; > --
> > Dario Strbenac
> > University of Sydney
> > Camperdown NSW 2050
> > Australia
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/
ersity of Sydney
> Camperdown NSW 2050
> Australia
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Michael Lawrence
Principal Scientist, Director of Data Science and Statistical Computi
uot;integerOrMissing"),
> 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
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 exampl
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 us
s from work - ~ ~~ ~ - https://mastodon.technology/@charles_plessy
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Michael Lawrence
Principal Scientist, Director of Data Science and Statistical Computing
Genentech, A Member of
,
Michael
--
Michael Lawrence
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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhz
______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Michael Lawrence
Senior Scientist, Data Science and Statistical Computing
Genentech, A Member of the Ro
gt;
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Michael Lawrence
Senior Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 2
etImageRegistry/202
> > Calls: render ... -> assert_image -> ->
> > magick_image_trim
> >
> >
> > ## Bioc-devel (3.11) Linux and Windows fails
> >
> >
> http://bioconductor.org/checkResults/release/bioc-LATEST/regionReport/malbec1-buildsrc.html
>
_isName
> Referenced 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, Bioinformatic
9024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax:(206) 667-1319
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Michael Lawren
b/libRblas.0.dylib
> >
> > 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
> >
> >
> > at
any cases 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 Instit
st be a vector, not a `test2` object
> > Run `rlang::last_error()` to see where 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
&g
N instead (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.c
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, Bio
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 Ro
urOav62YTOmxYcYZ4000MY8&e=>.
> >
> > 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
> >> af
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,
klayer::import.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
github), but first 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, Adity
edsrf)[
> !is.na(gene_id),
> 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 back
behalf of 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 encounter
.@mpi-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
r function read_bed, based on 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 Bha
o use S4 and 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:
`extraCols` 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..
I am 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: Bh
# Plot and return
> title <- paste0(providerVersion(bsgenome), ': ', basename(bedfile))
> if (plot) plot_karyogram(gr, title)
> gr
> }
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://sta
el [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`
>
>
ays
>
> #' Slop granges for both strands, merging overlaps
> #' @param gr \code{\link[GenomicRanges]{GRanges-class}}
> #' @param leftstart number
> #' @param rightend number
> #' @return \code{\link[GenomicRanges]{GRanges-class}}
>
> > 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
t necessarily
> 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.
> >
> > O
nome
> #' @export
> methods::setAs( "BSgenome",
> "GRanges",
> function(from) from %>%
> GenomeInfoDb::seqinfo() %>%
> as('GRanges'))
>
> Thankyou for feedba
3V3xDy55M&s=oBSScH5uD5j0vCAaj4dfWepjiNGtHm9q5gA8eaIudZ4&e=
> > > and redirected here following Martin's suggestion)
> > >
> > > Thankyou :-)
> > >
> > > Aditya
> > >
> > > [[alternative HTML version deleted]]
>
row.names=NULL, optional=optional, ...)
>
> }
>
>
>
> setMethod("as.data.frame", "Vector",
>
> function(x, row.names=NULL, optional=FALSE, ...)
>
> {
>
> x <- as.vector(x)
>
> as.dat
Sgenome')
>
> That loads all these 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
rt.bioconductor.org/p/124442/>
> and redirected here following Martin's suggestion)
>
> Thankyou :-)
>
> Aditya
>
> [[alternative HTML version deleted]]
>
> _______
> Bioc-devel@r-project.org mailing list
>
selection = GenomicRanges::reduce(regs),
> + as = 'RleList'
> + )
> > identical(result, result2)
> [1] TRUE
>
> library('sessioninfo')
> options(width = 120)
> session_info()
>
> ## Same as yesterday except:
> rtracklayer1.45.320
-11-05 [1] CRAN (R 3.6.0)
> # SummarizedExperiment 1.15.62019-07-31 [1] Bioconductor
> # 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] CRA
t; and
> > >>> 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 a
code. 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
>
>
>
>
> &
gt; If you go down 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> wrot
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 fo
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,
>>
&g
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
> the
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:
&g
n Tue, 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
> > re
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 Z
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
> bui
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 t
>
> Message: 1
> 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 Lawr
bloat to the
> methods 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 th
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 exam
switch back to the setMethod("colSums",
> 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
x,ANY,ANY-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
> >
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")
>set
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 was
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,
along
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 ca
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 no
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 Her
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" <
> bioc-devel-bo
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 of
I think you're doing the right thing, suggesting the data package from the
software package. This might require some manual intervention on the build
system side to ensure that the software package is installed before passing
full check, so that the data package can be installed/checked and finally
Another concern with kent utils (as opposed to kent lib) is the
non-open-source licensing.
Michael
On Sat, Aug 18, 2018 at 10:11 AM, Tim Triche, Jr. wrote:
> Vince beat me to it. Don’t use Kent utils unless you have to. If you have
> something like a bigBed parser, I could perhaps help clean it
Hi Leonardo,
I'm aware that the new ggplot2 is breaking ggbio. I haven't yet
convinced myself to actually fix it, even though I know there's no way
to avoid it. ggbio represents a big piece of technical debt, and I'm
not sure how to pay it off.
Michael
On Wed, Jun 6, 2018 at 1:03 PM, Leonardo Co
netics
> Stübeweg 51, Freiburg
>
> From: Bhardwaj, Vivek
> Sent: Saturday, May 19, 2018 10:35 AM
> To: Michael Lawrence; Martin Morgan
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?
>
>
>
On Fri, May 18, 2018 at 2:26 PM, Martin Morgan
wrote:
> You can create a plain text file in the root directory of your package
> .BBSoptions with the line
>
> UnsupportedPlatform: win
>
> Your package will not be available on Windows, losing about 1/2 your
> potential audience.
I'm not sure how
Only if Rsubread is used unconditionally.
On Fri, May 18, 2018 at 2:00 PM, Gabe Becker wrote:
> Vivek,
>
> Why (ie in what sense) is the package suggested? Is it used in your tests,
> examples, or vignette?
>
> If so, those would also fail during R CMD check if the package is not
> available even
nt.
> I have some functions that take as input a single range -> calculate number
> of reads that overlap the range -> subset the range into K number of
> segments based on coverage patterns across the range.
>
> Thanks!
> Jack
>
>
> Michael Lawrence wrote:
>
Just out of curiosity, why are you looping over a GRanges in the first place?
On Mon, May 14, 2018 at 7:28 AM, Jack Fu wrote:
> Hey all,
>
> I think some of the recent changes to GRanges has affected using the
> apply class functions with GRanges objects:
>
> o GenomicRanges now is a List subcl
>
> I opted for a simpler workaround, for now, renaming my abstract class to
> avoid the collision.
>
> - Paul
>
> > On May 8, 2018, at 8:25 AM, Michael Lawrence
> wrote:
> >
> > Thanks Paul.
> >
> > I've made improvements to the methods package
just calls the next
method. Ideally though Gviz would just drop its one.
Michael
On Mon, May 7, 2018 at 11:14 AM, Paul Shannon <
paul.thurmond.shan...@gmail.com> wrote:
> Hi Michael,
>
> > On May 4, 2018, at 1:36 PM, Michael Lawrence
> wrote:
> >
> > Do you have a
Do you have a reproducible example of this? It's probably a bug in the
methods package.
Thanks,
Michael
On Fri, May 4, 2018 at 10:52 AM, Paul Shannon <
paul.thurmond.shan...@gmail.com> wrote:
> I just discovered a class name collision - AnnotationTrack, in Gviz and my
> new package igvR. wish
ds.
>
> Thanks,
> H.
>
>
> On 04/30/2018 01:43 PM, Michael Lawrence wrote:
>>
>> It's checked into devel now. Thanks for the well documented examples,
>> Hervé.
>>
>> On Mon, Apr 30, 2018 at 10:26 AM, Michael Lawrence
>> wrote:
&
It's checked into devel now. Thanks for the well documented examples, Hervé.
On Mon, Apr 30, 2018 at 10:26 AM, Michael Lawrence wrote:
> I've fixed it and will push to R-devel as soon as it passes checks.
>
> Michael
>
> On Sun, Apr 29, 2018 at 9:04 PM, Michael Lawrenc
It would be great to be able to define a matrix-like abstraction
independent of 'matrix' and 'DelayedMatrix'. It could also encompass
objects from the Matrix package and potentially other things. So you
could define a parent class of 'matrix' using setClassUnion() and then
use setIs() to establish
I've fixed it and will push to R-devel as soon as it passes checks.
Michael
On Sun, Apr 29, 2018 at 9:04 PM, Michael Lawrence wrote:
> Just noticed this thread. I will look into this and hopefully fix it.
>
> On Sun, Apr 29, 2018 at 6:12 PM, Hervé Pagès wrote:
>> Hi,
>
Just noticed this thread. I will look into this and hopefully fix it.
On Sun, Apr 29, 2018 at 6:12 PM, Hervé Pagès wrote:
> Hi,
>
> I made progress on this. This has actually nothing to do with Java.
> You get the same thing with the flexmix package. What rJava and flexmix
> have in common is tha
out renaming Annotated? Isn't having 2 classes around with the
>>> same name fundamentally a bad situation? No amount of workarounds will
>>> change that.
>>>
>>> H.
>>>
>>>
>>> On 04/12/2018 04:06 PM, Michael Lawrence wrote:
>>&
;
> is(Biobase::ExpressionSet(), "ExpressionSet") # TRUE
>
>
> is(Biobase::ExpressionSet(), Biobase %c% ExpressionSet) # TRUE
>
>
>
>
>
>
> On Thu, Apr 12, 2018 at 3:57 PM, Michael Lawrence
> wrote:
>>
>> Hi Davide,
>>
>> We can ge
ectors implement the
> workaround that you mentioned?
>
> Happy to create a pull request on Github if that helps.
>
> We’re trying to solve this to fix the clusterExperiment package build on
> Bioc-devel.
>
> Thanks,
> Davide
>
>
> On Apr 12, 2018, at 1:27 PM, Micha
gt; > 3R6_2.2.2
>> > [33] XML_3.98-
>> > 1.10 purrr_0.2.4tidyr_0.8.0reshape
>> > 2_1.4.3
>> > [37] magrittr_1.5 codetools_0.2-
>> > 15 assertthat_0.2.0 bold_0.5.0
>> > [41]
>> > taxize_0.9.3
I'm surprised that DelayedMatrix inherits from DataTable. Originally
at least, DataTable was meant to represent a data.frame-like object,
not a matrix-like object. Since rbind2() and cbind2() assume that
DataFrame is a valid default implementation of DataTable, they will
coerce the matrix to a Data
The problem with requiring explicit tensor flow installation is that
it is tantamount to a system dependency in many ways, and those are
annoying. Herve points out the problems with installing at load time.
My suggestion was to install the package the first time someone tries
to e.g. load an R matr
Presumably the installation of tensor flow only has to happen once, so you
could factor your interface such that it installs tensor flow lazily.
Michael
On Wed, Mar 28, 2018 at 9:23 AM, Kieran Campbell
wrote:
> Hi all,
>
> Rstudio have released the Tensorflow package for R -
> https://tensorflo
Agreed about encapsulating plot parameters. I was thinking in terms of user
convenience, relying on defaults.
On Wed, Mar 14, 2018 at 12:40 PM, Paul Shannon <
paul.thurmond.shan...@gmail.com> wrote:
> Hi Michael,
>
> Set me straight if I got this wrong. You suggest:
>
> > There should be no nee
You could look at the rtracklayer API. For example, using gets functions
like track<-() and range<-() to set track and region may be more natural to
R users. Then again, if there were endomorphic functions add_track() and
set_range(), the API would support chaining. There should be no need to
expli
On Fri, Mar 9, 2018 at 12:36 PM, Cook, Malcolm wrote:
> Hi,
>
>
> > -Original Message-
> > From: Bioc-devel On Behalf Of
> > Michael Lawrence
> > Sent: Friday, March 09, 2018 1:49 PM
> > To: Paul Shannon
> > Cc: Gabe Becker ; bioc-deve
tious, though, about pushing limits and using the latest websocket
> extension, and found the fallback to local files quite adequate for now.
>
> I’ll look at ucsc.R.
>
> - Paul
>
>
> > On Mar 9, 2018, at 11:48 AM, Michael Lawrence
> wrote:
> >
> > Couple
Couple of things:
1) Check out epivizr and the surrounding infrastructure (maybe Hector can
chime in). It's able to serve up data directly from R; would be nice if we
could do that with IGV, instead of writing out to files. That would require
it to talk to some standard API, like the old DAS.
2)
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