Re: [Bioc-devel] Flexibility for submitting a new ExperimentData-package

Hi Teemu Daniel, Those packages were developed before ExperimentHub. Please follow the current standard for experiment data packages at https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html You may want to take a look at curatedTCGAData as an

Re: [Bioc-devel] Flexibility for submitting a new ExperimentData-package

Hi Teemu Daniel, Those packages were developed before ExperimentHub. Please follow the current standard for experiment data packages at https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html You may want to take a look at curatedTCGAData as an

Re: [Bioc-devel] Package dependencies error during BiocCheck

Hi Sarvesh, The error has something to do with an interaction between internal base R code and checking for dependencies in BiocCheck with `loadNamespace`. Either way, this check in BiocCheck is redundant with R CMD check. It will soon get removed but for now, you can disable it by running:

Re: [Bioc-devel] Interpreting BiocCheck output

after the build. > > Just for reference the package is ISAnalytics and the BiocCheck > version is the latest one. > > Thanks again, > > Giulia > > *From: *Bioc-devel on behalf of > Marcel Ramos > *Date: *Wednesday, 2022October5 at 23:48 > *To: *bioc-devel@r-

Re: [Bioc-devel] EXTERNAL: Interpreting BiocCheck output

Hi Giulia, Are you using a recent version of BiocCheck? If so, check the bottom of the BiocCheck::BiocCheck(): --- See the .BiocCheck folder and run     browseVignettes(package = 'BiocCheck') for details. --- Can you provide more details, e.g., the repository of the package? Thanks. Best

Re: [Bioc-devel] Vignettes with many output graphics - How to fulfill the Bioc build requirements, best practises?

ng list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel --- Marcel Ramos Bioconductor Core Team Roswell Park Comprehensiv

Re: [Bioc-devel] EXTERNAL: R: release of new version of package

l.S.Orsola-Malpighi, via Massarenti 9, >> >> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >

Re: [Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document

_______ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel --- Marcel Ramos Bioconductor Core Team Roswell Park Comprehensive Cancer Center Dept. of Biostatistics & Bioinformatic

Re: [Bioc-devel] EXTERNAL: Re: Too many dependencies / MultiAssayExperiment + rtracklayer

; Assistant Professor, Department of Molecular Biophysics, University of >>>> Toronto >>>> shraddhapai.com; @spaiglass on Twitter >>>> https://pailab.oicr.on.ca >>>> >>>> >>>> *Ontario Institute for Cancer Research* >>>> MaRS Centre, 661 University Avenue

Re: [Bioc-devel] EXTERNAL: ERROR: Avoid references to external hosting platforms

00LJmMuq-7m2YvCs1NyxzR8ls2M5q/https%3A%2F%2Fgithub.com%2Fmartaint%2FInterCellar-reproducibility>" >                                                ), >  notificationItem( >  text="Bioconductor package", >  icon=icon("cube"), >  status="primary",

Re: [Bioc-devel] EXTERNAL: ERROR: Avoid references to external hosting platforms

rsion deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel Marcel Ramos Bioconductor Core Team Roswell Park Comprehensive Cancer Care Dept. of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

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

ote? Or is there another mistake I am making? > > -Eric > > > > > [[alternative HTML version deleted]] > > _______ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel --- Marcel Ramo

Re: [Bioc-devel] EXTERNAL: Not possible to create runnable examples for package

; we provide justification for it? > > Thank you, > Kelsey > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel --- Marcel Ramos Bioconductor Core

Re: [Bioc-devel] EXTERNAL: Build errors when running examples that call circlize

files on disk, should I skip such tests on Windows? > Thank you > Giulia Pais > > [[alternative HTML version deleted]] > > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel --- Mar

Re: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq

ion or need help. >>>> >>>> This is very problematic. If no action is taken over the next few weeks >>>> we will begin the deprecation process for your package. We appreciate your >>>> assistance on pushing changes to remedy these errors. >>&g

Re: [Bioc-devel] SummarizedExperiment assays() gives HDF5Array error in Rstudio

methodsS3_1.8.1 >>>> [75] dbplyr_2.1.1 locfit_1.5-9.4 >>>> [77] utf8_1.2.1RJSONIO_1.3-1.4 >>>> [79] howmany_0.3-1 tidyselect_1.1.1 >>>> [81] rlang_0.4.11 softImpute_1.4-1 >

Re: [Bioc-devel] EXTERNAL: [BULK] genefu Warning

jMdBCESkhqsfPrcWfc8Ab0kjvn_Z_XrrywP-PCmcemZQIcG9qS5MN2iEXcHw16ZoAOf-To94IhLrODOlwxcAI8b36l90cL8uTmDa7F2eBjvSqKN49SkTyST48O4qon7Zqy5URTI0-Wo8ieqL1l5jMEgIt1yMIlo_9vSl6CuEpz30Ypcz6_LoGl-amdxx7WVeqaqDzUC3_f5UcFZHsqCQnQ8BWkaLyZdedEwzoQZsecXMJK-HyQv6dVV-r6gxwEz92Or-13j2tjyQR0tTN3ZDDTqRlwUUgL5LAW391b2uQMxKpRvt7dELVUbyaz7KwN6rAVI83Qh4EEs8lGu6KE3YvngyknLH9zdV4XbIscFxYp

Re: [Bioc-devel] EXTERNAL: Re: Best practice use pkgdown, docker with Bioconductor

lternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!OToaGQ!_F80SByafvC57ELoYJd6XPyuR_x33strnd_Fwdc5FIVN_HA8qpkOhRdwccPX4pandd

Re: [Bioc-devel] EXTERNAL: Resolve mismatch between master and release branches

University, Footscray Park Campus, VIC 3011 Australia > *Email*: sarah.voisin.ae...@gmail.com > *Office phone*: +61 3 9919 5744 > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > ht

Re: [Bioc-devel] EXTERNAL: %>%.html': Invalid argument Multiple platform

Laboratory > > The Walter Eliza Hall Institute of Medical Research > > +61 (0)466452544 > > [[alternative HTML version deleted]] > > _______ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel --- Ma

Re: [Bioc-devel] bioconductor_docker:devel missing MAE and GenomeInfoDb

4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=Jc5VJ3OtF73XPxF86RvZ%2FKjuJdCaabu4SC6aMnTIOwA%3Dreserved=0 > -- > Robert Castelo, PhD > Associate Professor > Dept. of Experimental and Health Sciences > Universitat Pompeu Fabra (UPF) > Barcelona Biomedical Research Park (P

Re: [Bioc-devel] EXTERNAL: Re: Encountering Issues with Github sync

repository. >> >> Please make sure you have the correct access rights >> and the repository exists. >> error: Could not fetch upstream >> >> Thanks, >> Krithika >> kb...@georgetown.edu >> >> [[al

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

cases of not specifying the sampleMap. I've opened an issue at https://github.com/waldronlab/MultiAssayExperiment/issues/291. --- Marcel Ramos Bioconductor Core Team Roswell Park Comprehensive Cancer Center Dept. of Biostatistics & Bioinformatics Elm St. & Carlton St. Buffalo, New Yo

Re: [Bioc-devel] Unsure about why package is not updating

fo/bioc-devel --- Marcel Ramos Bioconductor Core Team Roswell Park Comprehensive Cancer Center Dept. of Biostatistics & Bioinformatics Elm St. & Carlton St. Buffalo, New York 14263 This email message may contain legally privileged and/or...{{dropped:2}} ___

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

Hi Lara, I often recommend the use of the `Authors@R` field in the DESCRIPTION file which will give you more control: ``` Authors@R: c(     person(given = "Lara", family = "Selles Vidal", ...),     ...     ) ``` Best, Marcel On 4/22/20 4:00 PM, Selles Vidal, Lara wrote: > Dear Bioconductor

Re: [Bioc-devel] rankprod package update

Hi Francesco, Please wait at least 24 hours before seeing an effect on the build report. We should have a build report with your changes later today. Check around 2 PM EST or https://everytimezone.com/s/3eab3407 Best regards, Marcel On 2/14/20 11:32 AM, Francesco Del Carratore wrote: > Dear

Re: [Bioc-devel] EXTERNAL: Re: warning: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic

Hi Stefano, I'm no roxygen expert either but you could try using the `usethis::use_pipe(export = TRUE)` functionality developed by actual roxygen experts ;) Best, Marcel On 2/13/20 2:28 AM, Felix Ernst wrote: > Hi, > > I am certainly not a roxygen expert, but if \code{\link{\%>\%}} is to >

Re: [Bioc-devel] EXTERNAL: MultiAssayExperiment silently converting RangedSummarizedExperiments into SummarizedExperiments.

Hi Charles, Thank you for your post and for providing a reproducible example. I was able to reduce the example to behavior from the coerce method on `list`/`ANY` objects to `SimpleList`. Here is the reduced example: ``` r suppressPackageStartupMessages({     library(SummarizedExperiment) })

Re: [Bioc-devel] Dashes in GFF attributes

Hi Valentino, You will have to provide more details concerning the issue. It may be as simple as removing the dashes with `gsub` before using `featureCount`. Please review the posting guidelines for a better idea on how to get help: https://bioconductor.org/help/support/posting-guide/ And

Re: [Bioc-devel] BiocManager updates / changes

. of Biostatistics & Bioinformatics Elm St. & Carlton St. Buffalo, New York 14263 On 08/31/2018 01:28 PM, Marcel Ramos wrote: > Dear bioc-devs, > > Thank you to all maintainers who have made appropriate changes to their > packages *in devel*. > > This is an ongoing effort to replace

[Bioc-devel] BiocManager updates / changes

devel/bioc/html/RaggedExperiment.html Best regards, Marcel -- Bioconductor Core Team Roswell Park Comprehensive Cancer Center Dept. of Biostatistics & Bioinformatics Elm St. & Carlton St. Buffalo, New York 14263 On 07/13/2018 05:11 PM, Marcel Ramos wrote: > Dear bioc-devs, > > About 4 w

Re: [Bioc-devel] BiocManager now on CRAN

06 PM Gabe Becker wrote: Ah, of course. I should have realized that. Makes sense. I'll get that fixed in devel soon. Thanks and sorry for the noise. ~G On Mon, Jul 16, 2018 at 9:37 AM, Marcel Ramos wrote: Hi Gabe, Please note that we are only making changes to packages in *bioc-devel*. B

[Bioc-devel] BiocManager now on CRAN

packages: https://gist.github.com/LiNk-NY/44cc844a169d5d96c777a69037dae653 Best regards, Marcel Bioconductor Core Team Roswell Park Cancer Institute Dept. of Biostatistics & Bioinformatics Elm St. & Carlton St. Buffalo, New York 14263 On 06/20/2018 12:23 PM, Marcel Ramos wrote: Dear b

[Bioc-devel] BiocManager now on CRAN

Dear bioc-devs, A month ago we notified you about our "next generation" changes to BiocInstaller. Thanks to all beta testers and those who provided feedback and suggestions for a new package name. I am pleased to inform you that BiocManager is now on CRAN:

Re: [Bioc-devel] EXTERNAL: Re: Cannot update my development package to Bioconductor

Hi Christian, It looks like you have to do *git pull upstream master * according to your `git remote -v`. Regards, Marcel On 05/14/2018 04:21 PM, cstrato wrote: > Dear Nitesh, > > Thank you for your fast reply. Here is  what I tried now, > including using 'git pull': > > $ cd

Re: [Bioc-devel] EXTERNAL: Fwd: [Bioconductor/Contributions] GIGSEA (#720)

Hi Shijia, I am assigned to the submission and will be reviewing your package soon. Please send further correspondence as comments to the issue on GitHub. Best regards, Marcel On 04/18/2018 08:31 PM, Shijia Zhu wrote: > Hi Everyone, > > My package just passed the check, without errors or

[Bioc-devel] EXTERNAL: Accessing package citation info programmatically without running R?

Hi Ryan, Thanks for pointing this out. I'm not sure what you mean by "structured" or "format". We do have public facing citations which can be found at: http://bioconductor.org/packages/3.7/bioc/citations/BiocFileCache/citation.html (Thanks Lori for locating these pages!) And even with a

Re: [Bioc-devel] appveyor CI failing with biocparam

Hi Vivek, Make sure you are using the appropriate version of R. Your appveyor code says you're using 3.4.4. https://ci.appveyor.com/project/vivekbhr/icetea#L22 Add a chunk like: ``` environment:   global: ...   matrix:     - R_VERSION: devel ``` after your "global:" tag under the

Re: [Bioc-devel] EXTERNAL: Re: [R-pkg-devel] DESCRIPTION file building problem

Hi Dario, Gabe is right, you shouldn't be building within the package directory. Although AFAIK, you should be able to do so. Perhaps if you point us to your package, we might be able to see the issue... Regards, Marcel On 03/21/2018 06:15 PM, Gabe Becker wrote: Dario, Does this ever

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

> registered email address :/ > > Kind regards, > Kevin > > On Tue, Mar 20, 2018 at 5:03 PM, Marcel Ramos > <marcel.ra...@roswellpark.org <mailto:marcel.ra...@roswellpark.org>> > wrote: > > Hi Kevin, > > Being that I am unable to fully reprodu

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

Hi Kevin, Being that I am unable to fully reproduce the issue, I can only say that I have been successful in running the steps in the Wercker build for a different package. Please do a *clean* pull of the Bioconductor image from docker hub by removing any stale images first. Here is the

Re: [Bioc-devel] EXTERNAL: amplican tokay2 i386 error

Hi Kornel, I downloaded your package from our git repo and ran check locally on Windows 7. It seems like there are some issues with the `data.table` (version 1.10.4-3) package. Here is my result for the `i386` architecture: >>> R CMD check --force-multiarch --no-vignettes amplican_1.1.6.tar.gz

Re: [Bioc-devel] EXTERNAL: Re: unknown build error novel bioc. package

2.1    GenomicRanges_1.28.6  > [41] RaggedExperiment_1.0.0 SummarizedExperiment_1.6.5 > [43] mime_0.5   xtable_1.8-2  > [45] colorspace_1.3-2   httpuv_1.3.5  > [47] stringi_1.1.6  RCurl_1.95-4.8  

[Bioc-devel] unknown build error novel bioc. package

Hi Maarten, It appears that your vignette is pointing to a package that doesn't exist in the build system. Please reference `package = "brgedata"` instead. Regards, Marcel *Note. Apologies if you've received this email twice. On 12/13/2017 02:09 PM, Maarten van Iterson wrote: > Dear all, >

Re: [Bioc-devel] EXTERNAL: unknown build error novel bioc. package

Hi Maarten, It appears that your vignette is pointing to a package that doesn't exist in the build system. Please reference `package = "brgedata"` instead. Regards, Marcel On 12/13/2017 02:09 PM, Maarten van Iterson wrote: > Dear all, > > Our new package, omicsPrint, has been accepted and

Re: [Bioc-devel] MultiAssayExperiment Subsetting Fails if Column Data Has One Column

d packages: > [1] S4Vectors_0.15.7BiocGenerics_0.23.1 > MultiAssayExperiment_1.3.34 > > -- > Dario Strbenac > University of Sydney > Camperdown NSW 2050 > Australia > > ________

Re: [Bioc-devel] ExperimentList Contructor Failing

Hi Dario, You're using a different version of MultiAssayExperiment which might make the original problem less reproducible. I was not able to reproduce the error on the release version of MultiAssayExperiment. If you do find the issue again. Please let me know. As a side note, we are using the

Re: [Bioc-devel] ExperimentList Contructor Failing

-8" "3.2.3" "0.9-8" > Repository > rJava "https://cran.rstudio.com/src/contrib; > > update with biocLite() > > Error: 1 package(s) out of date > > The same example works on another computer using Windows operating system. > What's

Re: [Bioc-devel] test coverage of a shiny app

Hi Sam, This is a pertinent issue to shiny app development and there are continuing efforts to create unit tests for shiny applications. At the moment, there is a package dedicated to providing tests for shiny applications but it has not been published. See: https://github.com/rstudio/shinytest

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

-project.org>mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel> -- Marcel Ramos Bioconductor Core Team Member Roswell Park Cancer Institute This email message may contain legal

Re: [Bioc-devel] SVN repo and git mirror for accepted package

Hi Lukas, You will be receiving SVN credentials soon for upload. Please expect a message from Martin Morgan. Regards, Marcel On Sat, Oct 15, 2016 at 10:02 AM Lukas Weber wrote: > Hi, > > Is there anything we need to do to set up the svn repository and git mirror > for new

Re: [Bioc-devel] "Feature-freeze" deadline for new packages

is October 12. I will get to it much sooner. Regards, Marcel Ramos Bioconductor Core Team On Fri, Sep 30, 2016 at 9:50 AM Lukas Weber <lukmwe...@gmail.com> wrote: Hi, I submitted a new package last week, which passed all the checks, but I haven't heard anything else back since then. I