
going to do right now. Then you'll be able to import the subset()
generic from BiocGenerics.
Cheers,
H.
Can anyone provide a pointer?
Thanks,
-steve
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message.
maybe this exists already
-Mike
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with GRCh37 annotations.
Is there a trick to transform a 'SNPlocs' object, such as
'SNPlocs.Hsapiens.dbSNP142.GRCh37', into an 'XtraSNPlocs'?
Ne remets jamais à demain... :p
Cheers,
Fred
Frederic Commo
Bioinformatics, U981
Gustave Roussy
De : Hervé Pagès [hpa
Gustave Roussy
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compatibility conflicts. But I wanted to know why R has
never had a float data type available?
Regards,
Charles
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Done in SummarizedExperiment 0.3.2.
Thanks for the feedback,
H.
On 06/29/2015 10:26 PM, Hervé Pagès wrote:
Hi Nico,
It seems reasonable indeed to support rowRanges- on
SummarizedExperiment0. It might be a little bit surprising for the
user that the setter changes the class of the object
: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
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in the internal representation of class A
always break serialized A and B objects, no matter what).
Cheers,
H.
Thanks again,
E.
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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
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PM, Hervé Pagès hpa...@fredhutch.org
mailto:hpa...@fredhutch.org wrote:
Elena,
On 06/18/2015 10:48 AM, Elena Grassi wrote:
Hi Hervé,
thanks for your kind answer - refactoring is always good, I've
lagged
behind in the last months not following
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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...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
was great and RSE is already better in some respects.
But with a clear roadmap and more input, I bet it (and a tight clean definition
of what it is and isn't supposed to do) would be better-er.
(Steps off soapbox)
--t
On Jun 18, 2015, at 10:25 AM, Hervé Pagès hpa...@fredhutch.org wrote:
Hi
interactiveDisplayBase_1.7.0
[31] httpuv_1.3.2 stringi_0.4-1
[33] RCurl_1.95-4.6 crayon_1.3.0
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Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
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Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667
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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...@fredhutch.org
Phone: (206) 667-5791
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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...@fredhutch.org
Phone: (206) 667-5791
Fax:(206
] S4Vectors_0.7.4 BiocGenerics_0.15.2
loaded via a namespace (and not attached):
[1] XVector_0.9.1
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