Re: [Bioc-devel] S4 Methods Documentation Convention Triggers Warnings

--- > > Dario Strbenac > > University of Sydney > > Camperdown NSW 2050 > > Australia > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailma

Re: [Bioc-devel] DataFrameList to Wide Format DataFrame

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 Computing Genente

Re: [Bioc-devel] S4 Method Slow Execution if Signature Has Multiple Class Unions

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

Re: [Bioc-devel] S4 Method Slow Execution if Signature Has Multiple Class Unions

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

Re: [Bioc-devel] Too many dependencies / MultiAssayExperiment + rtracklayer

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

Re: [Bioc-devel] rtracklayer::import (v 1.53.1) fails on xz-compressed files.

m 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 t

[Bioc-devel] git permissions

, 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

Re: [Bioc-devel] merging DFrames

> > 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

Re: [Bioc-devel] Resource temporarily unavailable error with rtracklayer

______ > 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

Re: [Bioc-devel] How to import a setAs method in one's package?

[[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) 225-7760 micha..

Re: [Bioc-devel] regionReport error leads to ggbio & biovizBase issues, confusingly not on all OS though

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

Re: [Bioc-devel] Installing libsbml for rsbml on a mac?

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

Re: [Bioc-devel] Question regarding the error from build report

> 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 Lawrence Senior Scientist, Bioinformatics

Re: [Bioc-devel] proper way to define an S4 method for 'plot'

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

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

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

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

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 >

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

(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/

Re: [Bioc-devel] Compatibility of S4 and tidyverse

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,

Re: [Bioc-devel] How to speed up GRange comparision

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

Re: [Bioc-devel] How to speed up GRange comparision

> > > > 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

Re: [Bioc-devel] How to speed up GRange comparision

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,

Re: [Bioc-devel] rtracklayer::import.bed(genome = Seqinfo)

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

Re: [Bioc-devel] plyranges group_by

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-

Re: [Bioc-devel] plyranges group_by

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

Re: [Bioc-devel] read_bed()

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. >

Re: [Bioc-devel] read_bed()

-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

Re: [Bioc-devel] read_bed()

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

Re: [Bioc-devel] read_bed()

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

Re: [Bioc-devel] read_bed()

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

Re: [Bioc-devel] read_bed()

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

Re: [Bioc-devel] read_bed()

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

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

[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

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

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('\

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

> 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

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

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

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

;BSgenome", > "GRanges", > function(from) from %>% > GenomeInfoDb::seqinfo() %>% > as('GRanges')) > > Thankyou for feedback, > > Aditya > > ___

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

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

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

ames=NULL, optional=optional, ...) > > } > > > > setMethod("as.data.frame", "Vector", > > function(x, row.names=NULL, optional=FALSE, ...) > > { > > x <- as.vector(x) > > as.data.fra

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

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

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

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

Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

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

Re: [Bioc-devel] rtracklayer::import.bw error situation when there's repeated input ranges in the "selection", leads to S4Vectors

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) > #

Re: [Bioc-devel] InteractionSet for structural variants

; >>> 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

Re: [Bioc-devel] When to use generics?

. 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

Re: [Bioc-devel] When to use generics?

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: >> >

Re: [Bioc-devel] When to use generics?

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

Re: [Bioc-devel] Pushing towards a better home for matrix generics

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, >> >>

Re: [Bioc-devel] DataFrame: replacement error

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 >

Re: [Bioc-devel] Pushing towards a better home for matrix generics

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: >

Re: [Bioc-devel] Unclear build failure ‘logical subscript contains NAs’

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

Re: [Bioc-devel] Unclear build failure ‘logical subscript contains NAs’

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

Re: [Bioc-devel] Unclear build failure ‘appending gaps’

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 >

Re: [Bioc-devel] How critical is package style for bioconductor?

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

Re: [Bioc-devel] Pushing towards a better home for matrix generics

; 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

Re: [Bioc-devel] SetMethod to dispatch on class in unattached package

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

Re: [Bioc-devel] SetMethod to dispatch on class in unattached package

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

Re: [Bioc-devel] Pushing towards a better home for matrix generics

> 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

Re: [Bioc-devel] Pushing towards a better home for matrix generics

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

Re: [Bioc-devel] Pushing towards a better home for matrix generics

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") >

Re: [Bioc-devel] Plans for multi-feature SingleCellExperiment?

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

Re: [Bioc-devel] Controlling vignette compilation order

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

Re: [Bioc-devel] Controlling vignette compilation order

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

Re: [Bioc-devel] Controlling vignette compilation order

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

Re: [Bioc-devel] BioC 3.9 devel builds

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,

Re: [Bioc-devel] Questions about some checks in the latest BiocCheck

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

Re: [Bioc-devel] Manually editing man/.Rd files to pass BiocCheck

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

Re: [Bioc-devel] Possible to export coerce2() from S4Vectors?

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

Re: [Bioc-devel] Possible to export coerce2() from S4Vectors?

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

Re: [Bioc-devel] Possible to export coerce2() from S4Vectors?

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

Re: [Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?

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" < >

Re: [Bioc-devel] Error : object 'lengths' is not exported by 'namespace:BiocGenerics'

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 ? >

Re: [Bioc-devel] Problem with setClassUnion and DelayedArray

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

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

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

Re: [Bioc-devel] Question

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

Re: [Bioc-devel] ggplot2 update coming on June 25 and how it affects ggbio + other packages

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

Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?

ax Planck Institute of Immunobiology and Epigenetics > 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_FO

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 >

Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?

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

Re: [Bioc-devel] GenomicRanges List subclass and apply

is on each element. > 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 Law

Re: [Bioc-devel] GenomicRanges List subclass and apply

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

Re: [Bioc-devel] class name collision in cache: igvR and Gviz

ckage. > > 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 <lawrence.mich...@gene.com> > wrote: > > > > Thanks Paul. > > > > I've made improve

Re: [Bioc-devel] class name collision in cache: igvR and Gviz

s 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 <lawrence.mich...@gene.com> > wrote: >

Re: [Bioc-devel] class name collision in cache: igvR and Gviz

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

Re: [Bioc-devel] Error: node stack overflow

or the BioC 3.8 builds. > > 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 <micha...@

Re: [Bioc-devel] Error: node stack overflow

It's checked into devel now. Thanks for the well documented examples, Hervé. On Mon, Apr 30, 2018 at 10:26 AM, Michael Lawrence <micha...@gene.com> 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, Mi

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

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

Re: [Bioc-devel] Error: node stack overflow

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 <micha...@gene.com> 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 <hp

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

et) # FALSE > > > is(Biobase::ExpressionSet(), "ExpressionSet") # TRUE > > > is(Biobase::ExpressionSet(), Biobase %c% ExpressionSet) # TRUE > > > > > > > On Thu, Apr 12, 2018 at 3:57 PM, Michael Lawrence > <lawrence.mich...@gene.com> wrote: >>

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

with push permission to S4Vectors 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

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

RCurl_1.95-4.10 >> > [45] zoo_1.8-1 >> >> > >> > On Apr 11, 2018, at 10:25 AM, Elizabeth Purdom <epurdom@stat.Berkel >> > ey.EDU> wrote: >> > >> > Hello, >> > >> > Our package clusterExperiment has suddenly started produci

Re: [Bioc-devel] Tensorflow support for bioconductor packages

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

Re: [Bioc-devel] Tensorflow support for bioconductor packages

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

Re: [Bioc-devel] IGV VCF demo, other suggestions? [was Re: IGV - a new package in preparation]

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

Re: [Bioc-devel] IGV - a new package in preparation

On Fri, Mar 9, 2018 at 12:36 PM, Cook, Malcolm <m...@stowers.org> wrote: > Hi, > > > > -Original Message- > > From: Bioc-devel <bioc-devel-boun...@r-project.org> On Behalf Of > > Michael Lawrence > > Sent: Friday, March

Re: [Bioc-devel] IGV - a new package in preparation

ocket data exchange. I > am cautious, 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 <l

Re: [Bioc-devel] IGV - a new package in preparation

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)

Re: [Bioc-devel] giggle and bioc

25x faster for what it does I guess, which appears to be counting overlaps to an indexed database of BED files. It's nice to see an indexing scheme that unlike tabix is actually useful for something other than finding an offset to a compressed block. On Tue, Feb 27, 2018 at 10:03 AM, Vincent

[Bioc-devel] hail and bioc

Has anyone made a bioc interface to Hail yet? If not I might try to make one, just for fun. Michael [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] as.list of a GRanges

ona, Barcelona, Spain >>> b...@igtp.cat <mailto:b...@igtp.cat> >>> www.germanstrias.org <https://urldefense.proofpoint >>> .com/v2/url?u=http-3A__www.germanstrias.org_=DwMDaQ=e >>> RAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJK >>> aaPhzWA=Wwl42

Re: [Bioc-devel] as.list of a GRanges

ion)? >> > > Bioconductor devel only. > > >> > On 02/15/2018 08:37 AM, Michael Lawrence wrote: >> > > So is as.list() no longer supported for GRanges objects? I have >> found it >> > > useful in places. >> > >> > Very few

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