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
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
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
> 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
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
&
/ 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
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." -
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
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
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.
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
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
> 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
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With thanks in advance-
Wolfgang
---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany
wolfgang.hu...@embl.de
http
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
/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
, 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
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
.
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
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
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
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Wolfgang
---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany
wolfgang.hu...@embl.de
h
to more
detailed doc elsewhere
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---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laborat
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
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
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
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
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With thanks in advance-
Wolfgang
---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany
wolf
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
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
_
omicsPrint.
Regards,
Maarten
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Wolfgang
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s://mailtrack.io/install?source=signature=en=shakilmoham...@gmail.com=22>
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---
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Principal Investigator, EMBL Senior Scientist
European Molecular B
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
, 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
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
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
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
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
>
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
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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
__
/cbg/cbg-news/ascona-2017.html
Niko Beerenwinkel
Peter Bühlmann
Wolfgang Huber
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Perhaps interesting for some:
http://www.turing-gateway.cam.ac.uk/tgmw39.shtml
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(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
> 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.
t;legend", "mtext", "par", "plot", "title")
>
> Thank you,
> Yasir
>
> ------
> Confidentiality Notice: This e-mail message, including a...{{dropped:10}}
>
> ___
> Bioc-
/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
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
>>>>>> It could take total `Nb of downloads` from the right table like here
>>>>>>> http://bioconductor.org/packages/stats/bioc/RTCGA.html
>>>>>>>
>>>>>>> Best,
>>>>>>> Marcin
>>>>
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
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
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Wolfgang
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biolo
would like to see support in ggraph, please let me know…
>
> best
>
> Thomas
> [[alternative HTML version deleted]]
>
> ___
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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.
>
>
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
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
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
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
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
. 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
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
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
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
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,
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
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
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
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
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
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
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?
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
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
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
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
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
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
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
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
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
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
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
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