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

2023-11-23 Thread Wolfgang Huber
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] Package problems due to results() function from other package?

2023-10-31 Thread Wolfgang Huber
such 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 change

Re: [Bioc-devel] BiocManager::install

2023-05-14 Thread Wolfgang Huber
nnecessary 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 (d

Re: [Bioc-devel] BiocManager::install

2023-05-12 Thread Wolfgang Huber
> 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

Re: [Bioc-devel] BiocManager::install

2023-05-11 Thread Wolfgang Huber
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 >>>> Bioconductor developer should be R-devel, and BoicManager &

Re: [Bioc-devel] BiocManager::install

2023-05-07 Thread Wolfgang Huber
/ 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 > Subject: R

Re: [Bioc-devel] BiocManager::install

2023-05-06 Thread Wolfgang Huber
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 BioConductor." -

[Bioc-devel] BiocManager::install

2023-05-06 Thread Wolfgang Huber
ome 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 best wishes W

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

2023-02-22 Thread Wolfgang Huber
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

Re: [Bioc-devel] Package name

2021-11-08 Thread Wolfgang Huber
n 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's easy.

Re: [Bioc-devel] Package name

2021-10-22 Thread Wolfgang Huber
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

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

2021-05-04 Thread Wolfgang Huber
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

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

2021-02-10 Thread Wolfgang Huber
> 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

Re: [Bioc-devel] RFC: Bioc repository for single-version packages

2018-11-13 Thread Wolfgang Huber
___ 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

[Bioc-devel] Ascona Workshop 2019 -- Statistical Challenges in Medical Data Science, 16–21 June 2019

2018-10-25 Thread Wolfgang Huber
Penn), Michael Snyder (Stanford), Matthew Stephens (U Chicago), Yinyin Yuan (ICR London). Application will open in January 2019. For more information, please refer to https://www.bsse.ethz.ch/cbg/cbg-news/ascona-2019.html Niko Beerenwinkel (ETH Zurich) Peter Bühlmann (ETH Zurich) Wolfgang Huber

[Bioc-devel] Can ExperimentHub packages contain non-R data formats?

2018-09-11 Thread Wolfgang Huber
/CreateAnExperimentHubPackage.html [2] https://github.com/Bioconductor/GSE62944/blob/master/inst/extdata/metadata.csv With thanks in advance- Wolfgang --- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.hu...@embl.de http

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

2018-03-31 Thread Wolfgang Huber
, 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 (EMBL) Heidelberg, Germany wolfgang.hu...@embl.de

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

2018-02-02 Thread Wolfgang Huber
eate 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 <wolfgang.hu...@embl.de> wrote: Th

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

2018-02-02 Thread Wolfgang Huber
.   Not sure if it is better or worse, just different On Fri, Jan 26, 2018 at 2:39 PM, Wolfgang Huber <wolfgang.hu...@embl.de> 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 inst

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

2018-01-26 Thread Wolfgang Huber
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' package contains a

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

2018-01-07 Thread Wolfgang Huber
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

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

2018-01-07 Thread Wolfgang Huber
__ 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 h

Re: [Bioc-devel] workflow page reorganization

2017-12-17 Thread Wolfgang Huber
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 European Molecular Biology Laborat

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

2017-10-06 Thread Wolfgang Huber
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 <wolfgang.hu...@embl.de <mailto:wolfgang.hu...@embl.de>> wrote: On Mac OSX 10.12.16: $ ulimit -Sn 256 so the maximum value of R_MAX_NUM

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

2017-10-06 Thread Wolfgang Huber
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 <wolfgang.hu...@embl.de> wrote: Breaking up long wor

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

2017-10-05 Thread Wolfgang Huber
on of another? -Aaron ---- *From:* Wolfgang Huber <wolfgang.hu...@embl.de> *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() cal

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

2017-10-05 Thread Wolfgang Huber
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 <bioc-devel-boun...@r-project.org> on behalf of Wolfgang Hub

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

2017-10-04 Thread Wolfgang Huber
_ 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 wolf

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

2017-09-19 Thread Wolfgang Huber
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 than

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

2017-09-19 Thread Wolfgang Huber
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.huber.embl.de _

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

2017-07-21 Thread Wolfgang Huber
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 Investigator, EMBL Senior Scient

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

2017-07-17 Thread Wolfgang Huber
s://mailtrack.io/install?source=signature=en=shakilmoham...@gmail.com=22> [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- With thanks in advance- Wolfgang --

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

2017-05-18 Thread Wolfgang Huber
native 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 Investigator, EMBL Senior Scientist European Molecular B

Re: [Bioc-devel] Question about R functions

2017-03-31 Thread Wolfgang Huber
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

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

2017-03-10 Thread Wolfgang Huber
, 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] R long vectors not supported yet on R 3.3.2

2017-03-10 Thread Wolfgang Huber
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] any interest in a BiocMatrix core package?

2017-03-03 Thread Wolfgang Huber
r 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 needed for? I'm asking b/c

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

2017-03-02 Thread Wolfgang Huber
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

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

2016-12-28 Thread Wolfgang Huber
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 >

[Bioc-devel] .git folders in the repository

2016-12-15 Thread Wolfgang Huber
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 ___

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

2016-11-01 Thread Wolfgang Huber
@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel Wolfgang Huber Principal Investigator, EMBL Senior Scientist Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.hu...@embl.de http://www.huber.embl.de __

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

2016-10-18 Thread Wolfgang Huber
/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

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

2016-10-04 Thread Wolfgang Huber
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: Statistical Challenges in Single-Cell Biology, April 30 to May 5, 2017, Monte Verità, Ascona, CH

2016-08-29 Thread Wolfgang Huber
(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

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

2016-08-18 Thread Wolfgang Huber
> 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.

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

2016-08-06 Thread Wolfgang Huber
t;legend", "mtext", "par", "plot", "title") > > Thank you, > Yasir > > ------ > Confidentiality Notice: This e-mail message, including a...{{dropped:10}} > > ___ > Bioc-

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

2016-06-11 Thread Wolfgang Huber
/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

[Bioc-devel] Workflows for Bioconductor channel at F1000R

2016-06-02 Thread Wolfgang Huber
the 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] downloads number status shields for packages

2016-05-08 Thread Wolfgang Huber
>>>>>> It could take total `Nb of downloads` from the right table like here >>>>>>> http://bioconductor.org/packages/stats/bioc/RTCGA.html >>>>>>> >>>>>>> Best, >>>>>>> Marcin >>>>

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

2016-03-25 Thread Wolfgang Huber
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

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

2016-03-19 Thread Wolfgang Huber
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

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

2016-02-18 Thread Wolfgang Huber
___ > 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 Biolo

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

2016-02-06 Thread Wolfgang Huber
would like to see support 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

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

2016-01-04 Thread Wolfgang Huber
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. > >

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

2015-06-18 Thread Wolfgang Huber
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

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

2015-05-27 Thread Wolfgang Huber
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

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

2015-05-14 Thread Wolfgang Huber
frequently a package is used, and how it performs, in real contexts. Frederic Commo Bioinformatics, U981 Gustave Roussy De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de Wolfgang Huber [whu...@embl.de] Date d'envoi : samedi 9 mai 2015

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

2015-05-09 Thread Wolfgang Huber
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

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

2015-04-14 Thread Wolfgang Huber
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 Tue, Apr 14, 2015 at 7:23 AM, Wolfgang Huber whu...@embl.de wrote: Is it possible to ship individual R

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

2015-03-31 Thread Wolfgang Huber
. 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 whu...@embl.de mailto:whu...@embl.de wrote: Dear Jesper this is maybe not the answer you want to hear, but stuffing in 4, 5, … dimensions may not be all

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

2015-03-24 Thread Wolfgang Huber
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

[Bioc-devel] Short URLs for packages?

2015-03-23 Thread Wolfgang Huber
the package was yet 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

Re: [Bioc-devel] recalling methods

2014-12-06 Thread Wolfgang Huber
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

[Bioc-devel] SummarizedExperiment vs ExpressionSet

2014-11-26 Thread Wolfgang Huber
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] plotPCA for BiocGenerics

2014-11-02 Thread Wolfgang Huber
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

Re: [Bioc-devel] rhdf5 help

2014-11-01 Thread Wolfgang Huber
For the record: see https://support.bioconductor.org/p/62283 which includes a reply. On 25 Oct 2014, at 21:07, Joseph Nathaniel Paulson jpaul...@umiacs.umd.edu 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] Add a new developer/maintainer

2014-10-03 Thread Wolfgang Huber
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

[Bioc-devel] Workflows

2014-09-29 Thread Wolfgang Huber
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

Re: [Bioc-devel] Workflows

2014-09-29 Thread Wolfgang Huber
GMT+2, Dan Tenenbaum dtene...@fhcrc.org ha scritto: - Original Message - From: Wolfgang Huber whu...@embl.de To: bioc-devel@r-project.org Sent: Monday, September 29, 2014 12:24:54 PM Subject: [Bioc-devel] Workflows Sorry if I have overlooked something… referring to http

Re: [Bioc-devel] support site

2014-09-26 Thread Wolfgang Huber
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

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

2014-04-24 Thread Wolfgang Huber
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?

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

2014-04-24 Thread Wolfgang Huber
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

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

2014-03-12 Thread Wolfgang Huber
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

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

2014-02-27 Thread Wolfgang Huber
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

[Bioc-devel] org-mode vignettes

2013-08-28 Thread Wolfgang Huber
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

[Bioc-devel] svn and package version numbers

2013-06-30 Thread Wolfgang Huber
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

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

2013-06-20 Thread Wolfgang Huber
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

[Bioc-devel] \VignetteIndexEntry

2013-05-20 Thread Wolfgang Huber
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. empy title 2. Additional plots for: Independent filtering

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

2013-03-14 Thread Wolfgang Huber
Mar 13, 2013, a las 10:41 am, James F. Reid rei...@gmail.com 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 be surprised if the saving was worth

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

2013-03-12 Thread Wolfgang Huber
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

[Bioc-devel] Webpage spring cleaning - Package submission

2013-02-22 Thread Wolfgang Huber
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, and

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

2013-02-21 Thread Wolfgang Huber
described as normalize 2- 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: Hi is it clear that all these different functions (methods) share