raphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.25.2
loaded via a namespace (and not attached):
[1] tools_3.4.0
>
--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public
.2.3.tar.gz'
> Content type 'application/x-gzip' length 2139642 bytes (2.0 MB)
> ======
> downloaded 2.0 MB
>
> Val
>
> On 12/27/2016 02:00 PM, Levi Waldron wrote:
> > I don't seem to be able to install hgu133plus2.db in bioc-deve
Not sure anyone will be able to help with this, but I can no longer install
packages from bioc-devel using a current R-devel and biocLite() on my
OSX Yosemite 10.10.5. I can still install from the command line `R CMD
INSTALL` and `install.packages()`. Here is the error - the package lazyeval
is jus
On Sun, Jan 29, 2017 at 11:36 PM, Martin Morgan
wrote:
>
>
> can you try to find out what file it is trying to read and what function
> call, e.g.,
>
> options(error=recover)
> biocLite("lazyeval")
>
> That should get the call stack; choose readRDS and look for the 'file'
> variable for the
On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan
wrote:
> It seems like this is a local cache of the rstudio file that describes the
> mac repository. Maybe your vanilla execution of install.packages() does not
> use the repository that BiocInstaller does. So maybe
>
> install.packages("lazyeva
does. So maybe
One more note, I am doing all this from a terminal - I think the only
association with RStudio is that its mirror was my default.
--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US:
exiting and starting R again creates a new tmp directory
so gives another free invocation. Sorry for blaming it on biocLite().
--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616 S
I am getting this error from a basic phyloseq function, which doesn't
appear in the build system's check. Is this some strange thing wrong with
my installation? From a fresh R session:
> library(phyloseq)
> example("sample_data")
smpl_d> #
smpl_d> data(soilrep)
smpl_d> head(sample_data(soilrep
On Sun, Feb 19, 2017 at 2:54 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
>
> It is a variant of
>>
>> https://stat.ethz.ch/pipermail/bioc-devel/2017-February/010463.html
>>
>> and requires re-installation of one or more of your Bioconductor
>> packages that depend directly or indirect
On Tue, Feb 21, 2017 at 2:02 PM, Hervé Pagès wrote:
> Hi Levi,
>
> Were you able to sort this out? I think we should emphasize the
> importance of re-installing packages *from source* (i.e. with
> biocLite(..., type="source")). This is because some of the package
> binaries we distribute seem to
Rfactor or vector_OR_factor matches anything in the R/ directory of
phyloseq. But, my phyloseq installation is working again.
On Tue, Feb 21, 2017 at 5:33 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> On 02/21/2017 03:24 PM, Levi Waldron wrote:
>
>> On Tue, Feb 21,
On Feb 22, 2017 1:42 PM, "Vincent Carey" wrote:
might there have been an object that references the obsolete class around?
There were no objects in the environment, ie being loaded from an .RData,
if that's what you mean.
[[alternative HTML version deleted]]
__
ch happened
> in S4Vectors), the information contained in its cache of class
> definitions is also out-of-sync.
>
> I just bumped phyloseq version so new Windows and Mac binaries will
> be made and they'll have up-to-date class definitions in their cache.
>
> H.
>
>
> On
//stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616 Skype:
levi.waldron
[[alternative HTML version deleted]]
___
Running and updated Bioc 3.5:
> library(survival)
> set.seed(1)
> cens <- sample(0:1, 100, replace=TRUE)
> time <- rnorm(100)
> df = DataFrame(time=time, cens=cens, y=Surv(time, cens))
> df[1:3, ] #OK
DataFrame with 3 rows and 3 columns
time cens y.from
It works for me when I have an existing cache, but not after removing the
cache:
> unlink("~/.ExperimentHub", recursive=TRUE)
> suppressPackageStartupMessages(library(curatedMetagenomicData))
> ExperimentHub()
updating metadata: retrieving 1 resource
|=
tionHub >= 2.9.4.
>
> Val
>
>
> On 06/03/2017 05:55 AM, Levi Waldron wrote:
> > It works for me when I have an existing cache, but not after removing the
> > cache:
> >
> >> unlink("~/.ExperimentHub", recursive=TRUE)
> >> suppressPackageSt
On Tue, Jun 20, 2017 at 7:24 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:
> This is now fixed.
>
> Valerie
>
Thank you Val! curatedMetagenomicData is back under review now, so much
appreciated.
http://biorxiv.org/content/early/2017/06/21/103085
[[alternative HTML v
//git-lfs.github.com/:
git lfs track "*.rda"
git add .gitattributes
git commit -a
Does this seem correct, and is there anything else to know for experimental
data packages with large files?
--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Publi
Also, can I now remove external_data_store.txt?
$ cat external_data_store.txt
data
inst/extdata
On Tue, Sep 5, 2017 at 4:38 PM, Levi Waldron
wrote:
> Are a couple extra commands needed at https://www.bioconductor.
> org/developers/how-to/git/maintain-github-bioc/ for experimenta
>
> Nitesh
>
> > On Sep 5, 2017, at 4:49 PM, Levi Waldron
> wrote:
> >
> > Also, can I now remove external_data_store.txt?
> >
> > $ cat external_data_store.txt
> > data
> > inst/extdata
> >
> >
> > On Tue, Sep 5, 2017 at 4:38
Thanks, Nitesh! See below:
On Thu, Sep 7, 2017 at 4:21 PM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:
> Hi Levi,
>
> I’m not sure what you mean by tracked vs checked.
>
Sorry, I meant whether there are any differences in the way software and
experimental data packages are handled by
base package directory, and that is the only option I was able
to make show up on
https://bioconductor.org/packages/devel/data/experiment/news/curatedMetagenomicData/NEWS
when I played with it a couple months ago. Just want to get it straight.
-Levi
--
Levi Waldron
http://www.waldronlab.org
Assi
ROBEID"])))
>>>>return(z[!isd,,drop=FALSE])
>>>>z
>>>>},
>>>> signIsStrand = TRUE, # verify that signs of addresses define
>>>> strand
>>>> ucsdChrnames = TRUE# pre
xperiment” > as(mouseData,
"ExpressionSet") Error in updateOldESet(from, "ExpressionSet") : no slot of
name "pData" for this object of class "AnnotatedDataFrame" >
On Mon, Sep 11, 2017 at 6:58 AM, Martin Morgan <
martin.mor...@roswel
On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:
> I guess we discussed this with Davide Risso @Bioc2017 in the
> MultiAssayExperiment workshop.
>
> > SummarizedExperiment(mouseData)
>
> puts the eSet (rather counterintuitively) into `assays` of
> `S
On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès wrote:
> Hi,
>
> I added coercion from ExpressionSet to SummarizedExperiment in
> SummarizedExperiment 1.7.6.
>
Thank you Hervé!
> The current behavior of the SummarizedExperiment() constructor
> when called on a ExpressionSet object doesn't make mu
Thanks Ludwig and Kasper. This old presentation from Martin also helped me
a lot:
https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf
But I still wonder, why provide the coercion for ExpressionSet, if
providing it for eSet would work not only for Exp
of it in Powerpoint and part in Beamer, and used pdftk to
concatenate these! In practice I would do the Beamer part as a live-demo,
and take advantage of some animations in PPT)
--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +
>
> On Wed, Oct 18, 2017 at 10:26 AM, Ryan Thompson
> wrote:
>
>> I think the main reason for reusing/subclassing core classes that users
>> can
>> appreciate is that it makes it much easier for users to integrate multiple
>> packages into a single workflow. Only the most basic of pipelines uses
>
Thanks for all your thoughts Joey, and I hope I didn't come across as
critical of phyloseq in particular. In fact, the couple packages I created
as a post-doc (doppelgangR and ffpe) did exactly the same thing, but unlike
phyloseq have never been used enough for it to make much difference :).
This c
If your assays don't "match up" in
this way, then MultiAssayExperiment. Of course, the ExperimentList elements
of a MultiAssayExperiment can be SummarizedExperiments...
--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School
Just realized my answer yesterday went to Francesco and not the list:
Since it sounds like you have two matrices of the same dimensions, why not
represent these as two assays in a SummarizedExperiment? E.g.:
> statvals <- matrix(rnorm(100), ncol=5)
> pvals <- pnorm(statvals)
> library(Summarized
On Oct 24, 2017 6:14 AM, "Francesco Napolitano" wrote:
I'm converting gene expression profiles to "pathway expression
profiles" (https://doi.org/10.1093/bioinformatics/btv536), so for each
pathway I have an enrichment score and a p-value. I guess it would be
like modeling gene expression data whe
f I build one SummarizedExperiment for
> each database, I have to replicate the common metadata across all of
> them, and also lose most of the features that going through the burden
> of modeling my data with SE were all about :-/.
>
> Note I'm considering all this for a packag
On Mon, Oct 23, 2017 at 9:15 PM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> Are you discussing statistics of the same dimension as the data (unusual)
> or summary statistics? We should think about a MAE version of summary
> statistics, but that is not captured in current represe
Any thoughts about how to implement optional or "extra" unit tests, that
are too resource intensive to be part of the Bioconductor daily builds, but
that should be run once in a while, say with major updates?
[[alternative HTML version deleted]]
___
BioC build machines. The test will otherwise be run
> (e.g., during local development). There are some other `testthat::skip*()`
> functions that may also be useful.
> Cheers,
> Pete
>
> On Wed, 25 Oct 2017 at 12:47 Levi Waldron
> wrote:
>
>> Any thoughts about how to im
AM, Michael Lawrence <
>>> lawrence.mich...@gene.com> wrote:
>>>
>>> Looks like BiocCodeTools should start checking whether people are using
>>>> that and at least make a NOTE of it.
>>>>
>>>> On Tue, Oct 24, 2017 at 8:17
On Thu, Mar 8, 2018 at 12:29 AM, Paul Shannon
wrote:
> Thanks, Gabe.
>
> You make an excellent point: bioc objects get first class support. In
> some instance, base R data types deserve that also, and data.frames lead
> the list for me, being useful, concise, universally available, expressive.
>
Submissions are now open at
http://bioc2018.bioconductor.org/call-for-abstracts for:
-
Call for posters and short contributed talks (submit an abstract)
-
Call for workshops (submit a syllabus)
-
Call for Birds of a Feather / Special Interest Groups (submit an Issue
on GitH
On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon
wrote:
> Have I missed the deadline for the latest release? I have created a
> package, that runs great but there are a number of errors still from R CMD
> check that I am sorting out.
>
> This is my first R package so I'm not sure if development is
gt;
> On Tue, Apr 3, 2018 at 8:06 AM, Levi Waldron
> wrote:
>
>> On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon
>> wrote:
>>
>> > Have I missed the deadline for the latest release? I have created a
>> > package, that runs great but there are a
to limit reuse possibilities.
>
> See
>
> https://github.com/Bioconductor/BiocStickers/issues/54
>
> for details.
>
> Best wishes,
>
> Laurent
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.
It would be useful to be able to use BiocManager to install
the Depends/Imports/Suggests of a source package not on Bioconductor, e.g.:
BiocManager::install("Bioconductor/BiocWorkshops") #works but only if all
Depends/Imports are already installed
or:
BiocManager::install_deps("Bioconductor/Bio
Thanks Pariksheet and Martin! It seems that in fact both of these
approaches work, e.g. (I made a simpler test case to figure this out):
devtools::install_github("lwaldron/nothing", repos =
BiocManager::repositories(), dependencies = TRUE)
remove.packages(c("nothing", "ABCp2"))
BiocManager::instal
1), R 3.5.1 (2018-07-02)
Installing github package(s) 'lwaldron/nothing'
Downloading GitHub repo lwaldron/nothing@master
Skipping 3 packages not available: curatedTCGAData, GenomeInfoDbData,
mirbase.db
Installing 1 packages: TCGAutils
ERROR: dependencies *‘mirbase.db’, ‘curatedTCGAData’* are n
On Fri, Jul 20, 2018 at 10:26 AM Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> I think it's a Mac thing, and it's decided to install binary (tgz), and
> the annotation packages are source (tar.gz).
>
> Have you set options(pkgType = "both") ?
>
Thanks Martin, and sorry for the slow repl
There are also weekly "long test" builds with a 6h timeout:
https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012326.html
[[alternative HTML version deleted]]
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o change the citation on
> Bioconductor?
> >
> > Many thanks for your great help!
> >
> > Xiangyu
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat
rely,
Levi
--
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
[[alternative HTML version deleted]]
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Bioc-devel@r-project.org mailing list
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John, is your new version number reflected on the devel version of the
package landing page and the build report? After you push a new version
number to master, it will propagate the next day after overnight
building/testing.
AFAIK, there are only a few explanations for why git pushes do not show
t; (Maybe FAQ?)
>
>
> Just a thought.
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Levi Waldron
http://www.waldronlab.io
Associate Professor of Biostat
On Wed, Oct 10, 2018 at 3:25 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:
> As far as Levi’s comment about PEP8. It’s possible to design something
> similar with Jim Hester’s “lintr” package, which purely defines a style
> guide for code.
>
> https://github.com/jimhester/lintr
As I
,
talks, and posters, to come soon.
--
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
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https://stat.ethz.ch/m
curatedMetagenomicData hasn't built yet on the new release or devel. I
believe this was originally because the required ExperimentHub database
update occurred after the last curatedMetagenomicData version bump, but
since I bumped the version on Thursday it still hasn't built. Can you
advise?
I remember now (I think) that experimental data packages are built on
Wednesday and *Saturday* nights - in which case I’ll just check again
tomorrow morning.
On Sat, Nov 3, 2018 at 8:59 AM Levi Waldron
wrote:
> curatedMetagenomicData hasn't built yet on the new release or devel. I
&
post:
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014281.html
>
> Valerie
>
> On 11/3/18 7:08 AM, Levi Waldron wrote:
> > I remember now (I think) that experimental data packages are built on
> > Wednesday and *Saturday* nights - in which case I’ll just ch
I opened an issue on BiocManager (
https://github.com/Bioconductor/BiocManager/issues/39) somewhat related to
Sean's recent post, about what BiocManager::install() should return, and it
occurs to me that I should mention it here too for feedback:
> Having `BiocManager::install()` return the "pkgs"
t;is not available|had non-zero exit status", w)))
quit("no", 1L)
}
On Tue, Jan 22, 2019 at 10:19 AM Levi Waldron
wrote:
> I opened an issue on BiocManager (
> https://github.com/Bioconductor/BiocManager/issues/39) somewhat related
> to Sean's recent post, abo
s of R and Bioconductor.
Apologies for cross-posting (https://support.bioconductor.org/p/118159/)
but I want to make sure no one misses this deadline accidentally.
--
Levi Waldron
https://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Levi Waldron
http://www.waldronlab.io
Associate Professor of BiostatisticsCUNY School of Public Health
US: +1 646-364-9616 Skype:
levi.waldron
[
Bioc2019 NYC registration has been very strong and we will likely have to
close registration soon. If you are planning to present, have made travel
plans, or otherwise have your heart set on it but haven't registered, I
highly recommend doing so in the next couple days. Early registration ends
May
Indeed, it's amazing. Thank you, Lori and core team.
Il gio 31 ott 2019, 1:11 PM Sean Davis ha scritto:
> Huge kudos to the team for another successful release.
>
> Sean
>
> On Wed, Oct 30, 2019 at 4:54 PM Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
> > Thanks to all developers an
scholarships
March 24 Notification of decision
July 1 Deadline for late posters and for Birds of a Feather meetings
July 10 Notification of decision for late posters
July 10 Last day of early registration (2x fees)
July 29-31 BioC2020 Meeting, Boston
--
Levi Waldron
Associate Professor
D
ntial
expression output. But my first impression is that it will be important
for you to directly support output from DESeq2, edgeR, and limma, since
those are where most Bioconductor users get differential expression output
from.
--
Levi Waldron
Associate Professor
Department of Epidemiolog
; > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
>
Dear developers, for your information, the Bioconductor Code of Conduct
committee's response to a violation reported at BioC2019 has been posted at
https://bioc2019.bioconductor.org/code_of_conduct.
--
Levi Waldron
Associate Professor
Department of Epidemiology and Biostatistics
way ?
>
> Have a nice day,
>
> Charles
>
> --
> Charles Plessy
> Akano, Uruma, Okinawa, Japan
>
> _______
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Levi Waldron
Associate Professor
Department of Epidemi
Last Changed Rev: 2991 / Revision: 2991
Last Changed Date: 2014-09-02 08:08:09 -0700 (Tue, 02 Sep 2014)
--
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
"PrinicpalComponent (1)
<http://bioconductor.org/packages/release/BiocViews.html#>" - I'm reviewing
an incoming package that spells it correctly, not sure if it should change
to the mis-spelled version (hopefully not) or if it can be corrected
in SomaticSignatures and BiocVie
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY
andom number generation:
http://cran.r-project.org/web/packages/rlecuyer/index.html
--
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 10035-4003
phone: 212-396-7747
www.wa
ented
natively in r-core's parallel library and suggested by the snow
library. I used it in my pensim library before transitioning to
parallel, and have tested its streams on hyperthreaded CPUs and
clusters.
--
Levi Waldron
Assistant Professor of Biostatistics
City University of New York
> --
> $ pom
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY
there could be a section in the TOC
for "pre-configured Bioconductor" that links to the AMIs and Docker
containers.
--
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
2180 3rd Ave Rm 538
New York NY 1003
build reports. Package web pages could also link back to the profiles of
their developer. Extra incentive to develop and maintain, and keep those
build reports error-free?
--
Levi Waldron
Assistant Professor of Biostatistics
City University of New York School of Public Health, Hunter College
ou have any questions.
>
>
> Thanks!
>
> Dan
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Levi Waldron
Assistant Professor of Biostatistics
City University of
Date: Mon, Jun 1, 2020 at 8:02 PM
Subject: Re: [cbioportal] Installation cBioPortalData error
To: mohammed imran Khan , Levi Waldron <
lwaldron.resea...@gmail.com>
Cc: JJ Gao , Marcel Ramos ,
cbiopor...@googlegroups.com
Hi,
Thank you for your quick responses. Unfortunately this did not resol
il and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
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>
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Levi Waldron
Associa
Gives me some nostalgia because I think simpleaffy was the first
Bioconductor package I used!
Il gio 27 ago 2020, 1:46 PM Shepherd, Lori
ha scritto:
> Thank you for letting us know. I will begin the deprecation process for
> the package. Thank you for your contributions.
>
>
> Lori Shepherd
>
>
ogram development, technical development of various platforms, Code of
Conduct enforcement, and local organizing in Seattle. If you are interested
in getting involved, fill out this short survey with your contact
information and interests: https://forms.gle/Hb6WYxBzUJfqkq2D6
--
Levi Waldron
Asso
Hi Dario and Andrea, I don't think you'll have to do anything - it was
meant to be a feature that shouldn't have affected your use cases
of not specifying the sampleMap. I've opened an issue at
https://github.com/waldronlab/MultiAssayExperiment/issues/291.
--
Levi Waldron
Submit an abstract for a talk, digital poster, or Birds-of-a-feather
session, or a syllabus for a software demo or long workshop at BioC2021 on
Aug 4-6! The conference will most likely again be virtual this year.
https://bioc2021.bioconductor.org/submissions/
--
Levi Waldron
Associate
, Feb 18, 2021 at 4:52 PM Levi Waldron
wrote:
> Submit an abstract for a talk, digital poster, or Birds-of-a-feather
> session, or a syllabus for a software demo or long workshop at BioC2021 on
> Aug 4-6! The conference will most likely again be virtual this year.
> https://bioc2021.bioc
quot;))$tax_id
[1] 562
Any thoughts from the GenomeInfoDbData maintainer ("Bioconductor Maintainer
") about a pull request either to a) update
specData to add additional columns for all taxonomic levels, or b) creating
a new object? Or, another approach altogether? See
https://github.com/waldronl
I'd like to invite any interested members of the committee to get involved
in organizing BioC2022, planned to be in a hybrid format in Seattle
July 27-29, 2022. There is lots to be done, including sponsorship and
funding, outreach, website, workshop technical organization, program
development, code
ec 16, 2021 at 1:53 PM Levi Waldron
wrote:
> I'd like to invite any interested members of the committee to get involved
> in organizing BioC2022, planned to be in a hybrid format in Seattle
> July 27-29, 2022. There is lots to be done, including sponsorship and
> funding, outre
Anyone interested in helping formulate requirements for an API + web-based
(Experiment/Annotation)Hub submission system, we're setting a time to meet
next week at
https://doodle.com/poll/uu5ikxqun78twzzr?utm_source=poll&utm_medium=link.
--
Levi Waldron
Associate Professor
Depa
4417e5084e5ca46a4d9e),
would you still recommend it? I expect there to be some manual cleanup in
addition to adding BiocStyle markup, but the less the better.
3. If you or anyone you know wants to help out, let me know, I'll be
organizing a little group to work on this together.
-Lev
2,
verbose = TRUE,
BPPARAM = bpparam)
```
(returns lots of "Warning: Computed variance-covariance matrix problem: not
a positive definite matrix (and positive semidefiniteness is not
checked); returning
NA matrixboundary (singular) fit: see help('isSingular')" warnings)
--
Anatoly, delaying dependency on R 4.4 until October would mean 6 months of
Bioconductor release requiring an old release of R for users. Bioconductor
developers developing against r-devel means that users get a new Bioconductor
release that works immediately on the new R. And I think a main purp
Nice example of a reproducible bug report and rapid bug-fix!
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https://stat.ethz.ch/mailman/listinfo/bioc-devel
t;Download Stats" link. The file inst/NEWS exists in the
non-data repository but not in the data repository, should I add it to the
data repository instead?
Thanks!
-Levi
--
Levi Waldron
Post-doctoral fellow
Department of Biostatistics, Harvard School of Public Health
Department of Bi
Thanks, Dan!
On Wed, Apr 10, 2013 at 12:23 PM, Dan Tenenbaum wrote:
> On Wed, Apr 10, 2013 at 6:13 AM, Levi Waldron
> wrote:
> > Dear Bioconductors,
> >
> > I noticed that the NEWS from my new experimental data package
> > curatedOvarianData (
> >
> ht
and then be restarted with that object.
> >
> > Not sure if the place for such infrastructure is inside shiny itself,
> > or perhaps in a BioC infrastructure package.
> >
> > What are your thoughts?
> > Dan
> >
> > __
I just noticed that there is no mention on
http://bioconductor.org/install/of how to upgrade from the previous
Bioconductor. I think it would be
helpful to advise that it can be done with biocLite("BiocUpgrade").
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On Fri, Jan 10, 2014 at 9:59 AM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:
> Unfortunately, you may want to be careful about making it too robust
> (depending on what you mean). For example filtering methods could very
> well be seen as replacing one matrix with a smaller one.
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