uence of some
> other change?
>
> Thanks,
> —Russell Almond
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______
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Senior Princ
---
> > Dario Strbenac
> > University of Sydney
> > Camperdown NSW 2050
> > Australia
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailma
Sydney
> Camperdown NSW 2050
> Australia
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Michael Lawrence
Principal Scientist, Director of Data Science and Statistical Computing
Genente
gt; function(A = c('L', 'M', 'N'), B = 500, C = 100, D, E, F, G, H)
> {
> if(missing(A)) A <- 'L' # Mimick match.arg.
> if(missing(B)) B <- 500L # Hack to implement parameter defaults not
> specified by generic.
> if(missing(C)) C <- 100L
> new("ParamsSet", A = A, B = B)
> })
&g
psed
> 760.018 15.093 775.090
>
> Strangely, if I rerun this code again, it works quickly the second time.
>
> > system.time(CrossValParams("Leave-k-Out", leave = 2))
>user system elapsed
> 0.145 0.000 0.145
>
> I haven't been able to come up with a minimal reproducile example
Hi Shraddha,
>From the rtracklayer perspective, it sounds like Rsamtools is
(indirectly) bringing in those system libraries. I would have expected
zlibbioc to cover the zlib dependency, and perhaps bz2 and lzma
support is optional. Perhaps a core member could comment on that.
In the past, I've
m work - ~ ~~ ~ - https://mastodon.technology/@charles_plessy
>
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Genentech, A Member of t
,
Michael
--
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Senior Scientist, Director of Data Science and Statistical Computing
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
micha...@gene.com
Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
> > Bioc-devel@r-project.org mailing list
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TUxwEgK30pAlKpQ6SAJcnT6kPVktHlJ-9R_Al6ri-Mg=uqmel2bDfLejAXpRYsi-PFcG
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se an error, or at least warning?
> >
> > Best Regards,
> > Jan Gorecki
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> __
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>
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Michael Lawrence
Senior Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
micha..
nux and Windows fails
> >
> >
> http://bioconductor.org/checkResults/release/bioc-LATEST/regionReport/malbec1-buildsrc.html
> >
> > However, I see at
> >
> http://bioconductor.org/checkResults/devel/bioc-LATEST/regionReport/malbec2-buildsrc.html
> > that the err
enced from: /usr/local/lib/libsbml.5.dylib
> Expected in: flat namespace
> in /usr/local/lib/libsbml.5.dylib
> Error: loading failed
> Execution halted
>
> Any hints?
>
> Thanks, Martin
>
--
Michael Lawrence
Senior Scientist, Bioinformatics and Computational
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax:(206) 667-1319
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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Michael Lawrence
Senior Scientist, Bioinformatics
t; LAPACK:
> >
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
> >
> >
> > locale:
> >
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> >
> > attached base packages:
> >
> > [1] stats
or do you
> foresee a lot of changes coming in the 4.* series?
>
> On Tue, Feb 25, 2020 at 3:39 PM Michael Lawrence via R-devel
> wrote:
>>
>> This seems to work as expected (returning "hi!") in R-devel, but there
>> have been so many destabilizing cha
This seems to work as expected (returning "hi!") in R-devel, but there
have been so many destabilizing changes to methods that it would be
tough to port this to release. Probably should just wait for 4.0.
Michael
On Tue, Feb 18, 2020 at 8:00 PM Michael Lawrence wrote:
>
> T
r/local/lib/R/lib/libRblas.so
> > LAPACK: /usr/local/lib/R/lib/libRlapack.so
> >
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> > [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>
ases where a CRAN package migrated to
> Bioconductor after complying with the ecosystem policies.
>
> Thanks a lot.
>
> Best wishes.
>
> Stefano
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Med
here the error occurred.
> > ```
> >
> > Could you please advise whether a tidyverse based package can be
> > hosted on
> > Bioconductor, and if S4 classes are really mandatory? I need to
> > understand
> > if I am forced to submit to CRAN instead (although Bioconductor would
>
(although Bioconductor would be a
> good fit, sice I try to interface transcriptional analysis tools to tidy
> universe)
>
>
> Thanks a lot.
> Stefano
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/
Yep that about sums it up.
On Wed, Feb 5, 2020 at 8:37 PM Stefano Mangiola
wrote:
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Michael Lawrence
Senior Scientist,
gt; > poverlaps(GRanges("chr1:11-15"), GRanges("chr1:16-20"))
> Error in isSingleNumber(minoverlap) : object 'minoverlaps' not found
>
> H.
--
Michael Lawrence
Senior Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Of
> >
> > Best,
> >
> > Tobias
> >
> > Am 29.01.20 um 18:02 schrieb Pages, Herve:
> >> Yes poverlaps().
> >>
> >> Or pcompare(), which should be even faster. But only if you are not
> >> afraid to go low-level. See ?rang
eq_along(query)) out[i] <- (overlapsAny(query[i], subject[i]))
> out
>
> # Approach 3 (wrong results)
> as.numeric(overlapsAny(query, subject))
> as.numeric(overlapsAny(split(query, 1:4), split(subject, 1:4)))
>
>
> Maybe someone has an idea to speed this up?
>
>
> Best,
> > substitute(x1)
> x1
>
>
> Best regards,
> Daniel
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Michael Lawrence
Senior Scientist, Bioinformatics and Computational Biolog
I defied is somehow interfering with the "index" class union in
> > Matrix, R/AllClass.R, line 809
>
> > 3. Why should the class union I defined interfere with the inner workings
> > of a separate package?
>
> There is no good reason ...
>
> > 4.
t; SEXP vec = PROTECT(ScalarString(char_));
> SEXP call = PROTECT(lang3(sym_inherits, x, vec));
> bool ans = LOGICAL(eval(call, R_GlobalEnv))[0]==1;
> UNPROTECT(2);
> return ans;
> }
>
> ______
> R-devel@r-project.org ma
port.bed('SRF.bed', genome = 'mm10') # this works
>
> # But this doesn't
> seqinfo1<-
> GenomeInfoDb::seqinfo(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10)
> rtracklayer::import.bed('SRF.bed', genome = seqinfo1)
>
> So I am requesting feedback.
> I thought to u
tions for doing so?
>
> Thank you
> Travers
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Michael Lawrence
Scientist, Bioinform
t need your feedback as to whether
> you think that would be useful :-)
>
> Aditya
>
>
> --
> *From:* Stuart Lee [le...@wehi.edu.au]
> *Sent:* Thursday, October 17, 2019 3:01 AM
> *To:* Michael Lawrence
> *Cc:* Bhagwat, Aditya; bioc-devel@r-
d),
> gene_id := paste0(gene_id, collapse = ';'),
> by = c('seqnames', 'start', 'end', 'strand'))
>
> And was wondering, in general, whether it would be useful to have a
> data.table-based backend for plyranges::groupby()
> And, whether all of this is actually a on-issu
d reason; maybe someone from the R core team
> can shed some light on how they decide whether or not to include a function
> in base R?
>
>
> > Duncan Murdoch
> >
>
> [[alternative HTML version deleted]]
>
> __
&g
ecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> ///
>
> <https://www.inbo.be>
>
>
> Op vr 6 sep. 2019 om 17:16 sc
t; `@<-`(z, "x", value="newer")
> An object of class "Z"
> Slot "x":
> [1] "newer"
>
> > z
> An object of class "Z"
> Slot "x":
> [1] "orig"
>
> >
> > `slot<-`(z, "x", v
Bhagwat,
> Aditya [aditya.bhag...@mpi-bn.mpg.de]
> Sent: Wednesday, September 18, 2019 1:57 PM
> To: Michael Lawrence
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] read_bed()
>
> Hi Michael,
>
> That's a software design dilemma I've encountered a few times.
>
-bn.mpg.de]
> Sent: Wednesday, September 18, 2019 11:31 AM
> To: Michael Lawrence
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] read_bed()
>
> (Typo corrected to avoid confusion)
>
> Michael,
>
> rtracklayer::import.bed() indeed works perfectly for me, so I a
data.table::fread is
> doing the job, so I will stick to that .
>
> Thank you for all feedback,
>
> Cheers,
>
> Aditya
>
>
>
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat,
> Aditya [aditya.bha
nd whether to mix the two).
>
> Aditya
>
> ____
> From: Michael Lawrence [lawrence.mich...@gene.com]
> Sent: Tuesday, September 17, 2019 2:23 PM
> To: Bhagwat, Aditya
> Cc: Michael Lawrence; Shepherd, Lori; bioc-devel@r-project.org
> Subject: Re: [Bioc
aCols` argument explicitly, so it must be one of the ellipsis arguments,
> but `?rtracklayer::import` does not mention it. Should I say extraCols = 10
> (ten extra columns) or so?
>
> Aditya
>
> ____
> From: Michael Lawrence [lawrence.mich...@gen
curious as to why you feel that having additional columns in a bedfile
> would break it?
>
> Cheers,
>
> Aditya
>
> ____
> From: Michael Lawrence [lawrence.mich...@gene.com]
> Sent: Tuesday, September 17, 2019 1:41 PM
> To: Bhagwat
mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that
[bioc-devel-boun...@r-project.org] on behalf of Bhagwat,
> Aditya [aditya.bhag...@mpi-bn.mpg.de]
> Sent: Monday, September 16, 2019 10:30 AM
> To: Michael Lawrence
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`
>
> Hmm
Mmusculus
> #' gr <- read_bed(bedfile, bsgenome)
> #' gr
> #' slop_fourways(gr)
> #' @export
> slop_fourways <- function(gr, leftstart = -22, rightend = 22){
>
> # Comply
> . <- NULL
>
> # Slop
> if (verbose) cmessage('\
> Tobias
> >
> > _______
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> The University of Edinburgh is a charitable body, registered in S
essarily
> represented in seqnames(grl)).
>
> H.
>
> On 9/11/19 08:26, Hervé Pagès wrote:
> > The unique seqnames is what we call the seqlevels. So just:
> >
> >as(seqinfo(bsgenome)[seqlevels(grl)], "GRanges")
> >
> > H.
> >
> > On 9/1
;BSgenome",
> "GRanges",
> function(from) from %>%
> GenomeInfoDb::seqinfo() %>%
> as('GRanges'))
>
> Thankyou for feedback,
>
> Aditya
>
> ___
l@r-project.org mailing list
> > >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M=cEojiObibdSuzmh21opvy85D
ames=NULL, optional=optional, ...)
>
> }
>
>
>
> setMethod("as.data.frame", "Vector",
>
> function(x, row.names=NULL, optional=FALSE, ...)
>
> {
>
> x <- as.vector(x)
>
> as.data.fra
John Tukey
> ///
>
> <https://www.inbo.be>
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/l
dependencies.
> From your answer, I understand that there is currently no alternative to
> loading all these dependencies.
> I guess because these dependencies are needed to provide for all required S4
> methods for the BSgenome class, am I right?
>
> Is there a way to define a m
442/>
> and redirected here following Martin's suggestion)
>
> Thankyou :-)
>
> Aditya
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailm
sounds
> like a great design for strcapture with an atomic prototype.
>
> Best,
> CG
--
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
micha...@gene.com
Join Genentech on LinkedIn |
e to have in base. For example, MATLAB
> and Pandas regex both all
ow non-dropping empty matches (though of course I acknowledge Pandas is not a
base language).
>
> Best,
> CG
--
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Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche
___
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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Office +1 (650) 225-7760
micha...@gene.com
Join Genente
n = GenomicRanges::reduce(regs),
> + as = 'RleList'
> + )
> > identical(result, result2)
> [1] TRUE
>
> library('sessioninfo')
> options(width = 120)
> session_info()
>
> ## Same as yesterday except:
> rtracklayer1.45.32019-08-22 [1] Github
> (lawr
ctor
> # testthat * 2.2.1 2019-07-25 [1] CRAN (R 3.6.0)
> # usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.0)
> # withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
> # XML3.98-1.20 2019-06-06 [1] CRAN (R 3.6.0)
> #
gt; Khoury College of Computer Sciences
> Northeastern University
> kuwisdelu.github.io<https://kuwisdelu.github.io>
>
>
>
>
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-de
ing `[[.MYCLASS` 9 times ?
>
> Is there a way to avoid `class<-` to call `[[.MYCLASS` ?
>
>
> Thank you in advance for your help and suggestions.
>
> Gionata
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-proj
[[alternative HTML version deleted]]
>
> __
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--
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the
; >>> GRanges for inversions and copy number changes, but I don't know what
> > >>> would be the recommended way to store them all together using
> standard
> > >>> Bioconductor objects.
> > >>>
> > >>> And actually, is there an
. It's my understanding that that's a general
> trend. Now, do correct me if I'm wrong but IIRC, that doesn't work well
> with generics because they don't get registered. If so, that might be
> another consideration.
>
> Cheers,
> Boris
>
>
>
>
> > On 2019-05-01, at 12:18, M
own the generic route, think hard about the name.
>
>
> On Mon, Apr 29, 2019 at 10:38 AM Michael Lawrence via Bioc-devel <
> bioc-devel@r-project.org> wrote:
>
>> On Mon, Apr 29, 2019 at 6:55 AM Pages Gallego, M. <
>> m.pagesgall...@umcutrecht.nl> wrote:
>>
>
On Mon, Apr 29, 2019 at 6:55 AM Pages Gallego, M. <
m.pagesgall...@umcutrecht.nl> wrote:
> Dear all,
>
> I am currently developing a package and I am a bit confused in when one
> should define a generic. Let me propose an example:
> Suppose I have defined 3 classes: one for proteomics data, one
This should be in trunk and the 3.6 release branch.
On Thu, Mar 28, 2019 at 9:57 AM Michael Lawrence wrote:
> Not yet. Too busy breaking other things ;) I'll move it up on my TODO list.
>
> On Thu, Mar 28, 2019 at 9:16 AM Pages, Herve wrote:
>
>> Hi Michael,
>>
>>
Thanks for the report. It should be fixed in S4Vectors 0.21.22.
On Mon, Apr 1, 2019 at 12:01 PM Ludwig Geistlinger <
ludwig.geistlin...@sph.cuny.edu> wrote:
> I have a SummarizedExperiment with putatively user-annoted rowData.
> I have a function that does computation on this SE and appends
>
Not yet. Too busy breaking other things ;) I'll move it up on my TODO list.
On Thu, Mar 28, 2019 at 9:16 AM Pages, Herve wrote:
> Hi Michael,
>
> Did you get a chance to make this change?
>
> Thanks,
>
> H.
>
> On 2/11/19 08:07, Michael Lawrence wrote:
>
And it is used profusely by the methods package.
On Thu, Mar 28, 2019 at 4:53 AM Gábor Csárdi wrote:
> On Thu, Mar 28, 2019 at 11:43 AM Martin Maechler
> wrote:
> [...]
> >
> > Indeed... and as I mentioned I had never actively noticed the
> > use of topenv() at all...
>
> FWIW topenv() is used
Gabe described my main concern. Specifying a coercion function asserts that
the data (1) were what was expected and (2) were converted into what was
expected. Allowing a coercer to delegate to a "next method" is a good idea,
but keep in mind that any function that did that would not confer the
This has some nice properties:
1) It self-documents the input expectations in a similar manner to
colClasses.
2) The implementation could eventually "push down" the coercion, e.g.,
calling it on each chunk of an iterative read operation.
The implementation needs work though, and I'm not
Please file a bug on bugzilla so we can discuss this further.
On Tue, Mar 26, 2019 at 11:53 AM Kurt Van Dijck <
dev.k...@vandijck-laurijssen.be> wrote:
> Hello,
>
> I want to find out if this patch is ok or not, and if not, what should
> change.
>
> Kind regards,
> Kurt
>
>
Mar 26, 2019 at 1:35 PM Michael Lawrence <
> lawrence.mich...@gene.com>
> wrote:
>
> > DESeq2 seems to be working with S4Vectors 0.21.19. If you're using an
> > older version, you'll need to update once that version appears in the
> > repository. Sorry f
DESeq2 seems to be working with S4Vectors 0.21.19. If you're using an older
version, you'll need to update once that version appears in the repository.
Sorry for the mess. Trying to clean up the [<- stuff on DataFrame and
Vector to make them easier to extend.
On Tue, Mar 26, 2019 at 10:19 AM Yue
This is due to some buggy changes to the internals of the S4Vectors
package. I should be able to fix these today.
On Sat, Mar 23, 2019 at 7:41 AM Karl Stamm wrote:
> My package rgsepd has failed build recently.
>
> I don't understand the error message, and need some guidance. It says Error
>
t on the roadmap. The alias instability and the fact that the user
> has no way to know if s/he should do ?`foo,numeric-method` or
> ?`foo,numeric,ANY-method` to find the method has been a long-standing
> problem.
>
> H.
> On 3/21/19 21:29, Michael Lawrence wrote:
>
> If we
Y suffix in its signature gets added to the ecosystem. See my post about
> this to the Bioc-devel mailing list a couple of months ago:
> https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014603.html
>
> So overall isn't this truncation more trouble than it's worth?
>
> H.
Preferably the public API would be camel case for consistency with
other Bioconductor APIs (at least the core ones). It's not a huge deal
though.
On Tue, Feb 26, 2019 at 8:12 AM Turaga, Nitesh
wrote:
>
> As long as it’s consistent, you can use another style. Consistency helps
> reviewers read
; Date: Sun, 10 Feb 2019 13:36:43 +
> From: Aaron Lun
> mailto:infinite.monkeys.with.keyboa...@gmail.com>>
> To: "Pages, Herve" mailto:hpa...@fredhutch.org>>,
> Martin Maechler
> mailto:maech...@stat.math.ethz.ch>>
> Cc: Michael Lawrence
> mailto:lawrenc
package?
>
> My 2 cents,
>
> H.
>
>
> On 1/30/19 13:35, Michael Lawrence via Bioc-devel wrote:
> > Unrelated to the specific question, a generic function introduces more
> > vocabulary into the ecosystem. Since SingleCellExperiment defines the
> > standard inte
Unrelated to the specific question, a generic function introduces more
vocabulary into the ecosystem. Since SingleCellExperiment defines the
standard interface, why not make a new method on logcounts()?
Back on topic, what if the methods package were to support forward
class declarations? For
> signature(x="SomeClass"), ...) form, then I have to switch back all the
> aliases in all my downstream packages to the short form again!
>
> This fragility of the alias syntax was one of the motivations for me to
> put many setGeneric statements of the for
method} to
> \alias{colSums,dgCMatrix-method}).
>
> Anybody wants to try to make a patch for this?
>
> H.
>
> On 1/28/19 19:00, Michael Lawrence wrote:
> > I agree (2) is a good compromise. CC'ing Martin for his perspective.
> >
> > Michael
> >
> > On Mo
I agree (2) is a good compromise. CC'ing Martin for his perspective.
Michael
On Mon, Jan 28, 2019 at 6:58 PM Pages, Herve wrote:
>
> Hi Aaron,
>
> The 4 matrix summarization generics currently defined in BiocGenerics
> are defined as followed:
>
>setGeneric("rowSums", signature="x")
>
Hi Steve,
Pretty sure MultiAssayExperiment, containing SingleCellExperiments,
would fit the bill, but I'm not familiar with those data types.
Michael
On Tue, Jan 22, 2019 at 2:18 PM Steve Lianoglou
wrote:
>
> Comrades,
>
> Sorry if I'm out of the loop and have missed anything obvious.
>
> I
Thanks for the report. There is a comment from 2001 in the header for
reconcilePropertiesAndPrototype() that states:
"The prototype may imply slots not in the properties list. It is not
required that the extends classes be define at this time. Should it
be?"
But somewhere in the mid 2000's, I
ffects of running the controller.
>
> Are there any better ways to subvert the vignette building procedure to get
> the desired effect of running drake::make() and recognition of the resulting
> HTMLs as vignettes?
>
> -A
>
> > On 18 Dec 2018, at 17:41, Michael Lawrence
ing that the result object is generated by one
> vignette before it is needed by another vignette.
>
> -A
>
> > On 18 Dec 2018, at 14:14, Martin Morgan wrote:
> >
> > Also perhaps using BiocFileCache so that the result object is only
> generated once, then cached for
I would recommend against dependencies across vignettes. Ideally someone
can pick up a vignette and execute the code independently of any other
documentation. Perhaps you could move the code generating those shared
resources to the package. They could behave lazily, only generating the
resource if
Dear Val/Herve:
Does this mean that Bioconductor depends on C++14? Keeping up with the C++
standards is a struggle, at least for those maintaining deployments on
clusters with slow-moving enterprise linux distributions.
It would be helpful if someone could document the minimum C++ standard,
Argument matching is by name first, then the still missing arguments
are filled positionally. Unnamed missing arguments are thus left
missing. Does that help?
Michael
On Fri, Nov 30, 2018 at 8:18 AM Emil Bode wrote:
>
> But the main point is where arguments are mixed together:
>
> >
On Thu, Nov 29, 2018 at 8:32 AM Kasper Daniel Hansen
wrote:
>
> First, the issue with using class() is that the return is a vector possibly
> with >1 element. This _does_ happen. This is why is() etc is much better,.
>
And of course it also considers S4 inheritance.
> Second, why do you need
Whenever they are calling a primitive, because primitives match
arguments positionally. Of course, you then you need to introduce the
concept of a primitive.
You could also make an argument from the code clarity perspective, as
typically primitives have simple interfaces and/or are used
On Sun, Nov 18, 2018 at 9:16 PM L Rutter wrote:
>
> Hello all:
>
> I am preparing to submit a package to Bioconductor and have one note
> from R CMD BiocCheck that I have been unable to resolve. The note I
> receive is:
>
> NOTE: Consider multiples of 4 spaces for line indents, 40 lines(1%) are
t could solve my error as well, but the warnings about S4 dispatch on
> “...” are still a problem.
>
> -Kylie
>
> On Nov 14, 2018, at 12:38 PM, Michael Lawrence
> wrote:
>
> The use of c() in the implementation of [[<- is problematic, since [[<-
> has the semantic of
fic naming scheme. This proved
> fragile, difficult to maintain, and easily broken, so I am now using slots
> to contain this metadata so they can be validated independently of whatever
> user-supplied columns exist.
>
> Kylie
>
> ~~~
> Kylie Ariel Bemis
> College of Com
I don't want to derail this thread, but why is coerce2() necessary? Would
it be possible to fold its logic into as() without breaking too much?
Kylie,
It would help to see your code, with some pointers to where things break.
Michael
On Wed, Nov 14, 2018 at 5:36 AM Bemis, Kylie
wrote:
> Hi
For the general problem of understanding your package dependency structure,
see http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html.
On Mon, Nov 5, 2018 at 3:44 PM Martin Morgan
wrote:
>
>
> On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres" <
>
Yes, please follow Hervé's instructions.
On Fri, Nov 2, 2018 at 3:41 PM Håkon Tjeldnes
wrote:
> Just a quick question, in 3.8 we used biogenerics::lengths for ORFik,
> since it was much faster than base, for our dataset 1 second vs 30 minutes.
> We should change to S4 version of lengths now ?
>
This underscores how setClassUnion() can lead to unintended consequences.
Inheritance is an extreme form of coupling, and subclasses are expected to
obey the contract specified by the super class. By defining a class union,
the developer is essentially inventing a contract without any commitment
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