Re: [Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

Nice example of a reproducible bug report and rapid bug-fix! [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Important Bioconductor Release Deadlines

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

Re: [Bioc-devel] benchdamic TIMEOUT in merida1 and kunpeng2

rbose = 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) -- Levi Waldron As

[Bioc-devel] converting old Rnw vignettes to Rmd + BiocStyle

a46a4d9e), 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. -Levi -- Levi Wald

[Bioc-devel] Developing requirements for API + web-based *Hubs

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_medium=link. -- Levi Waldron Associate Professor Department

Re: [Bioc-devel] BioC2022 Seattle July 27-29 hybrid conference organizing committee

, 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, outreach, websi

[Bioc-devel] BioC2022 Seattle July 27-29 hybrid conference organizing committee

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,

[Bioc-devel] NCBI taxonomy annotation

oli"))$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

Re: [Bioc-devel] BioC2021 abstract/syllabus submissions

, 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

[Bioc-devel] BioC2021 abstract/syllabus submissions

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

Re: [Bioc-devel] Recent change in MultiAssayExperiment for inferred MAE-level colData

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 Associate Professor

[Bioc-devel] BioC2021 organizing committee

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 Associate

Re: [Bioc-devel] Request package deprecation

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 >

Re: [Bioc-devel] bioconductor_docker updates

mail message from your computer. Thank you. > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Levi Waldron Associate Professor Depart

[Bioc-devel] Fwd: [cbioportal] Installation cBioPortalData error

: 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 resolve my

Re: [Bioc-devel] How to add an experiment to an empty MultiAssayExperiment file ?

> > 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 Epidemiology

[Bioc-devel] BioC2019 Code of Conduct violation response

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 CUNY

Re: [Bioc-devel] Bioc2020 - Deadline for workshops/talk/poster TOMORROW

; [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] > > ___

Re: [Bioc-devel] Use of SummerisedExperiments or MultiAssayExperiments of many many Dataframes/ nested List objects

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 Epidemiology

[Bioc-devel] BioC2020 - mark your calendars!

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

Re: [Bioc-devel] Bioconductor 3.10 is released!!

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

[Bioc-devel] Bioc2019 NYC registration nearly full

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

Re: [Bioc-devel] package named spdeq causes error

ist > 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 [[alternative HTML version deleted]]

[Bioc-devel] BioC2019 talk/workshop/scholarship submission deadline MARCH 15

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 [[alternat

Re: [Bioc-devel] return value of BiocManager::install()

rep("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, about wh

[Bioc-devel] return value of BiocManager::install()

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

Re: [Bioc-devel] No curatedMetagenomicData build triggered

> 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 check again

Re: [Bioc-devel] No curatedMetagenomicData build triggered

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 > b

[Bioc-devel] No curatedMetagenomicData build triggered

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?

[Bioc-devel] BioC2019 June 24-27 in New York City

lks, and posters, to come soon. -- Levi Waldron http://www.waldronlab.io Associate Professor of BiostatisticsCUNY School of Public Health [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailm

Re: [Bioc-devel] Why bioconductor?

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

Re: [Bioc-devel] Why bioconductor?

aybe FAQ?) > > > Just a thought. > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Levi Waldron http://www.waldronlab.io Associate Professor of Biostatistic

Re: [Bioc-devel] Updating information on Bioconductor site

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

[Bioc-devel] Bioc2019 planning committee

-- Levi Waldron http://www.waldronlab.io Associate Professor of BiostatisticsCUNY School of Public Health [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Change the citation of my Bioconductor R package "BUScorrect"

nge the citation on > Bioconductor? > > > > Many thanks for your great help! > > > > Xiangyu > > > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz

Re: [Bioc-devel] Handling larger data in vignette

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]] ___ Bioc-devel@r-project.org mailing list

Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests

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

Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests

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 not available fo

Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests

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"))

[Bioc-devel] BiocManager to install Depends/Imports/Suggests

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:

Re: [Bioc-devel] BiocStickers license

mit 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.ch/ma

Re: [Bioc-devel] Missed deadline

it's not ready yet. > > On Tue, Apr 3, 2018 at 8:06 AM, Levi Waldron <lwaldron.resea...@gmail.com> > wrote: > >> On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon <roonysga...@gmail.com> >> wrote: >> >> > Have I missed the deadline for the latest release?

Re: [Bioc-devel] Missed deadline

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

Re: [Bioc-devel] "extra" unit tests

running on the 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 <lwaldron.resea...@gmail.com>

[Bioc-devel] MultiAssayExperiment compared to SummarizedExperiment (was: Why should Bioconductor developers re-use core classes?)

lnames, then you should use SummarizedExperiment. 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

Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

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

Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

> > 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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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 >

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

s(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...@roswellpark.org> wrote:

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

ROBEID"]))) >>>>return(z[!isd,,drop=FALSE]) >>>>z >>>>}, >>>> signIsStrand = TRUE, # verify that signs of addresses define >>>> strand >>>> ucsdChrnames = TRUE# prefix

[Bioc-devel] NEWS, inst/NEWS, NEWS.md

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 Assistant

Re: [Bioc-devel] experimental data packages and git-lfs

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

Re: [Bioc-devel] experimental data packages and git-lfs

est, > > Nitesh > > > On Sep 5, 2017, at 4:49 PM, Levi Waldron <lwaldron.resea...@gmail.com> > wrote: > > > > Also, can I now remove external_data_store.txt? > > > > $ cat external_data_store.txt > > data > > inst/extdata >

Re: [Bioc-devel] experimental data packages and git-lfs

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 <lwaldron.resea...@gmail.com> wrote: > Are a couple extra commands needed at https://www.bioconductor. > org/developers/how-to/git/maintain

[Bioc-devel] experimental data packages and git-lfs

-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 Public Hea

Re: [Bioc-devel] stale data experiment package builds

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

Re: [Bioc-devel] ExperimentHub broken in bioc-devel?

t;= 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) > >> suppressPackageStartupMessa

[Bioc-devel] ExperimentHub broken in bioc-devel?

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

[Bioc-devel] DataFrame errors with a Surv class column

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

Re: [Bioc-devel] Bioconductor mirror is gone

> https://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.

Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

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

Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

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, 2017 at 2:

Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

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

Re: [Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

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

[Bioc-devel] phloseq error: invalid class “sample_data” object: superclass "vectorORfactor" not defined in the environment of the object's class

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>

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

ng 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 Skype:

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

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:

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

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 >

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

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

[Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

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

Re: [Bioc-devel] hg133plus2.db

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-devel? > > > >> library(BiocInstal

[Bioc-devel] hg133plus2.db

cs 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 Heal

Re: [Bioc-devel] BioC 3.2 branch created

t us know if you have any questions. > > > Thanks! > > Dan > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Levi Waldron Assistant Professor of Biostatistics Ci

Re: [Bioc-devel] Package submission with library requirement

, implemented 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 School

[Bioc-devel] post-doc position

://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 10035-4003 phone: 212-396-7747 www.waldronlab.org [[alternative HTML version deleted

[Bioc-devel] mis-spelled BiocViews term

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 BiocViews? -- Levi Waldron

[Bioc-devel] daily build system behind

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

[Bioc-devel] upgrade instructions at http://bioconductor.org/install/

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). [[alternative HTML version deleted]]

Re: [Bioc-devel] shiny, Bioconductor, and reproducible research

/mailman/listinfo/bioc-devel -- Levi Waldron Post-doctoral fellow Department of Biostatistics, Harvard School of Public Health Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute Building 1, room 412C 655 Huntington Avenue Boston, Massachusetts 02115 mobile: (617

[Bioc-devel] broken links for curatedOvarianData package

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 Biostatistics