This is more of a support site question.
The stack() function is relevant here, but it won't fill in the missing columns.
Note though that there are some conveniences that might help a tiny
bit, like how colnames(DFL) returns a CharacterList, so you can do
unique(unlist(colnames(DFL))).
In theor
Hi Dario,
Thanks for the reproducible example. The time comes from building all
the possible signatures when dispatching the first time. The expense
comes from the length of the signature. After the first dispatch, the
table is cached and everything is fast.
Have you considered just using an ord
Hi Dario,
Thanks for bringing this up. The second time speed could be explained
by the caching that happens inside the methods package. If you are
able to come up with a smaller reproducible example, I would be happy
to help out.
Michael
On Mon, Nov 22, 2021 at 1:00 PM Dario Strbenac via Bioc-de
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
Hi Charles,
Thanks for reaching out. Please ensure that you have built R with xz
(lzma) support. If this does not resolve your problem, please post on
support.bioconductor.org.
Michael
On Thu, Sep 2, 2021 at 2:54 PM Charles Plessy
wrote:
>
> Hello
>
> on my R 4.1.0 system, rtracklayer version 1
Just got this when trying to push a change to IRanges:
Pushing to g...@git.bioconductor.org:packages/IRanges.git
FATAL: W any packages/IRanges m.lawrence DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Have git permissions changed?
Thanks,
Micha
Laurent,
Thanks for bringing this up and offering to help. Yes, please raise an
issue. There's an opportunity to implement faster matching than
base::merge(), using stuff like matchIntegerQuads(), findMatches(), and
grouping().
grouping() can be really fast for character vectors, since it takes
a
Please raise an issue on the rtracklayer GitHub.
Thanks,
Michael
On Sun, Jul 19, 2020 at 8:20 PM Charles Plessy wrote:
>
> On 15/07/2020 10:53, Charles Plessy wrote:
> > On 14/07/2020 19:56, Vincent Carey wrote:
> >> Can you post an example dataset that triggers the error reproducibly?
> >
> > h
setAs() defines methods on the coerce() generic, so you could write
importMethodsFrom(pkg, coerce). However, as() searches the namespace
associated with class(from) for coerce() methods. As long as that
namespace hasn't selectively imported methods on coerce(), it should
end up using the global tab
I bumped the version of ggbio which should propagate a recent fix.
Michael
On Thu, Apr 9, 2020 at 7:11 AM Leonardo Collado Torres <
lcollado...@gmail.com> wrote:
> Hi BioC-devel,
>
> I was able to trace a regionReport error back to ggbio & biovizBase.
> However, I'm completely clueless as to why
Does this work for you?
https://github.com/mythosil/homebrew-libsbml
Michael
On Fri, Apr 3, 2020 at 2:20 AM Martin Morgan
wrote:
> The INSTALL file for rsbml says
>
> ~/b/git/rsbml master$ cat INSTALL
> ...
>
> To build rsbml on the Mac, first install libsbml with:
> `brew install home
Try resending the email as plain text. The list strips HTML content,
so if the message has no text part, there will be no message.
On Thu, Mar 26, 2020 at 9:35 PM Hervé Pagès wrote:
>
> What is the question?
>
> On 3/26/20 17:36, 유도영 wrote:
> >
> > ___
At least with 2020-03-16 r77987 (Mac OS) I wasn't able to reproduce this.
Btw, there's no real need for an S4 method in this case. An S3 method would
work just as well.
On Mon, Mar 16, 2020 at 4:12 PM Henrik Bengtsson
wrote:
> Maybe it's related to:
>
> * The plot() S3 generic function is now in
I would urge you to make the package _directly_ compatible with
standard Bioconductor data structures; no explicit conversion. But you
can create wrapper methods (even on an S3 generic) that perform the
conversion automatically. You'll probably want two separate APIs
though (in different styles), f
There's a difference between implementing software, where one wants
formal data structures, and providing a convenient user interface.
Software needs to interface with other software, so a package could
provide both types of interfaces, one based on rich (S4) data
structures, another on simpler str
Martin's comments are great.
I'll just give some technical help. The "tbl_df" S4 class is already
defined by dplyr (and more properly), so omit the call to
setOldClass(). Then, things work a bit better.
> my %>% nest(-b) # had to fix this from your example
[some ugly result]
Warning messages:
1:
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, Bioinformatics and Computati
That sucks. It was broken since it was added in 2017... now fixed.
On Thu, Jan 30, 2020 at 11:20 AM Pages, Herve wrote:
>
> On 1/30/20 11:10, Hervé Pagès wrote:
> > Yes poverlaps() is a good option, as mentioned earlier.
>
> Well actually not. Looks like it's broken:
>
> > poverlaps(GRanges("chr
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
poverlaps()?
On Wed, Jan 29, 2020 at 7:50 AM web working wrote:
>
> Hello,
>
> I have two big GRanges objects and want to search for an overlap of the
> first range of query with the first range of subject. Then take the
> second range of query and compare it with the second range of subject
> a
Hi Aditya,
This is probably best asked on the support site. When you post there,
please include your sessionInfo().
Thanks,
Michael
On Tue, Oct 22, 2019 at 9:50 AM Bhagwat, Aditya
wrote:
>
> Dear Michael,
>
> Sorry for my incomplete email - the send button got hit too fast. Better this
> time.
I replied on the support site. Let's move the discussion there.
On Thu, Oct 17, 2019 at 1:24 AM Bhagwat, Aditya <
aditya.bhag...@mpi-bn.mpg.de> wrote:
> Thank you Stuart and Michael for your feedback.
>
> Stuart, in response to your request for more context regarding my use
> case, I have updated
Just a note that in this particular case, selfmatch(annotatedsrf) would be
a fast way to generate a grouping vector, like
plyranges::group_by(annotatedsrf, selfmatch(annotatedsrf)).
Michael
On Wed, Oct 16, 2019 at 2:48 AM Bhagwat, Aditya <
aditya.bhag...@mpi-bn.mpg.de> wrote:
> Hi Stuart, Michae
I'd suggest separating the operations on the data from the interface.
You can have both, one layer for programming and another for
interactive analysis.
On Wed, Sep 18, 2019 at 5:05 AM Bhagwat, Aditya
wrote:
>
> In the end I endeavour to end up with a handful of verbs, with which I can do
> all
I'm not sure if a function called read_bed() should be plotting or
printing. Is your BED file a known BED variant, i.e., maybe there is a
better name for the file type than "bed"?
On Wed, Sep 18, 2019 at 3:17 AM Bhagwat, Aditya
wrote:
>
> Actually,
>
> I will keep multicrispr::read_bed(), but wr
I think you probably made a mistake when dropping the columns. When I
provide the extraCols= argument (inventing my own names for things),
it almost works, but it breaks due to NAs in the extra columns. The
"." character is the standard way to express NA in BED files. I've
added support for extra
Having a "." in the function name does not make something "S3".
There's no dispatch from import() to import.bed(). Had I not been a
total newb when I created rtracklayer, I would have called the
function importBed() or something like that. Sorry for the confusion.
On Tue, Sep 17, 2019 at 5:34 AM B
The generic documentation does not mention it, but see ?import.bed.
It's similar to colClasses on read.table().
On Tue, Sep 17, 2019 at 5:15 AM Bhagwat, Aditya
wrote:
>
> Thankyou Michael,
>
> How do I use the extraCols argument? The documentation does not mention an
> `extraCols` argument expli
It breaks it because it's not standard BED; however, using the
extraCols= argument should work in this case. Requiring an explicit
format specification is intentional, because it provides validation
and type safety, and it communicates the format to a future reader.
This also looks a bit like a bed
I don't see an attachment, nor can I find the multicrispr package
anywhere. The "addressed soon" was referring to the BEDX+Y formats,
which was addressed many years ago, so I've updated the documentation.
Broken BED files will never be supported.
Michael
On Tue, Sep 17, 2019 at 4:17 AM Bhagwat, A
It's on the right track. The case where two ranges are produced is
problematic, because we would want this to be a parallel vector
operation, where the length of the input is the same as the length of
the output. So that last case I think might just ignore the leftend
and rightstart arguments with
Thanks for these suggestions; I think they're worth considering.
I've never been totally satisfied with (my function) flank(), because
it's limited and its arguments are somewhat obscure in meaning. You
can check out what we did in plyranges:
https://rdrr.io/bioc/plyranges/man/flank-ranges.html. Y
Third option: use Reduce() from base instead of purr::reduce().
On Thu, Sep 12, 2019 at 2:54 AM O'CALLAGHAN Alan
wrote:
>
> Hi,
>
> Two options.
>
> First option: import either purrr::reduce or GenomicRanges::reduce, and
> call the other with [pkg]::reduce.
>
> Second option: remove the import fo
Good call. Didn't know about seqlevelsInUse().
On Wed, Sep 11, 2019 at 8:29 AM Pages, Herve wrote:
>
> Or more accurately:
>
>as(seqinfo(bsgenome)[seqlevelsInUse(grl)], "GRanges")
>
> since not all seqlevels are necessarily "in use" (i.e. not necessarily
> represented in seqnames(grl)).
>
> H
So why not just do:
as(seqinfo(bsgenome)[unique(unlist(seqnames(grl)))], "GRanges")
Michael
On Wed, Sep 11, 2019 at 5:55 AM Bhagwat, Aditya
wrote:
>
> Thanks Michael,
>
> The important detail is that I want to plot the relevant chromosomes only
>
> relevant_chromosomes <- GenomeInfoDb::seqn
I'm pretty surprised that the karyoploteR package does not accept a
Seqinfo since it is plotting chromosomes. But again, please consider
just doing as(seqinfo(bsgenome), "GRanges").
On Wed, Sep 11, 2019 at 3:59 AM Bhagwat, Aditya
wrote:
>
> Hi Herve,
>
> Thank you for your responses.
> From your
port BSgenome class without attaching
> BiocGenerics (and others)?
>
>
>
> There are
>
> importMethodsFrom(PACKAGE, NAME_OF_METHODS)
>
> importClassesFrom(PACKAGE, NAME_OF_METHODS)
>
> to help with selective importing S4 methods/classes. See section 1.5.6 of
It sounds like you are trying to defer loading of namespaces in order
to save time when they are unnecessary? That's probably going to end
up a losing battle.
On Fri, Sep 6, 2019 at 5:47 AM Bhagwat, Aditya
wrote:
>
> Thank you Michael,
>
> Appreciate your time for helping me fill the gaps in my u
The way to keep a "clean namespace" is to selectively import symbols
into your namespace, not to import _nothing_ into your namespace.
Otherwise, your code will fill with namespace qualifications that
distract from what is more important to communicate: the intent of the
code. And no, there's no wa
Sorry about that. I bumped the version and ported to release.
On Thu, Aug 22, 2019 at 7:50 AM Leonardo Collado Torres
wrote:
>
> Hi Michael,
>
> That was using rtracklayer 1.45.3. However I see at
> https://github.com/lawremi/rtracklayer/commit/90d4209eae05ae2a4af550072c35cada662b4c89
> that you
Sorry, please try 1.45.3. If that works then I'll push it over to release.
On Wed, Aug 21, 2019 at 11:48 AM Leonardo Collado Torres
wrote:
>
> Dear Bioc-devel,
>
> In BioC 3.9 and 3.10 I've noticed some errors on recount which today I
> finally traced. It looks like the internals of
> rtracklayer
The new package StructuralVariantAnnotation is worth mentioning. It
operates on the general "breakend" notation so should be able to represent
any type of structural variant.
On Tue, May 21, 2019 at 3:22 AM Sean Davis wrote:
> On Tue, May 21, 2019 at 2:54 AM Aaron Lun <
> infinite.monkeys.with.k
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,
>>
>> Did you get a chance to make t
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:
> > I propose that we just fix the signatur
You'll just need to wait for that build error to resolve.
On Tue, Mar 26, 2019 at 10:45 AM Yue Zhao (Jason) wrote:
> Thanks, Michael. I saw this error in the bioC 3.9 package building step for
> my package, so I'm not sure how to specify the S4Vector version in that.
>
> On Tue, Mar 26, 2019 at
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
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
Along like the lines of Martin Morgan's comment, simpler signatures
mean simpler software. We can typically limit to single dispatch, and
it indicates how the generic is _meant_ to be used, separating the
data arguments from the modulating accessory parameters. I'm not sure
how valuable dispatching
That will have some consequences; for example, documentation aliases
will need to change. Not sure how many packages will need to be fixed
outside of Matrix, but it's not an isolated change. Martin might
comment on the rationale for the full signature, since he defined
those generics.
On Mon, Jan
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
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