[Bioc-devel] Code of Conduct committee announcement

to making the Bioconductor community a safe and supportive space for everyone. Sincerely, Kevin Rue-Albrecht On behalf of the Bioconductor Code of Conduct Committee [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list

[Bioc-devel] News: Extended submission deadline for EuroBioc2020

Hello community! The EuroBioc2020 submission deadline is extended to Monday, November 16th! The organising committee welcomes submissions for talks, workshops, posters, and birds-of-a-feather session topics. The scope for submissions is far from limited to Bioconductor packages; we welcome contr

Re: [Bioc-devel] Build error for pwrEWAS

Hi Stefan, Pasting the reply from Mike Smith, a few hours ago, in the email thread "Error in building vignette for previously stable version": This looks like the same problem a few others have reported. The latest > advice was to wait for BiocStyle to be updated to reflect changes in > rmarkdow

[Bioc-devel] Fwd: TVTB problems reported in the Multiple platform build/check report for BioC 3.10

Hi, I've been getting a weird Latex-related error on the daily build recently, _although I haven't updated the package in ages_. https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/TVTB/malbec1-buildsrc.html I'm guessing some LaTeX package must have been updated recently and causes trou

Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

clearly doesn't work for all cases, thanks for reporting the > problems with seqCAT and TVTB. I've reverted the change so your packages > will build and will re-think the fix. > > Valerie > > > On 1/8/19 10:45 AM, Kevin RUE wrote: > > Hi all, &g

Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

Hi all, Same kind of error for my TVTB package ( https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/TVTB/malbec1-checksrc.html ). I'll run R CMD check locally ASAP to see whether I need to update TVTB or if it's something upstream. Best, Kevin On Tue, Jan 8, 2019 at 5:05 PM Obenchain,

Re: [Bioc-devel] 80% of man pages must have runnable examples (package with numerous Shiny apps)

and return the appDir object for the > user. Thanks again! > > Lindsay > On Mon, Nov 19, 2018 at 3:02 PM Kevin RUE wrote: > > > > Hi Lindsay, > > > > Check out https://github.com/csoneson/iSEE/blob/master/R/iSEE-main.R > function "iSEE" for an example

Re: [Bioc-devel] 80% of man pages must have runnable examples (package with numerous Shiny apps)

Hi Lindsay, Check out https://github.com/csoneson/iSEE/blob/master/R/iSEE-main.R function "iSEE" for an example of both the function return value, and the man page. First, I would suggest that your function _returns_ the "appDir" object to the user, and that you leave it to the user to call "shin

Re: [Bioc-devel] Several vignettes with links between them

Hi David, First off, I'd recommend introducing non-crucial changes like this one on the devel branch (3.9). The devel branch is the developers' primary playground. If you _really_ think that users can't live without those vignette updates before the next release, then you can always `git cherry-pi

Re: [Bioc-devel] EXTERNAL: Question about Wercker continuous integration

> - script: > name: Install devtools > code: R -e "install.packages(c('devtools', 'backports'))" > - jimhester/r-dependencies > - jimhester/r-check > - jimhester/r-coverage > ``` > > Also, the EXTERNAL tag is generated by th

Re: [Bioc-devel] EXTERNAL: Question about Wercker continuous integration

tall.packages('devtools')" > - jimhester/r-dependencies: > cran_dependencies: backports > - jimhester/r-check > - jimhester/r-coverage > > > *Note:*I removed the r-lint step because it was having some issues with > xml. > > > Regards, > >

[Bioc-devel] Question about Wercker continuous integration

Dear all, I'm usually a big Travis CI fan, but I'm having a go at Wercker, using the bioconductor/devel_core2 docker (I have also tried the rocker 'parent' ones without further success). I am running into the following issue: [...] * creating vignettes ... ERROR Error: processing vignette 'NewPac

Re: [Bioc-devel] Thanks to Andrzej...

As a user and package maintainer, I'm sure that I am only aware of the tip of iceberg in terms of contributions from good souls like Andrzej. Their kind help, advice, and feedback are a big part of what keeps the community spirit alive (personal experience at https://github.com/Bioconductor/BiocSty

Re: [Bioc-devel] R version check in BiocChech

ay I'm doing too, but supporting two branches different only > in R version looks ridiculous and unnecessary. > > -- > Alexey > > > > > > On Mon, Feb 19, 2018 at 12:48 PM, Kevin RUE wrote: > >> Dear Alexey, >> >> The reason is somewhat implic

Re: [Bioc-devel] R version check in BiocChech

Dear Alexey, The reason is somewhat implicitly given at https://www.bioconductor.org/developers/how-to/useDevel/ : "Package authors should develop against the version of *R* that will be available to users when the *Bioconductor* devel branch becomes the *Bioconductor* release branch." In other w

Re: [Bioc-devel] assay dimnames in SingleCellExperiment / SummarizedExperiment

if you want, you can put in a > PR to override dim() and dimnames() for SingleCellExperiment to put some > names on the returned vectors or lists. If I had to choose, I would go with > "Features" and "Cells" for the rows and columns, respectively. (We already > use a RSE

[Bioc-devel] assay dimnames in SingleCellExperiment / SummarizedExperiment

Dear all, I cc-ed to this email individual package maintainer to directly 'notify' them of this thread and have their respective opinions, but I thought the common use of SummarizedExperiment was worth involving the community as well. Background: I was updating one of my workflow from SCESet to t

Re: [Bioc-devel] Search on www.bioconductor.org fails

Hi, I got the same issue yesterday if that can help track down the origin; it wasn't just today. I thought it was a transient glitch and didn't report it immediately. I hadn't checked today yet. Best Kevin On Mon, Aug 21, 2017 at 3:58 PM, Laurent Gatto wrote: > > Dear Bioconductor admins, > >

Re: [Bioc-devel] error with transfering SVN repo to git

Hi Samuel, Please see the recent email below from Nitesh (core team) yesterday on this mailing list. Best wishes, Kevin Hi Maintainers, > The beta phase for the GIT transition has now come to an end. All access > to the git.bioconductor.org server has been suspended till August 16th > 6pm EST.

Re: [Bioc-devel] Bioconductor Contribution 'GKnowMTest' (issue #436)

Dear Samsiddhi, I am not a core team member, but as developer/maintainer of two Bioc packages, I can assure you that the core team has not forgotten about your package submission and will review it as soon as humanly possible. They have quite a few packages in the review process at the moment, and

Re: [Bioc-devel] git transition for projects with prior git history

the > transition and then go from there. > > Once the git server is alive, you can make a new GitHub repo at that point. > > Nitesh > > > > On Aug 10, 2017, at 10:18 AM, Kevin RUE wrote: > > > > Hi all, > > > > I think I'm facing a similar sc

Re: [Bioc-devel] git transition for projects with prior git history

Hi all, I think I'm facing a similar scenario ("prior history"), although I have messed up my original GitHub repo (https://github.com/kevinrue/ TVTB/commits/master) beyond my ability to synchronise it back to a working state. Basically, a few months ago, a bad mix of `git svn rebase` and `git me

Re: [Bioc-devel] strange error in Jenkins build for singleCellWorkflow

Hi all, I had this same issue a few months ago (in the weeks leading up to the release of R-3.4.0), when building an Rmarkdown website on my own laptop. It seemed the session variables were cleaned up between markdown documents, but that packages remained loaded and accumulated to the point that I

Re: [Bioc-devel] condition tests on vectors with length greater than 1

2017 at 5:00 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 03/31/2017 08:21 AM, Kevin RUE wrote: > >> Hi Martin, >> >> Thanks a lot for systematically identifying the issue. >> >> Looking at the issue for GOexpress now, I realise that the is

Re: [Bioc-devel] condition tests on vectors with length greater than 1

Hi Martin, Thanks a lot for systematically identifying the issue. Looking at the issue for GOexpress now, I realise that the issue is not in GOexpress itself, but actually within the VennDiagram package that GOexpress imports. You actually captured that in your report: "GOexpress","*VennDiagram*

Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

On Wed, Nov 9, 2016 at 11:31 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 11/03/2016 08:14 AM, Kevin RUE wrote: > >> Apologies for the additional spam, for two reasons: >> >> * The diff files that I've previously sent had the base and modifi

[Bioc-devel] Problem with git-mirror

Dear all, Apologies for the confusing email below, but I'm not sure anymore which information can save the day. I'll provide all the information necessary to fix the situation! I think I've turned my GitHub/svn/GitHub-mirror repositories into a huge plate of spaghetti after encountering successi

Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

dated code would fail on packages that do not break any of the three guidelines. Best, Kevin On Thu, Nov 3, 2016 at 11:49 AM, Kevin RUE wrote: > Hi all, > > Please find attached the diff relative to the code that I cloned from > Bioconductor-mirror yesterday (please ignore the p

Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

Notes: - For demonstration purpose, I indented a handful of lines from the checks.R file itself with TAB characters. I assume that's OK, as some lines were already longer than 80 characters and not indented by a multiple of 4 spaces. All the best, Kevin On Wed, Nov 2, 2016 at 10:00 PM

Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

uot; that print *all* the offending lines? The data.frame also stores the content of the lines for the record, but does not print them. I think Kasper is right: filename and line should be enough to track down the line. All the best, Kevin On Wed, Nov 2, 2016 at 8:08 PM, Kevin RUE wrote:

Re: [Bioc-devel] A handful of check to follow up on R CMD BiocCheck

e: > I would prefer all line numbers reported, but on the other hand I am > indifferent wrt. the content of the line, unless (say) TABs are marked up > somehow. > > Kasper > > On Wed, Nov 2, 2016 at 3:17 PM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > &g

[Bioc-devel] A handful of check to follow up on R CMD BiocCheck

Dear all, Just thought I'd share a handful of scripts that I wrote to follow up on certain NOTE messages thrown by R CMD BiocCheck. https://github.com/kevinrue/BiocCheckTools They're very simple, but I occasionally find them quite convenient. Apologies if something similar already exists somewhe

Re: [Bioc-devel] Question about a package submission

nments")) I'll keep digging... :) Kevin On Fri, Oct 28, 2016 at 1:48 PM, Kevin RUE wrote: > (What puzzles me most is that it builds fine on Travis CI > <https://travis-ci.org/kevinrue/TVTB>, just not on AppVeyor > <https://ci.appveyor.com/project/kevinru

Re: [Bioc-devel] Question about a package submission

(What puzzles me most is that it builds fine on Travis CI <https://travis-ci.org/kevinrue/TVTB>, just not on AppVeyor <https://ci.appveyor.com/project/kevinrue/tvtb>). MS Windows issue? Best, Kevin On Fri, Oct 28, 2016 at 12:30 PM, Kevin RUE wrote: > Thanks for sharing your s

Re: [Bioc-devel] Question about a package submission

o> wrote: > For me, running biocLite(c("rtracklayer", "S4Vectors", "XVector", > "IRanges", >"Biostrings", "GenomicRanges", "GenomicAlignments")) > Worked and solved the error. > > Ioannis > -- &

Re: [Bioc-devel] Question about a package submission

ng that it is fairly frustrating to leave it at that :) Kind regards, Kevin On Thu, Oct 27, 2016 at 1:28 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 10/27/2016 08:22 AM, Kevin RUE wrote: > >> Hi Ioannis, Vincent, >> >> I'm in the middle of d

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

Dear T.Wang. First of all, as a general rule, please include the sessionInfo() output and command that caused the error to facilitate useful replies. Here I will assume that you are using the devel branch of BioC on the latest R/BioC setup available. As far as I know, your problem is still a cons

Re: [Bioc-devel] Question about a package submission

Hi Ioannis, Vincent, I'm in the middle of debugging a similar situation myself, which may provide a reproducible example at a package level. I am in the process of setting up AppVeyor CI for my package, and my R CMD check fails because of the same error. https://ci.appveyor.com/project/kevinrue/t

Re: [Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

false > cache: packages > r_github_packages: > - jimhester/covr > after_success: > - Rscript -e 'covr::codecov()' > > The additional "covr" lines are for checking unit test code coverage with > codecov. > > Lukas > > > On Thu, Oct 20, 2016

Re: [Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

;covr::codecov()' > > The additional "covr" lines are for checking unit test code coverage with > codecov. > > Lukas > > > On Thu, Oct 20, 2016 at 4:51 PM, Kevin RUE wrote: > >> Actually, nevermind, I think I solved the issue of R-devel with the >&

Re: [Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

Actually, nevermind, I think I solved the issue of R-devel with the following YAML instructions: language: r r: devel before_install: - Rscript -e 'source(file = "http://bioconductor.org/biocLite.R ");tryCatch(useDevel(devel = TRUE), error = function(err){message(err)})' - if [[ "$TRAVIS_

Re: [Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

build fails because it doesn't have 3.4 installed. But I suppose that the BioC devel-build servers have R-3.4 installed, right? All the best, and sorry for the additional email, Kevin On Thu, Oct 20, 2016 at 3:07 PM, Kevin RUE wrote: > Hi all, > > First of all, thanks for the questi

Re: [Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

Hi all, First of all, thanks for the question and answers, it helped me a lot on my local machine. While we're on the topic, does anyone know when R-devel (R-3.4) will be available on Travis CI ? Because it is running R-3.3.1, and therefore produces the same error message when I instruct Travis t

Re: [Bioc-devel] Package "not supported" on some platforms, and dependent packages

84 requires tabix. > > Valerie > > > On 10/18/2016 04:01 PM, Kevin RUE wrote: > > Agh, I could have looked better in the Git mirror code ;) > > > > Anyway, thanks a lot for the tip! > > > > No worries about removing the file if the parent package gets su

Re: [Bioc-devel] Package "not supported" on some platforms, and dependent packages

lding successfully there. Might not be that easy. Anyway, future will tell, and I'll keep an eye out for it! Cheers Kevin On Tue, Oct 18, 2016 at 11:44 PM, Dan Tenenbaum wrote: > > > - Original Message ----- > > From: "Kevin RUE" > > To: "bioc-devel&qu

[Bioc-devel] Package "not supported" on some platforms, and dependent packages

Hi all, Heartless logic works as follows: - ensemblVEP is "not supported" on Windows (build report ). Completely understandable. - My package depends on ensemblVEP. - The build system reports an error on Windows fo

Re: [Bioc-devel] GitHub and svn

Dear Mani, That's actually where I think the git-svn bridge becomes useful. If you take the time once to synchronise the devel branch of your package from the Bioconductor-mirror to one of the branch on your GitHub repository (for me the master branch), you could then: 1) commit changes to your ow

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

"Original Post(er)" I assume? On 20 October 2015 at 16:15, James W. MacDonald wrote: > The OP needs to accept your answer. > > On Tue, Oct 20, 2015 at 10:14 AM, Kevin Rue-Albrecht < > kevin@ucdconnect.ie> wrote: > >> Dear all, >> >> Being

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

Dear all, Being on the developer side of things, I have resolved two items related to my package on the support website, and I would like to know how my answer could be marked as "accepted", so that it shows in the corresponding badge on my package web page. Kind regards Kevin -- Kévin RUE-ALBR

Re: [Bioc-devel] BioC 3.1 branch created

Hi Tiphaine, I have followed both of your links,. and they both work for me. Probably just a glitch in the connection ? Hi Dan, I have a quick question of my own, I would like to bridge the new release branch to my Github "release" repository, but: - In the dropdown of the bridge creation, r

Re: [Bioc-devel] development vs release version

Hi Dan, all Maybe a silly question, but: where is the R-alpha 3.2.0 ? So far, I have only pushed to the devel branch (3.1.x), hoping that all my commits (most recent: 19 Mar) will be integrated into the release version (3.2.0). This is only my second release cycle. I remember that the first time,

Re: [Bioc-devel] RSS package feeds not updated

Hi Stephanie, I am using rss2email ( http://www.allthingsrss.com/rss2email/getting-started-with-rss2email/), a script that I installed to track my package feed, and that is run by my Windows task scheduler every day, to send me the RSS news in an email (not as an RSS feed per se) Now, just like y

Re: [Bioc-devel] Change of schema of ENSEMBL biomart

Well spotted Tiphaine ! I just checked and this has affected my package (GOexpress) as well, as it fetches the external_gene_id to annotate gene features. This prevent the key analysis step from completing on my analysis of *Bos taurus* gene expression as well. Consequently, I will bug-fix the re

Re: [Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build

r answer as well. Might be useful in the future for other types of problems. Cheers Kevin On 16 October 2014 15:34, Dan Tenenbaum wrote: > > > - Original Message ----- > > From: "Robert Castelo" > > To: "Kevin Rue-Albrecht" > > Cc: bioc-dev

[Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build

Hi Bioconductors, I got the *BUILD* ERROR report below on all platforms last night. Given the fact that I didn't update my package since the last (successful) build, and the error ''BiocInstaller' package not in repository'', I have a feeling this is due to a problem on the build platforms ? In

Re: [Bioc-devel] Bioonductor package tracker has moved

Hi all, Tim, Just for a second validation, I can log in again too while I couldn't yesterday as described in this thread. Anyway, thanks for fixing it so rapidly! Cheers, Kevin On 16 October 2014 06:17, Tim Triche, Jr. wrote: > Looks like that fixed it, for me at least. Thanks! > > Statistics

Re: [Bioc-devel] no more commits allowed before release ?

citing phrase to hear in science, the one that heralds new > discoveries, is not "Eureka!" (I found it!) but "That's funny ..." - Isaac > Asimov > > > > > On Fri, Oct 10, 2014 at 11:15 AM, Dan Tenenbaum > wrote: > >> >> >> -

Re: [Bioc-devel] no more commits allowed before release ?

x27;t cover multiple scenarios to respect a reasonable CMD check time. But this bug fix probably proved me wrong. Thanks for your time Kevin On 10 October 2014 16:15, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Kevin Rue-Albrecht" > > To

Re: [Bioc-devel] no more commits allowed before release ?

Check ? In which case, I would need to add another testing dataset corresponding to the scenario that I fixed yesterday. Cheers Kevin On 10 October 2014 15:40, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Kevin Rue-Albrecht" > > To:

[Bioc-devel] no more commits allowed before release ?

Dear all, I fixed a bug affecting one particular situation in my package (GOexpress) yesterday, and pushed the changes to GitHub. However, the webhook did not trigger to update the page, due to the feature freeze if I understand the schedule correctly (http://www.bioconductor.org/developers/releas

[Bioc-devel] GOexpress: new package to visualise microarray and RNAseq data using gene ontology annotations

Dear all, I would like to introduce a recent addition to Bioconductor. I hope those of you working with transcriptomics data will find it useful for their own work. *GOexpress *is a package taking an *ExpressionSet *object minimally including *assayData *and *phenoData* corresponding to either mi

Re: [Bioc-devel] GenomicRanges::findOverlaps() ignoring chromosome information?

ee to give me feedback on this. Apologies for the spam and the relatively obvious mistake on my part. Cheers Kevin On 19 September 2014 12:21, Kevin Rue-Albrecht wrote: > Hi again, > > Update on my issue, although I haven't found the source of the error yet.. > I have correct over

Re: [Bioc-devel] GenomicRanges::findOverlaps() ignoring chromosome information?

x27;ll definitely bring a conclusion to this thread. Kevin On 19 September 2014 10:12, Kevin Rue-Albrecht wrote: > Dear maintainer, Dear all, > > *Situation* > I have used the findOverlaps(function) to annotate differentially > methylated regions (DRMs) obtained using the bsseq B

[Bioc-devel] GenomicRanges::findOverlaps() ignoring chromosome information?

Dear maintainer, Dear all, *Situation* I have used the findOverlaps(function) to annotate differentially methylated regions (DRMs) obtained using the bsseq Bioconductor package in the *Bos taurus* genome. (No, you won't steal my experimental design :-P ). I used the genome UMD3.1.75 as a reference

Re: [Bioc-devel] Question about inserting bibliographic references in a package vignette

, Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > >> I would recommend looking at existing vignettes, for example minfi, but >> there are tons of them. >> >> >> On Thu, Aug 7, 2014 at 12:38 PM, Kevin Rue-Albrecht < >> kevin@ucdconn

[Bioc-devel] Question about inserting bibliographic references in a package vignette

Dear all, My name is Kevin Rue-Albrecht and I am working to improve a package currently in review by Bioconductor. I am blocked while trying to add the final touch to the package. I was wondering about the recommended way of inserting bibliographic references in the body of the package vignette