Re: [Bioc-devel] How to integrate code from a package not available on bioconductor

> Il giorno 10feb2021, alle ore 14:31, Kern, Lori > ha scritto: > > Have you reached out to the maintainer of the github package to see if they > would plan on submitting to CRAN or Bioconductor? > If they do not, you could see if they are okay with you including the code > in your package

[Bioc-devel] Can anyone reproduce this? Possible bug or typo in BiocManager:::.version_map() or upstream

Hi, I get > BiocManager::install() Error: Bioconductor version '3.13' requires R version '4.1'; R version is too new; see https://bioconductor.org/install and this appears to be because of the last line in > BiocManager:::.version_map() BiocR BiocStatus RSPM MRAN …(29 lines omitted)

Re: [Bioc-devel] Package name

This is probably a niche concern, but I’d find it a pity if a good package name (*) became unavailable forever, esp. if it refers to a real-world concept not owned by the authors of the original package. Perhaps we could allow re-using a name after a grace period (say 1 or 2 years)? To be extra

Re: [Bioc-devel] Package name

hed in my view. > > I renamed my package. > > > From: Bioc-devel on behalf of Henrik > Bengtsson > Sent: 22 October 2021 14:02 > To: Wolfgang Huber > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] Package name > > For CRAN packages it

Re: [Bioc-devel] name for new BioC package

hich co-existed for several years. Thanks for the feedback on MOFA/MOFA2. I was a co-author of MOFA but not MOFA2, and it seems we did not follow the above advice. Sorry. Thanks and best wishes Wolfgang -- Wolfgang Huber EMBL https://www.embl.org/groups/huber > Il giorno 04.02.2023, alle

Re: [Bioc-devel] Question on prospective Bioc package

Dear Greg This sounds like a typical use case for a Bioconductor package. Simplicity is a not a bad thing—robust, well-engineered building blocks that do one thing really well are IMHO often more useful to many than big integrated complex jack of all trades. Thanks and best wishes Wolfgang

[Bioc-devel] BiocManager::install

o have become convoluted. One of the most helpful documentation resources on this topic btw is https://solutions.posit.co/envs-pkgs/bioconductor/ which cheerfully concludes "Working with BioConductor packages for code development is possible." Thanks and bes

Re: [Bioc-devel] BiocManager::install

make use of BioConductor packages to > Connect is not possible for this setup. > BiocManager::install() temporarily adds the BioConductor repository > for the duration of the install process. > During the publishing process rsconnect no longer has any knowledge > about BioConducto

Re: [Bioc-devel] BiocManager::install

ise from R / Bioconductor version mismatches. Are these less-common > scenarios the one that you are engaged in? > Martin > From: Bioc-devel on behalf of Wolfgang > Huber > Date: Saturday, May 6, 2023 at 9:43 AM > To: Vincent Carey > Cc: bioc-devel@r-project.org >

Re: [Bioc-devel] BiocManager::install

should, during the >>>> mid-April to mid-October release cycle, be using the >>>> **release** version of R. This combination of R and >>>> Bioconductor is supported by BiocManager. Similarly, in >>>> the mid-October to mid-April release cycle, the &

Re: [Bioc-devel] BiocManager::install

> Il giorno 12.05.2023, alle ore 04:43, Kasper Daniel Hansen > ha scritto: > > It seems totally sensible to be able to use BiocManager to install either > bioc-release or bioc-devel at any time, provided you're running R-devel. > First, by definition, R-devel is always >= the R used for rele

Re: [Bioc-devel] BiocManager::install

tal unnecessary frustration this causes? > Have a nice weekend. > Kind regards, > Klaus Schliep > > On Sat, May 6, 2023 at 10:40 AM Wolfgang Huber > wrote: > >> Hi, >> >> I am wondering whether: >> 1. it could be easier to install Bioconductor packages

Re: [Bioc-devel] Package problems due to results() function from other package?

uch a function converts it to a method for that generic. Thank you and kind regards Wolfgang -- Wolfgang Huber EMBL https://www.huber.embl.de/ > Il giorno 2023-10-28, alle ore 16:15, Christian Arnold ha > scritto: > > For my package SNPhood that did not receive any code c

[Bioc-devel] Ascona Workshop: Spatial and temporal statistical modeling in molecular biology. 8-13 Sep 2024 in Ascona, Switzerland

and posters! Pre-registration is open now until 22 April 2024. Instructions at https://spatialbio.net With kind regards from the organizers Niko Beerenwinkel, ETH Valentina Boeva, ETH Peter Bühlmann, ETH Wolfgang Huber, EMBL [[alternative HTML version deleted

Re: [Bioc-devel] serializing pairwise alignment objects

Hi, I can reproduce this on more recent versions of everything: > sessionInfo() R Under development (unstable) (2012-10-31 r61057) Platform: x86_64-apple-darwin12.2.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods

[Bioc-devel] Section~\ref{sec:bla} idiom in vignettes

Hi, In LaTeX, I like to use the tilde in connection with equation or section references, e.g. "Equation~(\ref{eq:bla})" or "Section~\ref{sec:blo}", to make sure they are not separated by a line break. This has worked well for two decades and still does on my system. However, in some vignettes

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

Hi is it clear that all these different functions (methods) share similar semantics and enough (conceptually) of their interface? Wouldn't the implication be that preemptively every possible string of characters should already be defined as a generic function in BiocGenerics? Best wish

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

- all functions "normalize" do perform an action that can be described with > that verb > > Without more details, I'd vote for 2. > > (more below) > >> >> LEo >> >> On 20 Feb 2013, at 16:14, Wolfgang Huber wrote: >> >>

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

> >>>> Of course, packages that define functions whose names clash with >>>> BiocGenerics will cause problems, and they would generally be best >>>> to avoid that, but really I don't think I would advocate any sort of >>>> prohibit

[Bioc-devel] Webpage spring cleaning - Package submission

I would like to suggest clarification of the information in the "Package Guidelines" [1] and the "Package Submission" [2] pages. 1. Information that is actually of type "guideline" is (only) stated on the submission page, which is confusing. Shouldn't one page describe the applied criteria, a

Re: [Bioc-devel] vectorize default dist2 function in genefilter

Dear James Thank you. What would the saved time be (e.g. compared to the overall runtime of arrayQualityMetrics)? I would be surprised if the saving was worth the added complexity, but am always happy to be surprised. A patch of the .R and .Rd file would be most welcome and expedite the change

Re: [Bioc-devel] vectorize default dist2 function in genefilter

Mar 13, 2013, a las 10:41 am, James F. Reid escribió: > Hi Wolfgang, > > On 12/03/13 21:11, Wolfgang Huber wrote: >> >> Dear James >> >> Thank you. What would the saved time be (e.g. compared to the overall >> runtime of arrayQualityMetrics)? I would b

[Bioc-devel] \VignetteIndexEntry

I am puzzled by the interpretation of the %\VignetteIndexEntry directive by the build system. On http://www.bioconductor.org/packages/devel/bioc/html/genefilter.html of the four vignettes for this package, two are listed with titles 1. 2. Additional plots for: Independent filtering increases

[Bioc-devel] -which() pitfall in subsetting exressions

[bioc-devel added and subject header changed] Dear List & Developers Mani's post reminded me of the pitfall posed by using expressions such as x = x[ -which(someExpression) ] which tends to have unintended consequences in particular if all elements of 'someExpression' are FALSE. Com

Re: [Bioc-devel] biocLite should warn when called from a non-current R version

Hi, there is benefit in having newest versions, but I think we shouldn't get carried away, and find Martin's suggestion reasonable. I don't want to be told to go get an iPhone 5 every time I update an app on my iPhone 4 - even if that same app would work much better there. People may have legiti

[Bioc-devel] svn and package version numbers

Hi All, just a reminder that it is good practice to bump up the package version when you commit a change to a package's source, even if you consider it 'trivial'. Version numbers are free, while the confusion ensuing from there being different versions of the software with ostensibly the same v

[Bioc-devel] "R CMD check" and par(mfrow=…) in vignettes

Hi one of my packages [1] has several places in its vignette where multi-panel figures are generated via the likes of "par(mfrow=c(4,2))" within <> code chunks. The package builds fine with 'R CMD build', and the vignette builds fine when calling Sweave manually. However, 'R CMD check' fails wi

[Bioc-devel] org-mode vignettes

Hi is there already a best practice (example?) for how to deliver vignettes written in org-mode (http://orgmode.org) in Bioconductor packages? (This would also require that emacs and its ESS and org modes are installed on the build servers.) Best wishes Wolfgang __

Re: [Bioc-devel] org-mode vignettes

Hi Martin, thanks! Both of these sound doable, we'll explore. What was the third one? Best wishes, Wolfgang On 28 Aug 2013, at 14:28, Martin Morgan wrote: > On 08/28/2013 02:50 AM, Wolfgang Huber wrote: >> >> Hi >> >> is there already a best practi

[Bioc-devel] R-version (was: IRanges: 'extractROWS' fails for 'RangedData')

Dear Julian thanks. Since this has come up here and elsewhere, and since the next Bioc release is coming up, let's remind ourselves that we should make development against 3.0.1 Patched (2013-09-03 r63824) -- "Good Sport". Martin - should this be noted on http://www.bioconductor.org/developers

[Bioc-devel] Nature Genetics - Call for data analysis papers

Perhaps of interest to some: http://www.nature.com/ng/journal/v46/n3/full/ng.2914.html Community standards for data access, interoperability and metadata only make sense if data are creatively reused to further research. We are therefore inviting the submission of Analysis papers that reformat a

[Bioc-devel] 'droplevels' argument in `[` method for SummarizedExperiment?

Hi Martin, Mike a DESeq2 user brought up the observation that when he subsets a ‘DESeqDataSet’ object (the class inherits from ‘SummarizedExperiment’) by samples, he often ends up with unused factor levels in the colData. (Esp. since the subsetting is often to select certain subgroups). Would e

Re: [Bioc-devel] r+w permissions in release branches

Hi Julian what if two Bioc packages require different version of the ‘same’ CRAN package? AfaIu, the infrastructure is not designed to deal with multiple versions of a package. Nor would I as a user expect to have less-than-the-most recent versions of CRAN packages in my library just because so

Re: [Bioc-devel] r+w permissions in release branches

Hi Martin to come back to the original trigger for this thread: it was not concerns for reproducibility, but the fact that a Bioc package in the current release stopped working because a CRAN package has changed in the meanwhile. What’s the most practical solution to this specific problem?

Re: [Bioc-devel] r+w permissions in release branches

, Kasper Daniel Hansen wrote: > Wolfgang, > > Alejandro did not have a problem with the current release, but with the most > recent prior release. His issue is precisely because it is no longer the > current (stable) release. > > Kasper > > > On Thu, Apr 24, 2

[Bioc-devel] CITATION on the Bioc package landing page?

I wonder whether the software that makes the package landing pages (e.g.: http://bioconductor.org/packages/release/bioc/html/minfi.html ) could be tweaked to display the actual citation suggested in a package CITATION file. Right now, it says 'To cite this package in a publication, start R and e

Re: [Bioc-devel] support site

0. Overall, the new site is great. Some of the threads now turn into valuable little mini-blogs or discussion pages on a specialized topic. 1. I tend to agree with Kasper. The site layout looks a bit too cluttered to me, with all these boxes of votes, views and response counts in different col

Re: [Bioc-devel] minor suggestion for BiocStyle?

AfaIcs everybody (incl. myself) involved in this so far is an amateur when it comes to graphics design and text layout. This not to minimize the technical achievement! Anyway, input from someone with graphics design / text layout credentials (also privately) is welcome. Wolfgang Il gio

[Bioc-devel] Workflows

Sorry if I have overlooked something… referring to http://www.bioconductor.org/developers/how-to/workflows Is there a standardized way to manage - dependencies - versions In principle, these could be automagically computed (?), but would still have to be exposed to workflow users using an afaI

Re: [Bioc-devel] Workflows

GMT+2, Dan Tenenbaum ha scritto: > > > - Original Message - >> From: "Wolfgang Huber" >> To: bioc-devel@r-project.org >> Sent: Monday, September 29, 2014 12:24:54 PM >> Subject: [Bioc-devel] Workflows >> >> >&g

Re: [Bioc-devel] Add a new developer/maintainer

Dear Setia just edit the “DESCRIPTION” file. For maintainers, note the CRAN Repository Policy at http://cran.r-project.org/web/packages/policies.html which I think we generally also apply in Bioconductor: "The package’s DESCRIPTION file must show both the name and email address of a single des

[Bioc-devel] European Bioconductor Developers' Meeting 12th-13th January 2015, Heidelberg

Logistic and registration details, and an overview of the programme are here: http://www-huber.embl.de/BiocEurope The meeting is aimed at bioinformaticians, programmers and software engineers who contribute to the Bioconductor project, or are inte

Re: [Bioc-devel] rhdf5 help

For the record: see https://support.bioconductor.org/p/62283 which includes a reply. > On 25 Oct 2014, at 21:07, Joseph Nathaniel Paulson > wrote: > > Hello, > > I'm in the process of writing a few wrappers for loading and writing out > files in the biom-format >

Re: [Bioc-devel] plotPCA for BiocGenerics

Just to bring the discussion back to the fact that there is a need to do /something/. A function plotPCA is defined in packages EDASeq, DESeq2, DESeq, affycoretools, Rcade, facopy, CopyNumber450k, netresponse, MAIT, with a real potential for needless user confusion. And BiocGenerics already defi

[Bioc-devel] SummarizedExperiment vs ExpressionSet

A colleague and I are designing a package for quantitative proteomics data, and we are debating whether to base it on the SummarizedExperiment or the ExpressionSet class. There is no immediate use for the ranges aspect of SummarizedExperiment, so that would have to be carried around with NAs,

Re: [Bioc-devel] recalling methods

Also some interest on our side to contribute. Perhaps in particular the rendering a useful index (or graph) of man pages on the fly in HTML / graphically. Is it too ambitious to “learn” which methods are most important for objects of a particular class from analysing (running) a large code base

[Bioc-devel] [workshop announcement]: Workshop Statistical Learning of Biological Systems - Ascona, Switzerland, May 31 to June 5, 2015

researchers. Niko Beerenwinkel, Peter Buehlmann, Darlene Goldstein, Wolfgang Huber ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Short URLs for packages?

released. This could be handy in papers or grants that mention packages. Wolfgang Wolfgang Huber Principal Investigator, EMBL Senior Scientist Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg, Germany T +49-6221-3878823 wolfgang.hu...@embl.de http

Re: [Bioc-devel] Short URLs for packages?

Before we start a religious war, can we make progress on the pragmatic goal of making it possible to provide such URLs to people? There are two concepts - ‘the package' - a specific version, running in a specific environment, ‘frozen’, etc. (Gabe) - ‘the package’ - as a concept and a living arti

Re: [Bioc-devel] Short URLs for packages?

> 5. At the end of the day I find myself casting my lot for landing pages with > the form > http://bioconductor.org/release/BiocGenerics/ > which leads to a little less typing but not the dynamic resolution that > started this (version) of the thread. But we already have dynamic resolution. Eve

Re: [Bioc-devel] SummarizedExperiment subset of 4 dimensions

colData covariates. Wolfgang Wolfgang Huber Principal Investigator, EMBL Senior Scientist Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg, Germany T +49-6221-3878823 wolfgang.hu...@embl.de http://www.huber.embl.de > On 30 Mar 2015, at 12:38, Jesper Gådin wr

Re: [Bioc-devel] SummarizedExperiment subset of 4 dimensions

colData to annotate that structure. It does not make the data > any less "tidy", but it does make it more structured. > > On Tue, Mar 31, 2015 at 4:14 AM, Wolfgang Huber <mailto:whu...@embl.de>> wrote: > Dear Jesper > > this is maybe not the answer you want t

[Bioc-devel] Docker granularity: containers for individual R packages, running on a normal R installation?

Is it possible to ship individual R packages (that e.g. contain complex, tricky to compile C/C++ libraries or other system resources) as Docker containers (or analogous) so that they would still run under a “normal”, system-installed R. Or, is it possible to provide a Docker container that conta

Re: [Bioc-devel] Docker granularity: containers for individual R packages, running on a normal R installation?

; those would need to include all R package dependencies, also). R would need > to run INSIDE the container, though, to get the benefits of the installed > complex dependencies. > > I imagine Dan or others might have other thoughts to contribute. > > Sean > > > On

Re: [Bioc-devel] Use and Usability metrics / shields

Dear Martin great idea. "Current build status” could perhaps be wrapped with "Cross-platform availability” into some sort of “Availability / Accessibility”? I wonder how informative it would be to make metrics such as (i) citations of the associated paper (ii) full-text mentions e.g. in PubmedCe

Re: [Bioc-devel] Use and Usability metrics / shields

>>> >>> Another useful information would be to point to other publications >>> where a given package was used, and cited. >>> I don't know if it's technically possible, but it would be greatly >>> informative to know how frequently a package is

Re: [Bioc-devel] Overloading subset operator for an S4 object with more than two dimensions

Dear Christian not sure this is a wise idea, it breaks the semantics of “[“. The number of elements stored in an array is the product of the extent of its dimensions. In your example, it is the sum. To put it less abstract, a[1:2, 2, 3:4, 1] for a regular array is a 2 x 2 matrix, whereas in your

Re: [Bioc-devel] best way to transition users to new version of package

Robert with the packages cellHTS, cellHTS2 and DESeq, DESeq2 (and with the functions vsn, vsn2 in the vsn package) I three times chose route 1, and am generally happy about it. In due time, you can deprecate and then defunct the old one. Option 2 seems needlessly disruptive (potentially). A lar

[Bioc-devel] Rendering of vignette R code on the website

Perhaps a buglet in the build system / the website code? -- When I follow the link to “R Script” on the page http://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html (i.e. http://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.R ) the result is a nearly empty f

Re: [Bioc-devel] Shouldn't we distinguish between package-specific and dependency errors?

It seems that the “build” shield on the package landing page conflates things that happen in the package, and in its dependencies. Do we have a clear spec of what the purpose of that shield is? Something to avoid IMHO is creating incentives for package developers to reduce dependencies to make t

Re: [Bioc-devel] Update released version of Package

Something for a developer FAQ? Kind regards Wolfgang > On 4 Jan 2016, at 19:35, Dan Tenenbaum wrote: > > Check out the release version from SVN at > > https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/YOURPACKAGENAME > > Make the fixes. > > Be sure to bump the vers

Re: [Bioc-devel] Classes to be supported by ggraph

port in ggraph, please let me know… > > best > > Thomas > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel Wolfgang Huber Principal In

Re: [Bioc-devel] specify the color in plotMutationSpectrum() of SomaticSignatures library

__ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel Wolfgang Wolfgang Huber Principal Investigator, EMBL Senior Scientist Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.hu...@embl.de http://www.hube

Re: [Bioc-devel] Package reference manuals in html

and session-independent anyway seems dubious to me. Re resources, we (I) should be able to find them (both CPU and disk) at EMBL HD or EBI. Kind regards Wolfgang Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) http://www.huber.embl.de

[Bioc-devel] Bioconductor-related papers -- special F1000R collection for Bioc2016

Bioconductor Developers: The Bioconductor channel on F1000Research< http://f1000research.com/channels/bioconductor > will be publishing a collection of articles in time for the BioC 2016 conference, and we would like to invite you to contribute. We are specifically looking to publish articles o

Re: [Bioc-devel] downloads number status shields for packages

t; >>>>>>> Best, >>>>>>> Marcin >>>>>>> >>>>>>> [[alternative HTML version deleted]] >>>>>>> >>>>>>> ___ >>&g

[Bioc-devel] Workflows for Bioconductor channel at F1000R

figures to Overleaf​ and in manually adding figure captions. I wish this could be further automated. Kind regards Wolfgang Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) http://www.huber.embl.de > On 1 Jun 2016, at 16:52, Susan Hol

Re: [Bioc-devel] Announcement of a new package called bacon

> >>>> >>>> >>>> >>> >>> 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 th

Re: [Bioc-devel] problem in building package GSAR

, "title") > > Thank you, > Yasir > > ------ > Confidentiality Notice: This e-mail message, including a...{{dropped:10}} > >

Re: [Bioc-devel] Is it OK for Rmd package vignettes to be rendered as PDF?

> On 17 Aug 2016, at 13:02, Henrik Bengtsson wrote: > > R CMD build, which is what triggers vignette building, only supports one > output file (HTML or PDF) per vignette. It will basically ignore duplicate > output formats. This is by design / legacy reasons. Technically it wouldn't > be hard

[Bioc-devel] Ascona workshop: Statistical Challenges in Single-Cell Biology, April 30 to May 5, 2017, Monte Verità, Ascona, CH

(Paris Descartes). We welcome your submissions for proposals for contributed presentations More details are available at https://www.bsse.ethz.ch/cbg/cbg-news/ascona-2017.html Registration to the workshop and submission of abstracts opens in October 2016. Niko Beerenwinkel Peter Bühlmann Wolfgang

[Bioc-devel] Statistical Scalability for Streaming Data - 1/2 day workshop in London

Perhaps interesting for some: http://www.turing-gateway.cam.ac.uk/tgmw39.shtml ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Ascona Workshop 2017: Call for abstracts

/cbg/cbg-news/ascona-2017.html Niko Beerenwinkel Peter Bühlmann Wolfgang Huber ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] FlipFlop Ignores Read Strand and Requires Antiquated File Formats

imported into R with functions provided by > rtracklayer. > > -- > Dario Strbenac > University of Sydney > Camperdown NSW 2050 > Australia > > ___ > Bioc-devel@r-project.org mailing list >

[Bioc-devel] .git folders in the repository

Today I get, after “svn up" whuber@boltzmann:~/madman/Rpacks$ find . -name .git -exec du -sh {} \; 17M./anamiR/anamiR/.git 56K./RareVariantVis/.git Probably the “.git" folders should not be checked in? Best wishes Wolfgang ___ Bioc-de

Re: [Bioc-devel] Add journal citation to a package

Dear Andrea Have a look at this: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#CITATION-files Many CRAN and Bioconductor packages are doing this, you could look at some of them for examples. Wolfgang > On 28 Dec 2016, at 15:49, Rodriguez Martinez, Andrea > wrote: > >

Re: [Bioc-devel] any interest in a BiocMatrix core package?

Aaron Can you describe use cases, i.e. intended computations on these matrices, esp. those for which C++ access is needed for? I'm asking b/c the goals of efficient code and abstraction from how the data are stored may be conflicting - in which case critical algorithms may end up circumventi

Re: [Bioc-devel] any interest in a BiocMatrix core package?

ver memory management. For a decent number of cells, this can make the difference between something being runnable or not. Cheers, Aaron On 02/03/17 18:09, Wolfgang Huber wrote: Aaron Can you describe use cases, i.e. intended computations on these matrices, esp. those for which C++ access is neede

Re: [Bioc-devel] R long vectors not supported yet on R 3.3.2

Two replies: 1. Downsampling? In case you want to use the Hilbert curve for visualisation, please note that you will need a graphics device with resolution 65536 x 65536 to display it. Many people have smaller screens, so binning the genome (e.g. into bins of 10x10=100nt) could be a practical

Re: [Bioc-devel] R long vectors not supported yet on R 3.3.2

, Wolfgang Huber wrote: Two replies: 1. Downsampling? In case you want to use the Hilbert curve for visualisation, please note that you will need a graphics device with resolution 65536 x 65536 to display it. Many people have smaller screens, so binning the genome (e.g. into bins of 10x10=100nt) could

Re: [Bioc-devel] Question about R functions

Thanks Juan; the .point used to be a way to do this, but since the introduction of namespaces to R, it is neither necessary nor sufficient for private functions. See e.g. .Hub in the AnnotationHub package, or the .Call function in base. See https://cran.r-project.org/doc/manuals/r-release/R

Re: [Bioc-devel] invalid PDF version and NULL vector errors in unchanged package

ance for any help! Regards, Sokratis [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- With thanks in advance- Wolfgang --- Wolfgang Huber Principal I

Re: [Bioc-devel] Bioconductor issue 396: Vignette building problem for OPWpaper package

/mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=shakilmoham...@gmail.com&idSignature=22> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://

Re: [Bioc-devel] adding multiple vignettes not all should be processed by the build-system

y under review and called omicsPrint. Regards, Maarten [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- With thanks in advance- Wolfgang --- Wolfgang Huber Principal Investi

Re: [Bioc-devel] [Untrusted Server]Re: [Untrusted Server]Re: strange error in Jenkins build forsingleCellWorkflow

ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or...{{dropped:2}} ___ Bioc-devel@r-project.org mailing list htt

Re: [Bioc-devel] strange error in Jenkins build forsingleCellWorkflow

19.9.17 18:16, Martin Morgan scripsit: On 09/19/2017 09:50 AM, Wolfgang Huber wrote: My 3 cents: - I think this is a more and more common problem that I'm also encountering in everyday work and that asks for a general solution. - I agree with Martin that setting R_MAX_NUM_DLLS is better

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- With thanks in advance- Wolfgang --- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.hu...@embl.de http://www.hube

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

call library at the beginning of each section and explained that the package was only a collection of analyses stemming from other packages, but that wasn't enough apparently. Laurent -Aaron ____ From: Bioc-devel on behalf of Wolfgang Huber Sent: Thursday, 5 Octobe

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

e execution of another? -Aaron -------- *From:* Wolfgang Huber *Sent:* Thursday, 5 October 2017 6:23:47 PM *To:* Laurent Gatto; Aaron Lun *Cc:* bioc-devel@r-project.org *Subject:* Re: [Bioc-devel] library() calls removed in simpleSingleC

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

0) that depends on the number of files you can have open at the same time (fd_limit), e.g. on my Ubuntu 16.04 I've got: $ ulimit -Sn 1024 so R_MAX_NUM_DLLS=614 is the maximum for me. /Henrik On Thu, Oct 5, 2017 at 11:22 AM, Wolfgang Huber wrote: Breaking up long workflows into several smal

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

ulimit and how it is set, but that is a pretty start difference. Best, Kasper On Fri, Oct 6, 2017 at 3:12 AM, Wolfgang Huber <mailto:wolfgang.hu...@embl.de>> wrote: On Mac OSX 10.12.16: $ ulimit -Sn 256 so the maximum value of R_MAX_NUM_DLLS is 153 ...

Re: [Bioc-devel] Package additional maintainers

thanks in advance- Wolfgang --- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.hu...@embl.de http://www.huber.embl.de ___ Bioc-devel@r-project.org mailing

Re: [Bioc-devel] workflow page reorganization

re for submitting a workflow, link to more detailed doc elsewhere ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- With thanks in advance- Wolfgang --- Wolfgang Huber Principal Investigator, EMBL Senior Scientist

Re: [Bioc-devel] differential expression tools for proteins

_ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- With thanks in advance- Wolfgang --- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.

Re: [Bioc-devel] search - was: differential expression tools for proteins

7.1.18 12:46, Wolfgang Huber scripsit: Thank you for your question. It would however be more appropriate for the support forum, not for the developer mailing list. Would you mind moving it there, perhaps also the responses so far? I just saw you posted on the forum, after browsing it. I had

[Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

sed out. A modern 'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package" https://cran.r-project.org/web/packages/RMySQL/index.html So is it time to heed that advice and migrate GenomicFeatures to RMariaDB ? With thanks in advance- Wolfgang

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

26.1.18 14:59, Martin Morgan scripsit: On 01/24/2018 03:38 PM, Wolfgang Huber wrote: GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL'

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

  Not sure if it is better or worse, just different On Fri, Jan 26, 2018 at 2:39 PM, Wolfgang Huber wrote: 26.1.18 14:59, Martin Morgan scripsit: On 01/24/2018 03:38 PM, Wolfgang Huber wrote: GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from s

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

ger than that. I haven't been able to recreate the problem at my end, I think the time taken is related as much to the internet connection as to the query, but I'll take a look at the failing example to see if I can shed any more light on it. Mike On 2 February 2018 at 10:41, Wolfgang Huber

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

nt in the future. Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this migration. Let us know if you have any question about this. H. -- With thanks in advance- Wolfgang --- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory

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