Re: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

S4Vectors_0.41.5 Biobase_2.63.0 BiocGenerics_0.49.1 These new packages are still on the builder, and have to be transferred over to the download repository, which I imagine will happen sometime next week. Best, Jim From: Anatoly Sorokin Sent: Thursday, April 18, 2024 11:01 PM To: James

Re: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

There was an error in the scripts used to generate the organism packages that excluded (among other genes) GRPEL1. We have rectified the error and are re-running. The updated packages should be available early next week. -Original Message- From: Bioc-devel On Behalf Of James W

Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

We have to re-generate these packages - there was an error that excluded 65 genes (total) from nine of the species. They will be available early next week. Sorry for the delay! Best, Jim -Original Message- From: Bioc-devel On Behalf Of Kern, Lori via Bioc-devel Sent: Thursday,

Re: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

It is the wrong place to send the request. This listserv is for package developers. If you want support please use support.bioconductor.org. -Original Message- From: Bioc-devel On Behalf Of Anatoly Sorokin Sent: Thursday, April 18, 2024 12:40 AM To: bioc-devel@r-project.org Subject:

Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

imes to get affy removed in lieu of oligo, to no avail. From: Tim Triche, Jr. Sent: Thursday, March 28, 2024 10:40 AM To: James W. MacDonald Cc: Vincent Carey ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available is this an argument in favor

Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

As well as > subsetByOverlaps(transcripts(Homo.sapiens), GRanges("chrM:1-16569")) 'select()' returned 1:1 mapping between keys and columns GRanges object with 37 ranges and 2 metadata columns: seqnames ranges strand | TXIDTXNAME | [1]

Re: [Bioc-devel] Unable to install "spoon" package due to R version 4.4 dependence

It depends on your OS. If you are on a Linux derivative not named macOS, you can get the sources here: https://cran.r-project.org/src/base-prerelease/ You want R-devel with the latest date. If you are on Windows, you can get the installer here

Re: [Bioc-devel] BiocCheck error

Are you subscribed to the bioc-devel mailing list? -Original Message- From: Bioc-devel On Behalf Of Marek Gierlinski (Staff) Sent: Thursday, January 25, 2024 5:51 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] BiocCheck error When running BiocCheck::BiockCheck() on my package,

Re: [Bioc-devel] How to push to release branch

It's not clear from your screenshot that you checked out the release branch, made the fix, and then tried to push? You don't want to push your devel branch onto the release branch. https://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel -Original

Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects

neAnnotation(TxDb = tx, OrgDb = org.Hs.eg.db) Best, Jim From: Christian Arnold Sent: Tuesday, December 12, 2023 9:35 AM To: Vincent Carey ; James W. MacDonald Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects Dear Vincent and others, thanks for t

Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects

I don't believe a different OrgDb is required. The OrgDb package is meant to provide annotations for genes such as gene symbol or GO term, etc, which are orthogonal to the sequence of the genome, so the current version should suffice. -Original Message- From: Bioc-devel On Behalf Of

Re: [Bioc-devel] Not getting emails from watched tags

Hi Stephanie, I didn't add the tags to the original post, but I did edit the post to highlight the code, and then I responded. I guess it's possible that either action caused the email to be generated? Best, Jim -Original Message- From: Bioc-devel On Behalf Of Stephanie Gogarten

Re: [Bioc-devel] maintenance question

See here https://contributions.bioconductor.org/git-version-control.html#bug-fix-in-release-and-devel -Original Message- From: Bioc-devel On Behalf Of Michael Shapiro Sent: Wednesday, April 19, 2023 8:32 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] maintenance question I

Re: [Bioc-devel] Request for advice on ANCOMBC package error messages in Linux platform

You have this in line 1093-1094 ```{r} samp_frac = out$samp_frac And yet it appears that there is no 'out' object ever generated. There is an 'output' object, that perhaps you meant to use? Also, the vignette building is skipped for Windows and MacOS, which is why it is passing check on those

Re: [Bioc-devel] updating pathwayPCA: "permission denied (publickey)"

That looks like you have the wrong RSA key. You should be able to check which key you are using by logging in here: https://git.bioconductor.org/BiocCredentials/login/ -Original Message- From: Bioc-devel On Behalf Of Gabriel Odom Sent: Thursday, February 9, 2023 1:56 PM To:

Re: [Bioc-devel] Use set.seed inside function

It appears that you don't actually want random colors, but instead you want the same colors each time. Why not just generate the vector of 'random distinct colors' one time and save the vector of colors? -Original Message- From: Bioc-devel On Behalf Of Meng Chen Sent: Monday, November

Re: [Bioc-devel] Bioconductor build system using old commit

You are pushing to the master repo, but then are checking the build results from the RELEASE_3_14 branch. Are you also checking out the release branch and making changes/pushing there as well? http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ Best, Jim

Re: [Bioc-devel] Bioconductor build system using old commit

Err. check that. Release is 3.13, so you should be checking out RELEASE_3_13 -Original Message- From: James W. MacDonald Sent: Friday, September 17, 2021 2:23 PM To: 'Kort, Eric' ; bioc-devel@r-project.org Subject: RE: Bioconductor build system using old commit You are pushing

Re: [Bioc-devel] Best practices for joint release/update of BioC packages

Webster lake. Has it been submitted yet? ;-D -Original Message- From: Bioc-devel On Behalf Of Steve Lianoglou Sent: Wednesday, August 25, 2021 12:02 PM To: Nitesh Turaga Cc: Russell Bainer ; Hervé Pagès Subject: Re: [Bioc-devel] Best practices for joint release/update of BioC

Re: [Bioc-devel] Regarding package nanotatoR

Perhaps this helps explain things? > z <- entrez_search("gtr","muscle_weakness", retmax = )$id > any(z %in% keys(org.Hs.eg.db)) [1] FALSE > zz <- entrez_summary("gene", z) > table(do.call(c,sapply(extract_from_esummary(zz, "organism"), > function(x) x$scientificname)))

Re: [Bioc-devel] Regarding package nanotatoR

Perhaps this helps explain things? > z <- entrez_search("gtr","muscle_weakness", retmax = )$id > any(z %in% keys(org.Hs.eg.db)) [1] FALSE > zz <- entrez_summary("gene", z) > table(do.call(c,sapply(extract_from_esummary(zz, "organism"), > function(x) x$scientificname)))

Re: [Bioc-devel] Updating stable release

The release version of your package is 1.8.0, and the devel is on increment ahead (e.g., 1.9.x). You cannot increment the middle version number of your release package because that makes it a devel package, hence the pre-release hook denying your changes. You should change the version to 1.8.1

Re: [Bioc-devel] problem pushing update to deltaCaptureC

You are looking at the devel version of your package on git, but the release on the Bioconductor website. /Rpacks/deltaCaptureC$ grep Version DESCRIPTION Version: 1.7.1 /Rpacks/deltaCaptureC$ git checkout RELEASE_3_13 Switched to branch 'RELEASE_3_13' Your branch is up-to-date with

Re: [Bioc-devel] %outside% on GRanges

Hi Oleksii, That function is just a simplification of the negation of overlapsAny: > getAnywhere("%outside%") A single object matching '%outside%' was found It was found in the following places package:IRanges namespace:IRanges with value function (query, subject) !overlapsAny(query,

Re: [Bioc-devel] updating released version of package

You also have a commit from yesterday in master that isn't yet reflected on the build machine, again because it takes time for the build machine to build stuff. IIRC we are over 24 hours per build, but that may be old news (FAKE NEWS!). On Thu, Dec 10, 2020 at 11:09 AM James W. MacDonald wrote

Re: [Bioc-devel] updating released version of package

ut not release. > > Here are links to the build reports if it's helpful. > > devel: https://bioconductor.org/checkResults/3.13/bioc-LATEST/cmapR/ > release: https://bioconductor.org/checkResults/3.12/bioc-LATEST/cmapR/ > > Thanks again, > Ted > > On Thu, Dec 10, 2020

Re: [Bioc-devel] updating released version of package

e > branch? > > I'm sure I must be missing something very basic, but any help would be > appreciated. > > Thanks in advance, > Ted > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list

Re: [Bioc-devel] RCurl on Windows

nk for me at the moment. Can the curl package do > what you need? > > On Mon, Nov 23, 2020 at 11:49 AM James W. MacDonald > wrote: > >> FYI, there appears to be a problem with RCurl on Windows, most likely due >> to building against an old version of OpenSSL. Or at

[Bioc-devel] RCurl on Windows

l version I sent the same to c...@r-project.org, which is the email for the maintainer. So they have been notified, but maybe somebody knows whomever is actually maintaining RCurl, and can pull a string? Best, Jim -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and

Re: [Bioc-devel] Question about org.Dr.eg.db package

I thought it was as it did not refer to a > specific genome, unlike TxDb packages, but then I found what I said in my > previous emails. > > > > Thank you very much, > > Gennady > > > > *From: *"James W. MacDonald" > *Reply-To: *"jmac...@u.washi

Re: [Bioc-devel] Question about org.Dr.eg.db package

Hi Gennady, That information should probably be cleaned up, and the BiMaps that point to the location data removed. While the OrgDbs do contain position information, it's been deprecated, which you would find if you tried to query using select(): > select(org.Dr.eg.db, "30037", "CHR") 'select()'

[Bioc-devel] Purpose of subsetted GO tables in OrgDb packages

re are any instances where anything but the go or go_all tables are used, but I can't find one, which makes me wonder why we even have these other tables? So maybe the real easy fix is to just back out the changes that Martin made, and maybe even remove the subsetted GO tables from the DBSCHEMA packages as

Re: [Bioc-devel] Author name displayed incorrectly in package landing page

use of this email message is prohibited. 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]] > > ___

Re: [Bioc-devel] GO.db package data source

Further to this point, when comparing to the latest OBO from geneontology, it looks like the current GO.db has just over 1000 GO IDs that are not in GO any longer, and almost 500 GO IDs are in the GO OBO file that are not in GO.db On Wed, Apr 1, 2020 at 12:11 PM James W. MacDonald wrote

[Bioc-devel] GO.db package data source

://geneontology.org/docs/download-ontology/) for the downloadable data, so we should consider switching. I bring this up because apparently the current release GO.db is missing terms that were added as far back as 2018. Best, Jim -- James W. MacDonald, M.S. Biostatistician University of Washington

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

think the point is clear. This package is full of data > frames and nested lists and it would be nice to use SE or MAE to tidy up > the global environment. Is there a way of turning many many data frames/ > nested lists into an SE or MEA object? If there is please do let me know

Re: [Bioc-devel] Annotation for Lactuca sativa (Lettuce)

nnotation to download but I am > not finding it. Do you have it available? > > Thank you, > Camila > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mail

Re: [Bioc-devel] Changes not applied in bioc source

> > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistici

Re: [Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages may be archived

he 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 immediately by > e-mail and delete this email message from your

Re: [Bioc-devel] BiocManager::install() downgrade installed packages

ngrade Bioc developers' Bioc packages? > > Thanks, > > Henrik > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician University of Washi

Re: [Bioc-devel] Error with compiling Rhtslib

g_2.0.3 bitops_1.0-6 > [61] lattice_0.20-38 purrr_0.3.2 > [63] GenomicAlignments_1.21.7 labeling_0.3 > [65] cowplot_1.0.0 bit_1.1-14 > [67] tidyselect_0.2.5 magrittr_1.5 > [69] R6_2.4.0 DBI_1.0.0 > [71] pillar_1.4.2

Re: [Bioc-devel] biomaRt and TxDb don't play nice together

; > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational

Re: [Bioc-devel] Using my own genome for CAGER

du I 508.523.0203 > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician University of Washing

Re: [Bioc-devel] Error for voom() in limma package

icme=icme=chrome..69i57j69i60j69i65l3j69i60.1858j0j7=chrome=UTF-8# > > > > [[alternative HTML version deleted]] > > _______ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician Univer

Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

Biobase_2.43.1 BiocGenerics_0.29.2 > > > > loaded via a namespace (and not attached): > > [1] Rcpp_1.0.1 digest_0.6.18 DBI_1.0.0 RSQLite_2.1.1 > > [5] blob_1.1.1 bit64_0.9-7 bit_1.1-14 compiler_3.7.0 > > [9] pkgconfig_2.0.2 memoise_1.1

Re: [Bioc-devel] BiocInstaller: next generation

> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmen

Re: [Bioc-devel] Package download when using functions from affy and oligo

ackage 'pd.hugene.1.0.st.v1' is available as a source package but not as a binary So maybe you are thinking of an older R installation, from back when we still made binary versions of annotation packages? Best, Jim > > -- James W. MacDonald, M.S. Biostatistician University of Washing

Re: [Bioc-devel] Package download when using functions from affy and oligo

this email message is prohibited. 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]] > > ___

Re: [Bioc-devel] Best practice on commit

chem-bla-ics.blogspot.com/ > PubList: https://www.zotero.org/egonw > ORCID: -0001-7542-0286 <http://orcid.org/-0001-7542-0286> > ImpactStory: https://impactstory.org/u/egonwillighagen > > [[alternative HTML version deleted]] > > __

Re: [Bioc-devel] Missing link files in Windows (release and devel)

l message may contain legally privileged and/or confidential > information. If you are not the intended recipient(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, > distr

Re: [Bioc-devel] annotation data not updated?

looks like the GO source date were outdated? Jim > > The files were updated but the rdatadateadded was not updated when I added > the new files. > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics &a

Re: [Bioc-devel] annotation data not updated?

Thank you. > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confiden

Re: [Bioc-devel] git push to devel versions

otechnology Institute of Grenoble (BIG)* > *CEA / Grenoble* > *17 avenue des Martyrs* > *F-38054 Grenoble Cedex 9* > */Tél. : 04.38.78.44.14/* > */Fax : 04.38.78.50.51/* > > http://www.edyp.fr/ > > [[alternative HTML version deleted]] > > _____

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

Never mind. It's all Patrick Aboyoun, for whom I think this should persist. Jim On Tue, Aug 22, 2017 at 4:13 PM, James W. MacDonald <jmac...@uw.edu> wrote: > Hi Martin and Nitesh, > > > On Tue, Aug 22, 2017 at 10:09 AM, Martin Morgan < > martin.mor...@roswellpark

Re: [Bioc-devel] Git transition -- regenerating repositories from svn

;> >> >> For a little more detail, the problem is manifest as 'unknown' authors in >> a git commit, e.g., in Biobase from svn user 'jmc' >> >> commit b5ae43bc8aae967b80062da13e5085a6a305b274 >> Author: unknown >> Date: Fri Dec 7 15:17:06 2001 + &

Re: [Bioc-devel] Question about creating a bulleted list without bullets in rstudio

numFeature: number of gene features within the gene > >That is to say, to create a a bulleted list without bullets. > >Does anyone has idea on how to change settings in test.R file? > > >Thank you, > >Aimin > > [[alternative HTML

Re: [Bioc-devel] Windows binaries for the new release?

On Wed, Apr 26, 2017 at 11:26 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 04/26/2017 11:23 AM, James W. MacDonald wrote: > >> >> >> On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan >> <martin.mor...@roswellpark.org <mailt

Re: [Bioc-devel] Windows binaries for the new release?

On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 04/26/2017 10:34 AM, James W. MacDonald wrote: > >> >> >> On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan >> <martin.mor...@roswellpark.org <mailto:m

Re: [Bioc-devel] Windows binaries for the new release?

On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 04/26/2017 10:00 AM, James W. MacDonald wrote: > >> I see the binaries on the respective web pages, but biocLite seems not to: >> > > I'm not 100% sure but can you try aga

[Bioc-devel] Windows binaries for the new release?

C_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.26.0 loaded via a namespace (and not attached): [1] compiler_3.4.0 tools_3.4.0 -- James W. MacDonald, M.S. Biostatistician Univ

Re: [Bioc-devel] Vignette update after change in git mirror repo

t;> Thanks in advance for your help. > >>>> > >>>> Maia > >>>> > >>>> [[alternative HTML version deleted]] > >>>> > >>>> ___ > >>>> Bioc-devel@r

Re: [Bioc-devel] Fwd: Gostats and custom list

ing, > Level 4, 4326-WS10, Building 2, > King Abdullah University of Science and Technology (KAUST), > > Thuwal 23955-6900, Kingdom of Saudi Arabia, > Phone: (+966 12) 808 0614, Mobile: (+966) 5 40375986, > Email Address: amit.subu...@kaust.edu.sa > > [[alternative HTML version deleted

Re: [Bioc-devel] Package not being built on Windows or Mac

than asking him to perform a post-mortem examination: he may be able to say > what the experiment died of. - Ronald Fisher > > [[alternative HTML version deleted]] > > _______ > Bioc-devel@r-project.org mailing list > https://stat.

Re: [Bioc-devel] developing R package for new release

they are consistently failing you might contact them and find out if you can help. Jim > > Best, > Nick Clark > > > > [[alternative HTML version deleted]] > > _______ > Bioc-devel@r-project.org mailing list > http

Re: [Bioc-devel] problem installing 'Affycoretools' in linux ubuntu

antAnnotation’, ‘rtracklayer’, ‘GenomicFeatures’, ‘OrganismDbi’, > ‘ensembldb’ are not available for package ‘ggbio’ > * removing ‘/home/deepti/R/x86_64-pc-linux-gnu-library/3.3/ggbio’ > ERROR: dependencies ‘Category’, ‘GOstats’, ‘annotate’, ‘GSEABase

Re: [Bioc-devel] plotPCA in affycoretools not working

_ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way N

Re: [Bioc-devel] destiny git mirror and SVN desynced

trying to find a workable way to add git functionality for those who prefer to work with git? -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

Re: [Bioc-devel] lumi package is not available

>> Pan Du has several packages. Is this an issue for all of those packages >> or just lumi? >> > > I think that's a reasonable conclusion. Martin > I am not sure I follow. What is the reasonable conclusion? That it's just this one package, or all of them? Jim

Re: [Bioc-devel] lumi package is not available

CwICAg=yHlS04HhBraes5BQ9ueu5zKhE7r >>> tNXt_d012z2PA6 >>> ws=k93hb-mTY3FnvPobw-XK7YsatsLioMulL2zwAXZNoRo=LgNbgBxYv >>> 1xoQVTZ41uDrgo >>> XiSE2MpwIrBuyrgPBGQQ=_cCwN-6SMimKn17T4EAM9tLSK8ouLKv-GtD9MKPf9_U= >>> >> >> __

Re: [Bioc-devel] BiomartGeneRegionTrack question

1.0.0 > [49] dichromat_2.0-0 Formula_1.2-1 > [51] cluster_2.0.4 Matrix_1.2-6 > [53] data.table_1.9.6 httr_1.2.1 > [55] R6_2.1.2 rpart_4.1-10 > [57] GenomicAlignments_1.8.4 nnet_7.3-12 > > > > Thank you for help, > Ho

Re: [Bioc-devel] Confusion on biocLite() with github and annotation data repo

t; > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.22.3 > > loaded via a namespace (and not attached): > [1] httr_1.2.0 R6_2.1.2tools_3.3.0 withr

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

06/09/2016 10:06 AM, James W. MacDonald wrote: > >> You should post this on the support site ( >> https://support.bioconductor.org), >> using the 'News' item description. This bioc-devel is intended for >> discussion of issues with development of packages, not really f

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

_ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt W

Re: [Bioc-devel] inconsistent results from applyPileups and pileLettersAt

king forward to hearing your thoughts, > Jesper > > [[alternative HTML version deleted]] > > _______ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician

Re: [Bioc-devel] topGO and cat() and print() statements in program code

who is going to review it if the maintainer does not have time? > > best > Witold > > > > > > -- > Witold Eryk Wolski > > _______ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel &g

Re: [Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db

On Jan 5, 2016 7:01 PM, "Tim Triche, Jr." wrote: > > 1) this is a support.bioconductor.org question > 2) don't use .db0 packages, you will rue the day you did Can you expand on this statement? Right now all of the ChipDb are built using a db0 package, so it's not clear to

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

*. >> >> It seems that the current philosophy for select() is to emit a note >> or a warning every time the output is not parallel to the input. >> Personally I find this too noisy and not that useful. >> >> Thanks, >> H. >> >> >> On 11/20/2015 02:3

[Bioc-devel] Behavior of select function in AnnotationDbi

ould duplicates be removed before querying the database, preferably with a message saying that dups were removed? 2. If the answer to #1 is yes, then to be consistent, I will just commit the patch I have made to both devel and release. Best, Jim -- James W. MacDonald, M.S.

Re: [Bioc-devel] Access check.log file after error

3 1532 > e-mail: blattm...@imsb.biol.ethz.ch<mailto:blattm...@imsb.biol.ethz.ch> > > > [[alternative HTML version deleted]] > > _______ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Accepting an answer on the support website

n > Ireland > http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -

Re: [Bioc-devel] Accepting an answer on the support website

Yes. The original poster 'owns' their post, and they AFAIK are the only one who can accept an answer. On Tue, Oct 20, 2015 at 11:34 AM, Kevin Rue-Albrecht < kevin@ucdconnect.ie> wrote: > "Original Post(er)" I assume? > > > > On 20 October 2015 at 16:15, Jam

Re: [Bioc-devel] IPI numbers in annotation packages

use of the crazy timing, before I left I build I pushed into devel a > fresh set of .DB0s and core packages (in late August) just in case it was > too crazy to do a refresh right now. But it sounds like you won't need > that. > > > Marc > > > > On Sun, Oct 4, 2015 at

Re: [Bioc-devel] IPI numbers in annotation packages

ot;smart"]]) Thanks! Jim On Mon, Oct 5, 2015 at 10:16 AM, Marc Carlson <mrj...@gmail.com> wrote: > You need to scroll down that script a ways... Look for 'yeast'. > > On Mon, Oct 5, 2015 at 6:11 AM, James W. MacDonald <jmac...@uw.edu> wrote: > >> Hi Marc,

Re: [Bioc-devel] Removed packages and package landing pages

previously removed? Thanks, Sean [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington

Re: [Bioc-devel] Changes in AnnotationDbi

this will represent an acceptable compromise. Marc On 06/05/2015 08:37 AM, James W. MacDonald wrote: I agree that a warning is probably not the way to go, as it does imply that there might have been something wrong with either the input or output. Plus, not everybody understands the distinction

[Bioc-devel] Changes in AnnotationDbi

about this? Best, Jim -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] ___ Bioc-devel@r

Re: [Bioc-devel] GEOquery Warnings When Reading SOFT File

of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences

Re: [Bioc-devel] Documentation of GenomicRanges::follow etc. very hard to find

contain confidential information and ...{{dropped:11}} ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational

Re: [Bioc-devel] About Hg38 BSgenome

]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative

Re: [Bioc-devel] BiocStyle on windows with spaces in path names

___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

Re: [Bioc-devel] RMarkdown for vignettes

://cran.r-project.org/web/packages/rmarkdown/ ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health

Re: [Bioc-devel] hedgehog Subversion server upgrade Tuesday 9/30

https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health

Re: [Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats

...@fhcrc.org wrote: Hi Jim, On 09/23/2014 09:42 AM, James W. MacDonald wrote: There is an issue on the support site having to do with the inability to import the summary function from the namespaces from the packages listed in the subject line. I see the same problem/errors with my

Re: [Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats

Never mind. Installing all of GOstats, Category, AnnotationDbi and ReportingTools fixed the issue. Thanks, Jim On Tue, Sep 23, 2014 at 1:55 PM, James W. MacDonald jmac...@uw.edu wrote: Hi Herve, No joy: biocLite(ReportingTools) BioC_mirror: http://bioconductor.org Using Bioconductor

Re: [Bioc-devel] Distinction between release and devel package websites

___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

Re: [Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called From A Package

Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA

Re: [Bioc-devel] question about affy::plotLocation - scripts

-- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc

Re: [Bioc-devel] error in summary method for KEGGHyperGResult

installation of bioc-devel 3.0 yet (mea culpa) but a quick glance at the source code tells me that the relevant summary method still calls getAnnMap with KEGG as it's second argument. Thanks, ~G -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational

Re: [Bioc-devel] Apparent error in illuminaHumanv4.db

version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100

Re: [Bioc-devel] AnnotationDbi and select function

]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

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