Re: [Bioc-devel] potential cache-related error

Thanks! On Thu, 1 Aug 2024 at 13:44, Kern, Lori wrote: > It has been refreshed. > > I'm looking into a fall back when the download gets corrupted so this will > be done automatically in the future. > > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer

Re: [Bioc-devel] potential cache-related error

It has been refreshed. I'm looking into a fall back when the download gets corrupted so this will be done automatically in the future. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets

[Bioc-devel] potential cache-related error

Dear Bioc team, build/check of my package results in errors on nebbiolo1 and palomino7 possibly due a corrupted file in cache.

[Bioc-devel] problems understanding build error

Hi Michael, Thanks for reporting. This has been fixed in the latest version of BiocCheck (1.41.9). Best regards, Marcel On 7/26/24 5:29 AM, Michael Shapiro wrote: > We are currently working through the submission of a new package, CatsCradle > (issue #3452). We get a build error from the

Re: [Bioc-devel] Change of maintainer for DeMixT

For clarification, Ruonan Li is the new maintainer and you need assistance on setting up push access to git.bioconductor.org? As I see Ruonan Li is already listed in the DESCRIPTION as maintainer. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center

Re: [Bioc-devel] Assistance Needed with Bioconductor Git Credentials

Private reply off list since it involves discussing credentials. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel

Re: [Bioc-devel] Second Maintainer

Would you please have Markus confirm this request? We can assist after this is achieved. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] Moving repository for Bioconductor package

Hi both, Thank you for the advice, I was able to successfully move the project and update the origin locally. I also went for the transfer and fork approach Henrik mentioned. Cheers, Alan. From: Henrik Bengtsson Sent: Friday 26 July 2024 17:32 To: Mike Smith

[Bioc-devel] Second Maintainer

Dear BioC Team, I would like to contribute to an existing package, SPONGE, in the future and also handle the current build error. So we discussed in our group that it would be best if I become co-maintaner together with the current maintainer, Markus List (cc). Could you advise us how to do

Re: [Bioc-devel] Moving repository for Bioconductor package

> Secondly, does anyone have a good approach for keeping a mirror of it at the > url in the lab's github since this is the link we reference in the > publication: https://neurogenomics.github.io/MungeSumstats? Maybe an alternative is to: 1. Transfer the existing repo to your GitHub name 2.

Re: [Bioc-devel] Moving repository for Bioconductor package

Dear Alan, I don't think there are any formal steps required to do this. Once a package is in Biocondcutor, it is effectively decoupled from whatever Git repository it was originally submitted from. For example, you could delete the existing GitHub repository entirely, and it wouldn't affect

[Bioc-devel] Moving repository for Bioconductor package

Hi all, I'm the maintainer for MungeSumstats package and I will be leaving my current lab in the near future. Currently, the package code is hosted in the lab github but I want to move it to my personal github - What are the steps for setting up

Re: [Bioc-devel] problems understanding build error

Dear Michael, The error means that length(which(cond)) > 1 I think this is a bug on BiocCheck on the internal function .getTokenTextCode (findSymbols.R L12 ). It checks if any condition

[Bioc-devel] problems understanding build error

We are currently working through the submission of a new package, CatsCradle (issue #3452). We get a build error from the Coding Practices section of the BiocCheck tests, namely Error in seq.default(which(cond) - length(notLookback), which(cond)) : 'from' must be of length 1 For whatever

[Bioc-devel] Assistance Needed with Bioconductor Git Credentials

Dear BioC Team, I recently changed to a new computer and need to sync the GitHub repository with Bioconductor. However, I was unable to log into Bioconductor Git Credentials as it stated that my account "is not associated with a maintainer of a Bioconductor package." I am indeed the maintainer of

Re: [Bioc-devel] Build Error for ANCOMBC Package on Linux

Hi Huang, That's because the latest version of CVXR (1.0-14, uploaded to CRAN on June 27) introduces a dep on the new clarabel package (also on CRAN since June 22): https://cran.r-project.org/package=clarabel Unfortunately clarabel has a bunch of system requirements that are not on our Linux

[Bioc-devel] Build Error for ANCOMBC Package on Linux

Dear BioC Team, I am the maintainer of the ANCOMBC package http://bioconductor.org/packages/release/bioc/html/ANCOMBC.html I recently received messages from the system indicating that ANCOMBC encountered a build error on the Linux system. The error message is as follows: ``` * installing to

[Bioc-devel] BioC2024: Virtual registration and Lightning Talk submissions open

BioC2024 starts next week (July 24-26)! Virtual registration remains open for the next few days and virtual registrants can also apply to give a lightning talk. Details below. Register for BioC2024 here The submission window for BioC2024

[Bioc-devel] EuroBioC2024 Carpentries workshops Sep 2-3

Hi everyone, We would be grateful if you could help spread the word about these workshops with your networks or anyone who might be interested. Join us for the EuroBioC2024 Carpentries Workshops! September 2-3, 2024 Oxford, UK Workshops: 1. Intro to Genomic Data Analysis with R and

[Bioc-devel] Final reminder: BioC2024 in-person registration ends tomorrow, July 10

Just a quick reminder that registration for in-person attendance at BioC2024 ends tomorrow, July 10. Don't miss out on this fantastic opportunity to engage with the Bioconductor community in Grand Rapids, Michigan, USA. Register here: https://www.bioc2024.bioconductor.org/registration Maria

Re: [Bioc-devel] [EXTERNAL] Deeptarget package

Dear Trinh and Martin, thanks for the update and for the suggestions how to deal in such situation. Best regards Kristian -- Kristian Ullrich, Ph.D. Max Planck Institute For Evolutionary Biology Scientific IT group Department of Evolutionary Genetics August Thienemann Str. 2 24306 Plön

Re: [Bioc-devel] [EXTERNAL] Deeptarget package

Dear Dr. Kristian, We consulted with experts at our NIH/NCI here and per their suggestion, we have added the following paragraph to the description and document of Workflow Demonstration as below: “The user of this package is required to agree to the terms and conditions of DepMap portal

Re: [Bioc-devel] Devel build report errors

Sorry to hear you are having problems. I tried to run the igblast example in a current installation. I set BASILISK_MINICONDA_VERSION=py311_23.11.0-2 to get faster mamba resolution (but this setting cannot be used on windows AFAIK, so is not used in build system) and I hit warning libmamba

Re: [Bioc-devel] Devel build report errors

On Mon, Jul 8, 2024 at 11:21 AM Martin Grigorov wrote: > Hi, > > > On Mon, 8 Jul 2024 at 11:14, Rodrigo Arcoverde Cerveira < > rodrigo.arcove...@gmail.com> wrote: > >> Hi all, >> >> We are trying to implement a new tool in scifer package, and I have a few >> questions about compatibility and

Re: [Bioc-devel] Devel build report errors

Hi, On Mon, 8 Jul 2024 at 11:14, Rodrigo Arcoverde Cerveira < rodrigo.arcove...@gmail.com> wrote: > Hi all, > > We are trying to implement a new tool in scifer package, and I have a few > questions about compatibility and build reports. > > 1. I am getting the following error in build for

[Bioc-devel] Devel build report errors

Hi all, We are trying to implement a new tool in scifer package, and I have a few questions about compatibility and build reports. 1. I am getting the following error in build for Linux (openEuler 22.03 LTS-SP1) / aarch64. ``` error: dependency ‘sangerseqR’ is not available for package

[Bioc-devel] Reminder: BioC2024 in-person registration closes soon (July 10)

Hi everyone, Just a friendly reminder about two opportunities: BioC2024 In-Person Registration The deadline to register for in-person attendance at BioC2024 in Grand Rapids, Michigan, is fast approaching! Don�t miss your chance to join the conference and expand your expertise. In-person

Re: [Bioc-devel] bioconductor support site problem

Dear Lori, Is the support site notification system by email working as intended? I just activated the "Email for every new thread (mailing list mode)" and I got emails from topics not in my Watched tags. When I had a weekly digest I too got emails from other topics, as reported on the github

Re: [Bioc-devel] Package version did not update correctly

Thank you so much! On Wed, Jul 3, 2024 at 12:38 PM Kern, Lori wrote: > It looks like this 1.1.3 version was just pushed and built today. It will > propagate today per the green radio button on the report. I imagine if you > try again in an hour or so that version will be available. There is

Re: [Bioc-devel] Package version did not update correctly

It looks like this 1.1.3 version was just pushed and built today. It will propagate today per the green radio button on the report. I imagine if you try again in an hour or so that version will be available. There is a little delay from the report to the propagation. Lori Shepherd - Kern

Re: [Bioc-devel] Package version did not update correctly

Hello all, I was hoping to use the devel version of my package "spoon" by installing it with the devel version of BiocManager. I installed Bioconductor version 3.20 (BiocManager 1.30.23), R 4.4.0 (2024-04-24) and then tried using BiocManager::install("spoon") to install the package. It installed

Re: [Bioc-devel] bioconductor support site problem

You don't have to create the tag. It will automatically be suggested once accepted. What you do need to do is add it to your watch list so you will be emailed/notified when someone uses the tag. To do this, go to your profile and select edit. There will be a field Watched Tags that you

[Bioc-devel] bioconductor support site problem

hi Bioc: It is the first time I submit R package to bioconductor, I need to complete the BiocCheck() check: register and then include my package name in the list of watched tags. But I don't know how to create tag on the support site, can you show me how to do it? thank you!

Re: [Bioc-devel] Fwd: SpliceWiz problems reported in the Multiple platform build/check report for BioC 3.19

I went on the builders to investigate and there is no such cache at that location. It seems like the cache is either not being created at all or is not being created where you think it is. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of

Re: [Bioc-devel] Package with restrictive licenses, not suitable for Bioconductor

Le Sun, Jun 30, 2024 at 08:28:34PM +, Laurent Gatto via Bioc-devel a écrit : > The Bioconductor contributions guide says: > > > Licenses restricting use, e.g., to academic or non-profit > > researchers, are not suitable for Bioconductor. > > but we have several packages with restrictive

[Bioc-devel] Package with restrictive licenses, not suitable for Bioconductor

The Bioconductor contributions guide says: > Licenses restricting use, e.g., to academic or non-profit > researchers, are not suitable for Bioconductor. but we have several packages with restrictive licenses: - RankProd: free for non-commercial users. Non-academic users MUST have requested

[Bioc-devel] Fwd: SpliceWiz problems reported in the Multiple platform build/check report for BioC 3.19

Hi there, I am getting errors in the SpliceWiz build on BIoc 3.19. However I cannot reproduce this issue on our local server using the bioconductor docker. The vignette failure appears to be due to a section of code that fetches a cached data file using BiocFileCache. The data files are

Re: [Bioc-devel] [EXTERNAL] Deeptarget package

I agree that it is important to only redistribute data in a way that is consistent with whatever terms are encountered when accessing the data. Some options I've seen include (1) using an API that allows authentication (the httr2 'auth' vignette provides workflows; I took the time recently to

Re: [Bioc-devel] [EXTERNAL] Deeptarget package

Dear Nguyen, Thank you for your response. I am just a bit puzzled, and no other developer has answered so far. E.g. in the description of the depmap package it says: "This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0))." Anyhow if you visit

Re: [Bioc-devel] Failed to load resource from AnnotationHub

I noted the same resource causing the same error for the OSCA books in BIoC 3.20 and Lori said she'll take a look at it tomorrow (only on Slack, sorry: https://community-bioc.slack.com/archives/CM2CUGBGB/p1719265237989709) On Tue, 25 Jun 2024 at 12:21, Shian Su via Bioc-devel <

[Bioc-devel] Failed to load resource from AnnotationHub

Hi BioC Developers, I have an error in the checks for my package Glimma that I hoped would go away on its own https://bioconductor.org/checkResults/release/bioc-LATEST/Glimma/nebbiolo1-checksrc.html Error: processing vignette 'single_cell_edger.Rmd' failed with diagnostics: failed to load

Re: [Bioc-devel] AnnotationHub failing to load on Mac

What is interesting is the resource can load fine on its own when accessed from AnnotationHub so it might be related to the way it is being access/loaded in DMRcate. > ah = AnnotationHub() snapshotDate(): 2024-04-30 > temp = ah[["AH116484"]] loading from cache > > head(temp)

[Bioc-devel] AnnotationHub failing to load on Mac

Hi Bioc, A couple of Macx86_64 users have contacted me with this error when using DMRcate::rmPosReps(), which looks like it's propagating from a failure to load AnnotationHub: Error: failed to load resource name: AH116484 title: EPICv2manifest reason: error in evaluating the argument 'x'

Re: [Bioc-devel] Hub Resource Access Downtime

I apologize, the correct date of the update is this Thursday June 20 Get Outlook for iOS From: Bioc-devel on behalf of Kern, Lori via Bioc-devel Sent: Monday, June 17, 2024 1:34:49 PM To: bioc-devel@r-project.org Subject: [Bioc-devel]

[Bioc-devel] Hub Resource Access Downtime

We plan to do updates and maintenance on our ExperimentHub and AnnotationHub resource location on Thursday June 17. There will be a period of time where hub resources will be unavailable. We apologize for any inconvenience. Lori Shepherd - Kern Bioconductor Core Team Roswell Park

Re: [Bioc-devel] Build fail due to "undefined color `fgcolor`"

Awesome, thank you so much! On Mon, Jun 17, 2024 at 3:29 PM Alvaro Cuadros < acuadros+bioc-de...@gmail.com> wrote: > On Sat, Jun 15, 2024 at 4:37 PM Xiangyu Luo wrote: > > Build error messages for my packages still exist after a few days. I am > > wondering how long the error will last. Thank

Re: [Bioc-devel] Build fail due to "undefined color `fgcolor`"

On Sat, Jun 15, 2024 at 4:37 PM Xiangyu Luo wrote: > Build error messages for my packages still exist after a few days. I am > wondering how long the error will last. Thank you so much for your great > help! Not Mike, but I noticed that BiocStyle was updated Monday last week on devel and last

Re: [Bioc-devel] Build fail due to "undefined color `fgcolor`"

Dear Mike, Build error messages for my packages still exist after a few days. I am wondering how long the error will last. Thank you so much for your great help! Many thanks! Xiangyu On Sat, Jun 15, 2024 at 10:35 PM Xiangyu Luo wrote: > Dear Mike, > > Build error messages for my packages

Re: [Bioc-devel] Package version did not update correctly

Thank you for the quick response, this is very helpful! On Thu, Jun 13, 2024 at 1:19 PM Kern, Lori wrote: > A few things. > > >1. Please keep in mind there is a delay from pushing to the >Bioconductor git and when it will be available via BiocManager. The >package must first get

[Bioc-devel] Package version did not update correctly

Hello, I made some small changes to a function in my package, "spoon", and wanted to update the patch version number to build the changes. https://github.com/kinnaryshah/spoon/tree/main I updated the version from 1.1.0 to 1.1.1 and pushed the changes to the Bioconductor and GitHub repositories.

Re: [Bioc-devel] Package version did not update correctly

A few things. 1. Please keep in mind there is a delay from pushing to the Bioconductor git and when it will be available via BiocManager. The package must first get built and propagated on our system. The checkResults page shows the timings of these reports currently twice a week.

Re: [Bioc-devel] [EXTERNAL] Re: Deeptarget package

Dear Kristian, This is very important question. Thanks for checking in. The manuscript is under review, and I believe that we already agreed and followed to Depmap’s policies. The input data we used in this package here contains only a subset of the data we used in the manuscript, and it is

Re: [Bioc-devel] Error in methylclockData package

I can't reproduce either of these and when I check the resources on the builders they load successfully so doesn't appear to be a caching issue. I would expect them to clear up on the next run of the builders. Let's see what happens on the next run and if they continue to error I can look

Re: [Bioc-devel] Error in methylclockData package

Dear BioC Team, I am receiving a similar error from the MouseThymusAgeing package: > smart.data <- MouseSMARTseqData(samples = "day1") see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for documentation loading from cache field not found in version - adding see ?MouseThymusAgeing

[Bioc-devel] Error in methylclockData package

Dear Bioconductor team, I have seen that the methylclockData package gives an error when loading the EH6082 resource, the error is: get_TestDataset() see ?methylclockData and browseVignettes('methylclockData') for documentation loading from cache Warning in grepl("RD[ABX][2-9]\n", magic) :

Re: [Bioc-devel] Deeptarget package

Dear Nguyen, I have a question related to the data that you use and I just bring it up here since I would also like to ask the bioconductor developers, how this can be handled properly. The depmap.org portal has a clear "Terms and Condition" statement that you need to

Re: [Bioc-devel] Deeptarget package

Thank You! Trinh From: Kern, Lori Date: Tuesday, June 11, 2024 at 12:19 PM To: bioc-devel@r-project.org , Nguyen, Trinh (NIH/NCI) [C] Subject: [EXTERNAL] Re: Deeptarget package Two things: 1. The package was accepted on Friday. Currently our software builds are only building twice a

Re: [Bioc-devel] Deeptarget package

Two things: 1. The package was accepted on Friday. Currently our software builds are only building twice a week Tue and Fri. You can see the schedule of all the different builds at https://bioconductor.org/checkResults/. Eventually devel Bioc will go back to daily builds but there are

[Bioc-devel] Deeptarget package

Dear Bioconductor team, Deeptarget package has been accepted. However, when I installed it has error of �package �DeepTarget� is not available for Bioconductor version '3.18'� Could you please give me some guidance? Thanks, Trinh [[alternative HTML version deleted]]

Re: [Bioc-devel] No bioc-git server access

Sorry for the inconvenience and the confusion. It looks like there was an error when your account was created. It has been remedied and you should now have a BiocCredentials account associated with the email. You will still have to activate your account to gain access. Let us know if there

[Bioc-devel] No bioc-git server access

Dear Bioconductor team, I am currently in the process of contributing a package to Bioconductor ( https://github.com/Bioconductor/Contributions/issues/3446). Today I wanted to implement the necessary changes for the pre-review check but I have trouble accessing the package on the bioc-git server.

Re: [Bioc-devel] Build fail due to "undefined color `fgcolor`"

This looks to be an issue introduced by changes in knitr 1.47.0, which lead to an incompatibility in the BiocStyle Rnw template. We're working on a patch to BiocStyle, which should be deployed on the build machines today, and will hopefully fix the issue in the affected packages. The is nothing

Re: [Bioc-devel] Build fail due to "undefined color `fgcolor`"

I also received the same error email for my packages BUScorrect and HIREewas. I don't know how to fix these "undefined color" issues. Thank you very much for all your help and replies! Best regards, Xiangyu On Sun, Jun 9, 2024 at 11:05 PM Martin Morgan wrote: > This seems to me like a change

Re: [Bioc-devel] Build fail due to "undefined color `fgcolor`"

This seems to me like a change in the xcolor package, but I'm not sure. I opened an issue on the BiocStyle package at https://github.com/Bioconductor/BiocStyle/issues/109. Martin From: Bioc-devel on behalf of Alvaro Cuadros Date: Sunday, June 9, 2024 at 5:00 AM To: bioc-devel@r-project.org

Re: [Bioc-devel] Build fail due to "undefined color `fgcolor`"

On Fri, Jun 7, 2024 at 10:23 PM Christian Mertes wrote: > > Dear Bioc Team, > > I got today a build error from OUTRIDER and FRASER with: > > LaTeX errors: > ! Package xcolor Error: Undefined color `fgcolor'. > > The same errror also pops up at other packages such as ggbio: > > output file:

[Bioc-devel] Build fail due to "undefined color `fgcolor`"

Dear Bioc Team, I got today a build error from OUTRIDER and FRASER with: LaTeX errors: ! Package xcolor Error: Undefined color `fgcolor'. The same errror also pops up at other packages such as ggbio: output file: ggbio.tex ! Package xcolor Error: Undefined color `fgcolor'. I assume this is

[Bioc-devel] EuroBioC2024 Registration is Open!

Hi everyone, We are excited to share that registration for EuroBioC2024 is open! Join us for the European Bioconductor conference in beautiful Oxford, UK, from September 4-6. This event focuses on cutting-edge bioinformatics and data analysis using R and Bioconductor. Secure your spot and take

[Bioc-devel] Final reminder: BioC2024 early registration ends tomorrow, May 31

Just a quick reminder that early registration for in-person attendance at BioC2024 ends tomorrow, May 31. Don't miss out on this fantastic opportunity to engage with the Bioconductor community in Grand Rapids, Michigan, USA. Register here: https://www.bioc2024.bioconductor.org/registration

Re: [Bioc-devel] Remote BigWig file access

Thanks Vince, understood about the Core's focus right now. I think this is something that Leo and I can fix among ourselves for the time being. Looking forward, as you brought up, if we were to refresh recount or produce a recount4 (discussed) we'd certainly consider additional coverage

Re: [Bioc-devel] Remote BigWig file access

We have been experimenting with other formats in our package ORFik, the fst format is also a good candidate, though the problem is that only R and Julia supports it currently. My biggest problems with bigwigs are the slow full file access time and not supporting multiple score columns (as far

[Bioc-devel] Legacy Bioconductor Installation

In the past Bioconductor provided an install script that was sourced directly from the Bioconductor.org website to install Bioconductor packages. We have since moved away from this practice in favor of BiocManager since sourcing in this way is a known security risk. The scripts have remained

Re: [Bioc-devel] Remote BigWig file access

thanks On Thu, May 23, 2024 at 5:36 PM Chris Wilks (gmail) wrote: > Thanks Vince, understood about the Core's focus right now. > > I think this is something that Leo and I can fix among ourselves for the > time being. > > Looking forward, as you brought up, if we were to refresh recount or >

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

I replied the wrong email sorry. Please ignore. On 5/23/24 11:40, Hervé Pagès wrote: > > Ok I downloaded the SecureLink Connection Manager (file > connection-manager.run) on my Linux laptop (got a big warning from > Chrome that this kind of file is dangerous, I found this pretty ironic). > >

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

Ok I downloaded the SecureLink Connection Manager (file connection-manager.run) on my Linux laptop (got a big warning from Chrome that this kind of file is dangerous, I found this pretty ironic). Then I started it with   bash connection-manager.run (you have to kind of figure out these

[Bioc-devel] Bioconductor Build System

Due to unforeseen circumstances, our daily builders and new submission builders are currently offline. We are sorry for the inconvenience and will restore as soon as possible Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics &

[Bioc-devel] BioC2024 Bioconductor Carpentries RNA-Seq Workshop July 22-23

Hi everyone, We would be grateful if you could help spread the word about this workshop with your networks or anyone who might be interested. Also, a reminder that BioC2024 early registration ends soon on May 31. Workshop: We're excited to announce the

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

On 5/22/24 02:16, Vincent Carey wrote: > ... > > > Q4: Do you think a separate ExperimentData package satisfying > the specifications laid out in Background 2 is warranted? This > could be included in a future version with > SummarizedExperiment/MetaboExperiment support. >

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

Dear Vilhelm, If you need to use/share (reasonably large) MS data, you could consider contributing data to the MsDataHub package [1], that is superseding msdata and makes use of ExperimentHub. Feel free to get in touch (ideally opening a GitHub) if this is of interest to you. Best wishes,

Re: [Bioc-devel] Remote BigWig file access

Really glad to see this discussion moving forward. I would say that the core is wrangling with some even lower-level technical concerns right now, so I can't jump in just now. I just want to raise the question of whether bigWig files are a technologically sound format to continue investing in

Re: [Bioc-devel] Remote BigWig file access

Thanks for sharing Leo, this does interest me, especially since so much is built on BigWig access via rtracklayer at least in the recount2 ecosystem. As you alluded to, Megadepth currently supports remote access of BigWigs (and BAMs) over HTTPS on all platforms (Linux, MacOS, and Windows),

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

> > ... > > > Q4: Do you think a separate ExperimentData package satisfying the > specifications laid out in Background 2 is warranted? This could be > included in a future version with SummarizedExperiment/MetaboExperiment > support. > It depends on the size of the data. For a software package,

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

Dear Vilhelm, notame seems to be an interesting package filling some gaps that currently exist in the untargeted metabolomics workflow. I would strongly suggest to support the SummarizedExperiment classes (in future). I would maybe suggest to keep it as generic as possible without dedicated

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

Hi, On 5/21/24 01:58, Vilhelm Suksi wrote: > Hi! > > Excuse the long email, but there are a number of things to be clarified in > preparation for submitting the notame package which I have been developing to > meet Bioconductor guidelines. As of now it passes almost all of the automatic >

[Bioc-devel] Remote BigWig file access

Hi Bioc-devel, As some of you are aware, rtracklayer::import() has long provided access to import BigWig files. Those files can be shared on servers and accessed remotely thanks to all the effort from many of you in building and maintaining rtracklayer. >From my side, derfinder::loadCoverage()

Re: [Bioc-devel] AnnotationHub: uniprot seqs ?

If you have many sequences to download, it can be very slow if you use Uniprot.ws to query the database. I used a walk-around method to download the proteome of a species using FTP in my dagLogo package: https://github.com/jianhong/dagLogo/blob/devel/R/prepareProteomeByFTP.R. Haibo

Re: [Bioc-devel] AnnotationHub: uniprot seqs ?

Thank you Haibo and Vincent : ) Yes, UniProt.ws is certainly there and did serve me well earlier. There are times when an offline solution is needed, when operations are done on larger sets. Followed my habit to check first whether a relevant AnnotationHub record exists. Given the absence of

Re: [Bioc-devel] AnnotationHub: uniprot seqs ?

We use Uniprot.ws to access the Uniprot data on demand: https://bioconductor.org/packages/release/bioc/html/UniProt.ws.html. Haibo -Original Message- From: Bioc-devel On Behalf Of Vincent Carey Sent: Tuesday, May 21, 2024 7:02 AM To: aditya.bhag...@uni-marburg.de Cc:

Re: [Bioc-devel] AnnotationHub: uniprot seqs ?

On Tue, May 21, 2024 at 4:18 AM Aditya Bhagwat via Bioc-devel < bioc-devel@r-project.org> wrote: > Hey guys, > > Do we have Uniprot sequences in AnnotationHub ? > That does not seem practical. Please see

[Bioc-devel] Question relating to extending a class and inclusion of data

Hi! Excuse the long email, but there are a number of things to be clarified in preparation for submitting the notame package which I have been developing to meet Bioconductor guidelines. As of now it passes almost all of the automatic checks, with the exception of formatting and some functions

[Bioc-devel] AnnotationHub: uniprot seqs ?

Hey guys, Do we have Uniprot sequences in AnnotationHub ? Not being able to find them. Thankyouverymuch : ) Aditya -- Aditya Bhagwat Translational Proteomics ∙ Philipps-University Marburg Biological Pharmacological Center ∙ Room A406 Tel.: +49 6421 28 27403

Re: [Bioc-devel] Change of decontX package maintainer

Hello, We can assist with this request. We will contact Joshua off list to verify the BiocCredentials account. Once Joshua has access it will be up to them to update the DESCRIPTIONS accordingly (which will change the listed maintainer on the package pages) and to appropriately sign up for

[Bioc-devel] Change of decontX package maintainer

Dear Bioconductor Team, I am Yuan and I am the current maintainer of decontX (https://bioconductor.org/packages/release/bioc/html/decontX.html). I would like to pass the maintainer role to another author Joshua Campbell (c...@bu.edu). Could you point me to any instructions on how to update

[Bioc-devel] Single Package Builder for new Bioconductor Submissions

Over the next few days, we will be transitioning the single package builder for new Bioconductor submissions to use Bioconductor 3.20 rather than 3.19 following the latest Bioconductor release on May 1. This may result in downtime to the build on demand functionality. We appreciate your

[Bioc-devel] Bioc2024 Nomination Deadline May 15

We are still accepting nominations for Bioc2024 Awards!! Please recognize an outstanding member of the Bioconductor community. We also dedicate one award to a junior developer or new package development. Award criteria can include but is not limited to: * Outstanding new package

[Bioc-devel] AMI Policy Change

In the past Bioconductor provided pre-configured AMI with certain Bioconductor releases, conferences, and workshops. We are moving these legacy AMI snapshots to a cold storage class. They will be available by request only; The time necessary for retrieval may range from 12 to 72 hours. These

Re: [Bioc-devel] Maintainer change

Thank you for reaching out. I will be in contact off list to help set up Camila Perico BiocCredentials account that will be needed to access. We will then grant push access to git.bioconductor.org. It will be up to Camila to adjust the package DESCRIPTION accordingly with a valid version

Re: [Bioc-devel] scaeData: not available for Bioconductor version '3.19'

It looks like it is clean on yesterday's report; normally it would be available shortly after propagation on a build day. We identified the issue and it should be made available shortly. We apologize for the delay. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive

[Bioc-devel] Maintainer change

Hi bioc-devel, I would like to request for me to be removed as maintainer of the rSWeeP package and for > to be added as maintainer. Thank you for your help. Kind regards, Danrley R. Fernandes -- *Danrley R Fernandes* Bacharel em Ciências Biológicas

[Bioc-devel] scaeData: not available for Bioconductor version '3.19'

Dear Core Team, I hope you are doing well. I am facing an issue installing |scaeData| via BiocManager on Bioconductor version '3.19'. Despite its presence in the list of newly accepted/released packages and an active RELEASE branch, I am encountering an error indicating that the package is

[Bioc-devel] Bioconductor 3.19 is Released!

Thanks to all developers and community members for contributing to the project! Please see the full release announcement: https://bioconductor.org/news/bioc_3_19_release/ Cheers, Sent on behalf of the Bioconductor Core Team This email message may contain legally privileged and/or

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