Hi, Pabita.
This question is better asked on the bioconductor support site (
HTTPS://support.bioconductor.org). However, finding no evidence for
differential expression is not uncommon. Whether it is expected or not is
hard to comment on without data.
Sean
On Jul 30, 2016 10:43, "Pabita Basnet"
> On Nov 30, 2016, at 4:13 PM, Martin Morgan
> wrote:
>
> On 11/30/2016 08:51 AM, Kasper Daniel Hansen wrote:
>> Full transcript please; you're compiling from source.
>
> Excuse my ignorance about the Mac world but shouldn't these be available for
> binary installation via the URL Andrea prov
Github allows you to set the branch for the docs directory if I recall.
Perhaps a separate branch with a docs directory (not master) is a viable way to
go?
Sean
> On Dec 23, 2016, at 12:16 PM, Laurent Gatto wrote:
>
>
> There's actually another side-effect for Bioconductor. The package
> we
Hi, all.
I am curious about what folks think about naming conventions for commonly
named functions, some of which are so common that even establishing a
generic would be difficult because of different use cases. Examples
include things like “filter”. One possibility is to use the Google Sheets
a
Hi, Welliton.
Great question. Just out of curiosity, what are the internet connection
requirements that preclude running examples? Is authentication required?
Or are you connecting to a server that runs only intermittently?
Sean
On Tue, Mar 7, 2017 at 1:57 PM, Welliton Souza wrote:
> Hi,
>
r FD in
>>> the
>>> R package.
>>>
>>>
>>>
>>> Could you please give me some suggestion how to do that?
>>>
>>>
>>>
>>> Thanks,
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
Hi, Maia.
The git mirror is not used for building packages. Instead, you will need
to commit to svn for changes to show up on Bioconductor. See here for
details of working with git and svn together.
https://www.bioconductor.org/developers/how-to/git-mirrors/
If I misunderstood what you are say
rror
> somewhere?
>
> Best,
> Maia
>
> On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis wrote:
>
>> Hi, Maia.
>>
>> The git mirror is not used for building packages. Instead, you will need
>> to commit to svn for changes to show up on Bioconduc
Sorry I lead you astray, earlier, Maia.
In general, you do not need to install the package in the vignette. The
first code block in the vignette where you did "eval=FALSE" is the way to
go. The second code block where you actually do the installation is
unnecessary. The package is installed by R
>> Suggestions?
>>
>> Thank you
>>
>> Greg Gloor
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
> This email message may contain
r | Epigenetics Research Laboratory |
> Genomics and Epigenetics Division
>
> Garvan Institute of Medical Research
>
> 384 Victoria St., Darlinghurst, NSW, Australia 2010
>
> Tel: +61 (2) 9295 8319
>
>
> [[alternative HTML version deleted]]
>
&
included. I think the distinct IPs are reset per
month for the monthly stats.
>
> Regards,
>
> Lluís
>
> [[alternative HTML version deleted]]
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.eth
)
> > Ingolstädter Landstr. 1
> > 85764 Neuherberg
> > www.helmholtz-muenchen.de
> > Aufsichtsratsvorsitzende: MinDir'in Bärbel Brumme-Bothe
> > Geschäftsführer: Prof. Dr. Günther Wess, Heinrich Baßler, Dr. Alfons
> Enhsen
> > Registergericht: Amtsgeri
ly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> http
e instructions available here:
> > >
> > > http://bioconductor.org/developers/how-to/git/sync-
> > existing-repositories/
> > >
> > > However, if I run the command *git remote add upstream
> > > g...@git.bioconductor.org:packages/COHCAP.gi**t*, then I get an error
> &g
uld not read from remote repository.
>>> > >
>>> > >
>>> > > Please make sure you have the correct access rights
>>> > >
>>> > > and the repository exists.
>>> > >
>>> > > error: Could not fetch upstream
20007
> Phone: (202) 687-1545
> Fax: (202) 687-5011
> http://icbi.georgetown.edu/boca
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman
not
machine-type dependent, although how to use ssh keys may vary a bit,
particularly on windows.
Sean
>
> ~/.ssh$ ssh -T g...@git.bioconductor.org
> Permission denied (publickey).
>
> Thanks,
> Charles
>
>
>
> On Mon, Sep 4, 2017 at 5:28 PM, Sean Davis wrote:
&
oneSENSE.html
>
>
> --
> Best Wishes,
> Tan Yong Kee
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Da
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seand
_
> >>>>>> Bioc-devel@r-project.org mailing list
> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>>
> >>>>>>
> >>>>> [[alternative HTML
[[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National
(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify th
Just in case some developers would like to review the Bioconductor build
report as computable data in R:
http://bit.ly/2zKL3M3
Sean
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https
-P
>
I leave that as an exercise for the reader. ; )
Sean
>
> Thanks,
> H.
>
>
> On 11/17/2017 12:16 PM, Sean Davis wrote:
>
>> Just in case some developers would like to review the Bioconductor build
>> report as computable data in R:
>>
>> https:/
oyee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immedia
vel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> ht
On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith wrote:
> Thanks for the speedy response Sean. I'll switch back to the version
> using a file name shortly.
>
No problem. Let me know if it does not work as expected.
Sean
>
> Cheers,
> Mike
>
> On 30 November 201
On Thu, Nov 30, 2017 at 10:01 AM, Janssen-10, R.R.E. <
r.r.e.janssen...@umcutrecht.nl> wrote:
> Dear Martin,
>
> Martin writes:
>
> > On 11/29/2017 11:14 AM, Janssen-10, R.R.E. wrote:
> >> Hi Martin,
> >>
> >> Thanks for your reply!
> >>
> >> Martin Morgan writes:
> >>
> >>> On 11/29/2017 09:58 AM
lt user_cache_dir may not be the
best choice there.
Sean
>
> thanks,
> Mike
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Inst
ser.
>
>
https://cran.r-project.org/web/packages/policies.html
Sean
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
hat_0.2.0
> [5] R6_2.2.2 magrittr_1.5 rlang_0.1.4 bindrcpp_0.2
> [9] limma_3.34.2 xml2_1.1.1 readr_1.1.1 glue_1.2.0
> [13] purrr_0.2.4 hms_0.4.0compiler_3.4.2 pkgconfig_2.0.1
> [17] bindr_0.1tibble_1.3.4
>
>
> On
This new NSF funding opportunity might interest a few folks on this list.
Sean
-- Forwarded message --
Subject: [SIAM-LS] New NSF funding opportunity: Rules of Life (RoL):
Forecasting and Emergence in Living Systems
Dear Colleagues:
NSF seeks to highlight the importance of resea
ctor is passing
> metadata along, or perhaps it's a problem with crosscite or something?
> I'm not sure. Any thoughts?
>
> Nathan Sheffield, PhD
> Assistant Professor
> Center for Public Health Genomics
> University of Virginia
> www.databio.org
>
> On 10/19/20
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12
[[alternative HTML version deleted]]
___
I'd be interested to see one. I don't think it has been done yet.
On Fri, Feb 23, 2018 at 9:19 AM Michael Lawrence
wrote:
> 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]]
>
> _
he right place in a more visual
> way...
>
>
> Cheers,
> Christian
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
--
Sean D
work.
Thanks,
Sean
(on behalf of the F1000Research Bioconductor Advisory Board)
--
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12
[[alternative HTML
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
&g
ed]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, M
ternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesd
el-capitan/contrib/3.6:
cannot open URL '
https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
trying URL '
https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/GEOquery_2.51.5.tgz
'
Content type 'application/x-gzip' length 1382
On Tue, May 21, 2019 at 2:54 AM Aaron Lun <
infinite.monkeys.with.keyboa...@gmail.com> wrote:
> > Thanks for your response. So far my intention is to to plot them and I
> > do not intend on performing any other operation. The first step would be
> > read in the VCF file and transform it into a mea
ture,
> Computational Genomics Group,
> IFOM - The FIRC Institute of Molecular Oncology,
> Via Adamello 16,
> 20139 Milano, Italy.
> Phone: +393441130157
> E-mail: koustav@ifom.eu
>
>
>
>
> [[alternative HTML version deleted]]
>
> ___
itation could allow any recipient to send a response
> to
> > the organizer and be added to the guest list, or invite others regardless
> > of their own invitation status, or to modify your RSVP. Learn more at
> > https://support.google.com/calendar/answer/37135#for
rohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.o
ernative HTML version deleted]]
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Heal
There are some good ideas here that would provide enhancement to
BiocPkgTools. I don't have the bandwidth to incorporate right now, but
filing issues or a pull request with a skeleton would be helpful to keep
track.
Sean
On Sun, Feb 9, 2020 at 7:31 AM Vincent Carey
wrote:
> On Sat, Feb 8, 2020
On Tue, Mar 17, 2020 at 11:48 PM Julian Flesch
wrote:
> Hi Bioc team,
>
>
> I am the maintainer of the package /waddR/.
>
> We have had built issues on the active branch recently, due a dependency
> being unavailable. After pushing a patch, the issues were resolved on
> the devel branch.
>
> Is i
On Fri, May 23, 2014 at 4:34 PM, Michael Lawrence
wrote:
> I like the idea about extracting important environmental information.
> Possibly the function that browses to the bug tracker could print out the
> sessionInfo for copy/paste.
>
> It is tempting to push the automation further, e.g. talking
Check in svn for the sources.
Sean
On Aug 8, 2014 8:58 AM, "Kevin Rue-Albrecht"
wrote:
> Hi,
>
> Thank you for your replying.
>
> Thanks Kasper, I had looked at other vignettes, but in the packages I
> looked at so far I only found the PDF end-result. (e.g. edgeR), or the
> sources. On the other
Hi, Arun. There is not such a system that covers the entire Bioconductor
project. Since packages are largely contributed by diverse developers,
there are many disparate bug tracking systems in use (and many packages
with no formal bug tracking). There is a facility in R to allow package
authors
The National Institutes of Health is now accepting applications for
tenure-track positions through the Earl Stadtman recruitment mechanism.
Details are available here:
http://goo.gl/vF95Pi
Sean
[[alternative HTML version deleted]]
___
Bioc-de
The National Institutes of Health is now accepting applications for
tenure-track positions through the Earl Stadtman recruitment mechanism.
Details are available here:
http://goo.gl/vF95Pi
Sean
[[alternative HTML version deleted]]
___
Bioc-de
Hi, Vince.
I'm coming a little late to the party, but I agree with Kasper's sentiment
that the less "magical" approach of using subsetByXXX might be the cleaner
way to go for the time being.
Sean
On Sat, Sep 20, 2014 at 10:42 AM, Vincent Carey
wrote:
>
> https://github.com/vjcitn/biocMultiAss
Hi, Vince.
Looks like a good start. I'd probably pull all the assays from
ExpressionSet into SummarizedExperiment as the default, avoiding data
coercion methods that are unnecessarily lossy. Also, as it stands, the
assayname argument is not used anyway?
Sean
On Sat, Sep 20, 2014 at 10:38 AM,
eries in each of these vocabularies
> > should, perhaps, be in the OrganismDb space? Once those are in place
> > no additional infrastructure is necessary?
> >
> > On Sat, Sep 20, 2014 at 12:49 PM, Tim Triche, Jr.
> > wrote:
> >
> > > Agreed with Se
Hi, Henrik.
This is the approach that I have been using, also, roughly summarized as:
- git svn clone from bioconductor svn (can take a LONG time, so use git svn
clone -r 4:HEAD to truncate history to rev4 in svn)
- git push to github
- setup git-svn bridge
- work with git as normal
Sean
I've been meaning to suggest the same thing. Istvan can probably clarify
the details of who can do what on biostars, but it really does improve the
site to have active moderation if that is technically feasible.
Sean
On Sep 24, 2014 2:00 PM, "Steve Lianoglou" wrote:
> Greetings,
>
> I'm curious
Hi, Leo.
I think you'll need to include the VignetteIndexEntry and VignetteEngine as
the first lines of your vignette, enclosed in an HTML comment. You'll also
need to adjust your DESCRIPTION file slightly. Though not meant to be
authoritative, I put together the details that worked for me here:
On behalf of a number of software developers, end-users, publishers
associated with the scientific analysis community, we would like to invite
all of you to review a document generated as a result of a NIH BD2K
supported meeting that focused on the opportunities and challenges of
developing a softw
Hi, Darin.
You might find these instructions useful:
http://www.bioconductor.org/about/mirrors/mirror-how-to/
Basically, you can use rsync to get the repository and keep it up-to-date.
Sean
On Thu, Oct 30, 2014 at 9:17 AM, Darin Perusich wrote:
> Hello All,
>
> Would it be possible to get a
On Sat, Nov 22, 2014 at 12:53 AM, Karl Stamm wrote:
> Question regarding gene name conversions. Once upon a time, I was doing a
> lot of gene name conversions, particularly from NM_ to HGNC symbol or
> Entrez GeneID. I used bioMaRt successfully, and developed a cache matrix so
> I could quick
d a double lookup to go from Refseq to EG to HGNC.
>
> I've reimplemented following your advice (Thanks Sean Davis and Vincent
> Carey). Examples with benchmarking are posted here:
> http://pastebin.com/HjNbtD1g
>
> Calling select() with a short vector of refseq IDs takes a si
Hi, Martin, Val, and Herve.
This looks like a little problem with the bitnames in
Rsamtools/GenomicAlignments. Perhaps this is related to some bitnames
being deprecated?
Thanks,
Sean
> library(GenomicAlignments)
> sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate = FALSE))
> x =
I am calculating coverage metrics of a BAM file on the CDS regions. When I
form the RangesList and do coverage(), the resulting coverage vector
applies the views to the regions from the RangesList without checking on
matching ordering or seqlevels of the RleList and the RangesList. This
results,
ing or error and results in an object that "works" but is
nonsensical. I simply want to protect myself from making the same mistake
twice by some checking inside the Views() method.
Sean
>
> Hope this helps,
>
> Malcolm
>
> On Fri, Feb 20, 2015 at 12:53 PM, Sean Davis
of the situation.
>
> Thanks for your feedback.
> H.
>
>
>
> On 02/20/2015 07:38 AM, Kasper Daniel Hansen wrote:
>
>> Clearly the Views method has to handle that, and in my opinion return it
>> in
>> the order of cds list in this case. Anything else is way
Hi, Marc.
Since Ensembl has switched to GRCh38 for their most recent builds, to get
access to GRCh37 data now requires a different host and port for biomaRt.
These are exposed in the makeTxDbFromBiomart, but not the accompanying
functionality to directly make a package. Would it make sense to add
Just so we don't lose the thoughts that have come before, here is a link to
a similar proposal from last year.
https://stat.ethz.ch/pipermail/bioc-devel/2014-February/005292.html
Sean
On Mon, Mar 23, 2015 at 6:17 AM, Wolfgang Huber wrote:
> I wonder whether it’d possible to have the website
Is this a use case for a "graphical" build report that displays the build
status on a graph/DAG?
http://www.bioconductor.org/packages/release/bioc/vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf
pkgDepTools, combined with a computable build report (a downloadable
version of the current build repor
Hi, Wolfgang.
One way to think of docker is as a very efficient, self-contained virtual
machine. The operative term is "self-contained". The docker containers
resemble real machines from the inside and the outside. These machines can
expose ports and can mount file systems, but something like .
Hi, Aileen.
This list isn't really the best place to ask questions like this and is
really reserved for discussion around package development. Could you
please post to:
https://support.bioconductor.org/
That way, you benefit from more eyes and everyone benefits from potential
answers.
Thanks,
The last Bioconductor development cycle visualized as a graph using gource
is available here:
https://youtu.be/-HZ4XOh49fw
Sean
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinf
On Tue, Jun 2, 2015 at 5:32 AM, Vincent Carey
wrote:
> I agree that this would be nice; not sure how feasible. Could a specific
> approach with containers provide a solution?
>
Unfortunately, containers are linux microkernels, so Windows and MacOS are
basically out.
> On Mon, Jun 1, 2015 at 1
Hi, Arne.
This question is best posted on the support site:
https://support.bioconductor.org/
To give a preview of the answer, though, while coverage and binned counts
are related concepts, they are not really identical. The csaw package is
looking for read counts.
Sean
On Tue, Jul 7, 2015 a
Hi, Vince.
It seems like knitr should be able to build a sweave vignette, particularly
if the stuff in the << >> has been converted from sweave to knitr format?
It might be easier to do that than to convert the original to Rmarkdown.
Sean
On Mon, Aug 3, 2015 at 6:57 PM, Vincent Carey
wrote:
Hi, Dan.
A user asked me a question about the DnaseR package. It appears to have
been removed from Bioc? Where would I find that out? What is the behavior
of the release/devel pages if a package has been previously removed?
Thanks,
Sean
[[alternative HTML version deleted]]
__
> all the way at the bottom: http://bioconductor.org/news/bioc_3_1_release/
>> .
>> That's a bit hands-on, as you sometimes have to go back several releases
>> to
>> see when it got removed, so hopefully Dan has a more reasonable approach.
>>
>> Jim
>>
>>
>
> On Sep 1, 2015, at 6:15 AM, Zhilong Jia wrote:
>
> Hello,
>
> I'm wonder it there a way to update a package in the current version of
> Bioconductor using the development version ot it? Thank you.
Hi, Zhilong.
See the following page under “committing to the release branch”.
http://biocondu
Forgive the really naive questions, but my C/C++ and Biostrings skills
are pretty rough. I have been playing with Rcpp to interface to an
external library for reading sequence formats. I am reading DNA
sequences one-at-a-time and would like to package a set of those up as a
DNAStringSet. I ha
Hi, all.
Sorry for the hiccup. The problem appears to have stemmed from NCBI GEO
switching to using https for GEO data tables. This is not a highly-used
feature, but it was enough to break the build. It should be fixed (cross
fingers) in Devel. If fixed in devel, I will backport to release.
Morais
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of
some larger packages from ‘Imports’ to
> ‘Suggests’, but to no avail.
>
> Best,
> Koen
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bio
o rewrite my package without
> d3heatmap? Or is there an easy alternative to d3heatmap?
>
> Thanks,
> Mani
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc
_
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> > --
> >
> > Levi Waldron
> >
> > Associate Professor
> >
> > Department o
[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://sea
__
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12
[[
deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https
Hi, Huang.
It looks like you might need to add the rmarkdown package in Suggests (and
version bump to catch the change):
http://bioconductor.org/checkResults/devel/bioc-LATEST/ANCOMBC/nebbiolo2-buildsrc.html
Since the windows binary version is building, I'm guessing that may fix the
issue.
Sean
Hi, Pariksheet.
For #1, I suspect that it might be challenging to publish a paper based on the
context you provide, but I do not have a good handle on the specific changes
you have proposed. To make your work publishable, you would probably need to at
least publish the software and it appears f
My sentiments exactly! Great work!
Sean
From: Bioc-devel on behalf of Steve
Lianoglou
Date: Tuesday, September 27, 2022 at 1:25 PM
To: Jennifer Wokaty
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Mac ARM64 binaries available
a yeah
thanks for the hard work, everybo
Hi, Amin.
You�ll have a more likely chance of an answer if you post to the Bioconductor
support site at https://support.bioconductor.org. This list is really focused
to development-related issues.
Best,
Sean
From: Bioc-devel on behalf of Amin Ali
Date: Monday, October 31, 2022 at 5:18 AM
T
Hi, Chiagozie.
This list is mainly for developer questions. Your best bet is to ask on
https://support.bioconductor.org/ where you'll get many more eyes on your
question and the broadest possible community will benefit from answers.
When you ask there, consider adding the output of sessionInfo() t
On Fri, Nov 16, 2012 at 10:33 AM, Hahne, Florian wrote:
> Sort of. My implementation assumes parLapply to be a generic function, and
> there is an object called SGEcluster, which in a way is equivalent to the
> 'cluster' class objects in the parallel package. Rather than providing a
> bunch of no
On Wed, Jan 23, 2013 at 1:41 PM, Frederic Fournier
wrote:
> Hello everyone,
>
> I recently submitted a package to bioconductor, and couple of days ago, the
> package started to fail the automated daily build on george2 and moscato2.
> Today I made some changes that work on my testing environment,
On Tue, Feb 26, 2013 at 1:23 PM, Julian Gehring wrote:
> Hi Richard,
>
> That is true that is not according to the specs. However, the 'ensemblVEP'
> package has the 'parseCSQToGRanges' method which extracts this kind of CSQ
> information from a 'VCF' object (as read in by 'readVcf') and fails at
On Tue, Mar 26, 2013 at 7:27 AM, Ulrich Bodenhofer wrote:
> On 03/26/2013 12:18 PM, Laurent Gatto wrote:
>
>> On 26 March 2013 09:26, Ulrich Bodenhofer
>> wrote:
>>
>>> Dear colleagues,
>>>
>>> One of my students is currently working on a package that we plan to
>>> submit
>>> to Bioconductor. I
On Thu, Jul 11, 2013 at 11:01 AM, Kasper Daniel Hansen
wrote:
> On Thu, Jul 11, 2013 at 9:57 AM, Henrik Bengtsson
> wrote:
>
>> On Wed, Jul 10, 2013 at 9:10 PM, Hervé Pagès wrote:
>> > Hi Kasper,
>> >
>> >
>> > On 07/10/2013 10:50 AM, Kasper Daniel Hansen wrote:
>> >>
>> >> On Wed, Jul 10, 2013
A little off-topic, I know
NHGRI has released a new RFI. There are a number of folks on this
list that may have input they want to share, so I am forwarding along
the Notice:
http://grants.nih.gov/grants/guide/notice-files/NOT-HG-13-014.html
Sean
___
1 - 100 of 113 matches
Mail list logo
