Re: [Bioc-devel] Important Bioconductor Release Deadlines

On Fri, Apr 5, 2024 at 12:56 AM Anatoly Sorokin wrote: > > Dear Levi, > > minor correction: not requiring but working with. Testing against r-devel > and requiring it for development are two different things. If the > development and maintenance of the Bioconductor package would be my only >

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

winging it here tim > select(Homo.sapiens, keys="ENSG0198727", keytype="ENSEMBL", columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) 'select()' returned 1:1 mapping between keys and columns ENSEMBL GENENAME SYMBOL CDSCHROM GENEID 1 ENSG0198727 cytochrome b CYTB

Re: [Bioc-devel] R package on Github uses Bioconductor depenencies and cant be installed.

What command was used? BiocManager::install should resolve the dependencies whereas straight use of install.packages would not. On Wed, Feb 28, 2024 at 9:07 AM Ruff, Sergej wrote: > Hello, > > > I have an R package on Github that uses Bioconductor dependencies: > > >

Re: [Bioc-devel] Build errors from recent breaking ggplot2 changes

thanks for the report, we will discuss this today. it should be possible to address this soon. On Tue, Feb 27, 2024 at 6:02 AM Stevie Pederson < stephen.pederson...@gmail.com> wrote: > Hi, > > I have the package ComplexUpset as a dependency for some packages and the > recent changes to ggplot2

Re: [Bioc-devel] Question about cstack usage error

can you build a reprex for gplots? we are stretched very thin right now and i am sorry to say i don't see this as actionable in our group. On Tue, Feb 27, 2024 at 2:36 AM Johannes Griss < johannes.gr...@meduniwien.ac.at> wrote: > Hi, > > We've been encountering a cstack related error on the

Re: [Bioc-devel] Check time on macOS (MIRit)

> > Il mer 7 feb 2024, 12:26 Vincent Carey ha > scritto: > >> Thanks Jacopo. You shouldn't have to struggle. We are aware of >> disparities of platform >> performance and are working to improve the build process. It will take >> time. I believe that >>

Re: [Bioc-devel] Check time on macOS (MIRit)

Thanks Jacopo. You shouldn't have to struggle. We are aware of disparities of platform performance and are working to improve the build process. It will take time. I believe that achievement of acceptable timings on the linux platform should be the key goal at this time. On Wed, Feb 7, 2024

Re: [Bioc-devel] hermes Bioconductor

at 9:51 AM Vincent Carey wrote: > I cannot reproduce this with a current pull of the devel container. > BiocManager installation > of S4Vectors succeeded. Please provide the version given in environment > variable > BIOCONDUCTOR_DOCKER_VERSION, I used 3.19.13 > > R Under

Re: [Bioc-devel] hermes Bioconductor

I cannot reproduce this with a current pull of the devel container. BiocManager installation of S4Vectors succeeded. Please provide the version given in environment variable BIOCONDUCTOR_DOCKER_VERSION, I used 3.19.13 R Under development (unstable) (2024-01-03 r85769) Platform:

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

eve 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

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

Good question. I believe these will be forthcoming soon. In the mean time you can create your own. See, for example https://github.com/vjcitn/BiocT2T/blob/devel/inst/scripts/makeTxDb.R It's an active area so you can pull a gff file from

Re: [Bioc-devel] Is my package suitable for Bioconductor?

agreedthis discussion is best discussed in the open On Tue, Oct 24, 2023 at 8:57 AM Lluís Revilla wrote: > Hi Tim, > > I think there is a mentorship program for cases like this (I am not sure if > it still accepts mentees): > https://www.bioconductor.org/developers/new-developer-program/ >

Re: [Bioc-devel] Including large files for the package

On Thu, Aug 31, 2023 at 7:28 AM Martin Grigorov wrote: > Hello, > > Perhaps you could use https://bioconductor.r-universe.dev/BiocFileCache to > download the big file on demand. > The benefit is that the file would be stored in ~/.cache/R/yourPackage/ > (for Linux; something similar for

Re: [Bioc-devel] Champ Analysis trouble

Thank you for your note. This list is for package development. Please register at support.bioconductor.org and post your question there On Fri, Jul 21, 2023 at 7:14 AM Keasiykan Selvaraju wrote: > Hi. I am having trouble analysing own data in champ. Error keep appearing > as pd file and green

Re: [Bioc-devel] Python module "tensorflow_probability" not found

ensorflow > >> = 2.2. That's a strong promise considering also the difference > > between GPU and CPU. > > > > In the meantime, in case the core build team wants some input, I have > some > > experience with tensorflow, although so far my experience is mostly > > fr

Re: [Bioc-devel] Python module "tensorflow_probability" not found

make sense with basiliskRun). I could also not find any advice on this > elsewhere. > Do you have a suggestion how to best handle this (or should it *just* work)? > > > On Tue, Jul 4, 2023 at 1:04 PM Vincent Carey > wrote: >> >> Sorry to hear about this.

Re: [Bioc-devel] Python module "tensorflow_probability" not found

Sorry to hear about this. Our informal outlook on python interoperation in Bioconductor packages is that the basilisk discipline should be used. This allows you to pin specific versions of all python dependencies and use python for your R functions from an insulated conda environment. There is

Re: [Bioc-devel] package failing

Please provide more details in the future. What is the name of the package, which branch of Bioconductor? The packages I can see seem to be in a warning state. * checking Rd \usage sections ... WARNING Documented arguments not in \usage in documentation object 'show,SampleSet-method': ‘...’

Re: [Bioc-devel] Urgent minor deployment of a release?

On Tue, Jun 20, 2023 at 1:34 AM Henrik Bengtsson wrote: > On Mon, Jun 19, 2023 at 5:46 PM Vincent Carey > wrote: > > > > Hi Adam, thanks for your note. > > > > Changes to release branch sources must be limited to bug fixes or doc > > improvement. Any new

Re: [Bioc-devel] Urgent minor deployment of a release?

Hi Adam, thanks for your note. Changes to release branch sources must be limited to bug fixes or doc improvement. Any new features must be introduced only in the devel branch. Any features to be removed must be indicated as deprecated for one release and then labeled as defunct. See

Re: [Bioc-devel] there is no package called ‘BiocStyle’

In SC3 you have Suggests: on two different lines in DESCRIPTION. The second one supersedes the first, I suppose. On Thu, May 25, 2023 at 6:06 AM Vladimir Kiselev < vladimir.yu.kise...@gmail.com> wrote: > Hello, > > Recently two of my packages (SC3 and scmap) started failing checks due to: >

Re: [Bioc-devel] BiocManager::install

Thanks for these observations Wolfgang, I am glad I read to the end, because as you say, https://solutions.posit.co/envs-pkgs/bioconductor/ has lots of interesting information. As I personally have no experience with renv or Connect much of the motivating detail is opaque to me. I would

Re: [Bioc-devel] Participating in the development of Bioconductor

Hi Franck, thanks for writing. I think it would be great to hear from users about performance concerns. We would like to do more profiling and instrumentation of key worksteps to help increase throughput and ensure available compute resources are used. In the cuda/gpu space we don't have

Re: [Bioc-devel] TCGAbiolinks fails

The problem is that it is in an error state --- re-building ‘subtypes.Rmd’ using rmarkdown Quitting from lines 114-121 (subtypes.Rmd) Error: processing vignette 'subtypes.Rmd' failed with diagnostics: object 'lgg.gbm.subtype' not found --- failed re-building ‘subtypes.Rmd’ so the standard

Re: [Bioc-devel] Installation of XCMS on R

please pose your question with details of error messages to support.bioconductor.org no telephone contacts should be provided or used On Thu, Feb 23, 2023 at 6:04 PM insaf ben wrote: > Hello, > > I have a problem installing the xcms library on my R studio 4.2. Could you > help me do this plz ?

Re: [Bioc-devel] DESeq2 package

You can read the description file (e.g., help(package="DESeq2")), but the best way is to pose a question at support.bioconductor.org as many people with good experience are reading that at all hours On Tue, Jan 24, 2023 at 7:13 AM Claudio A Bravo wrote: > Hi- > > Could you please direct me to

Re: [Bioc-devel] Proposing patch to Bioconductor package

Thanks for checking in Duncan. I don't believe we have a guideline on this. We have code.bioconductor.org that facilitates search of the entire codebase. If you provide a list of the functions that should not be used, I will see about making a focused message to the developers who need to

Re: [Bioc-devel] Large vignettes

t-class concerns and really require author commitment. > > Some authors already have books outside bioconductor to have extensive > examples of their packages. > They will also benefit from having them with the Bioconductor framework > and in sync with the packages released to the u

Re: [Bioc-devel] Support for Linux ARM64

On Thu, Jan 5, 2023 at 7:08 PM Vincent Carey wrote: > > > On Thu, Jan 5, 2023 at 1:44 PM Hervé Pagès > wrote: > >> Hi Martin, >> >> Linux runs on many architectures, ARM64 is just one of them. >> >> Our daily builds have traditionally focused on 3

Re: [Bioc-devel] Support for Linux ARM64

On Thu, Jan 5, 2023 at 1:44 PM Hervé Pagès wrote: > Hi Martin, > > Linux runs on many architectures, ARM64 is just one of them. > > Our daily builds have traditionally focused on 3 platforms: Intel-based > Linux (Ubuntu 22.04), Windows, and Intel-based Mac. Note that we > recently added

Re: [Bioc-devel] Bioconductor data packages containing very large files

I would like us to discuss this in the context of the HDF Scalable Data Service that we have running on the NSF cloud in jetstream2. Let's discuss off line and then report back to the list. On Thu, Jan 5, 2023 at 7:11 AM Heery Richard wrote: > Thank you Lori. > > I was wondering if there is

Re: [Bioc-devel] Support for Linux ARM64

On Thu, Jan 5, 2023 at 5:02 AM Martin Grigorov wrote: > Dear community, > > Happy and successful new year! > > Appologies if this has been discussed before but > https://stat.ethz.ch/pipermail/bioc-devel/ does not provide search > facilities and my googling didn't help much! > > I'd like to ask

Re: [Bioc-devel] Large vignettes

I am glad you brought this up here, and I welcome further discussion on this mailing list. It is important to understand the constraints on development that arise from Bioconductor's package guidelines. I don't think we want to change the limits on package payload size without understanding the

Re: [Bioc-devel] Multiple projects for submission to Bioconductor

to-github but perhaps further discussion is needed. At this time our build system works with git repositories that are jointly managed by us and by the package maintainer. Maintainers are responsible for ensuring that the git repository is up to date. Sincerely, Vincent Carey > T

Re: [Bioc-devel] Package "rmspc" failing on Bioconductor devel

At this time (and for the foreseeable future) messaging on changes to packages only occurs during the review process. Your version 1.5.1 is visible in git and will be tested in the next build cycle which should be very soon. Thank you On Wed, Dec 28, 2022 at 12:29 PM Meriem Bahda wrote: >

Re: [Bioc-devel] Developing a package that handle BAM file

On Sun, Dec 18, 2022 at 4:07 PM Hao Feng wrote: > Hi Bioconductor team, > > We’re developing a package to analyze a `new` type of high-throughput > sequencing data. We have some BAM files ready. We’d like the package to be > able to take BAM files as the input. In addition, to maintain our

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

Thank you for this note. We cannot modify the system to accept this package. If we can help with aspects of compatibility problems related to ExperimentHub let us know. On Thu, Nov 24, 2022 at 1:58 AM Daniel Laajala wrote: > Dear Bioconductor devs, > > thanks for all the hard work. Regarding

Re: [Bioc-devel] Fwd: Package "SingleCellSignalR" failing on Bioconductor devel

When testing on the devel branch at this time, you must use R-devel (R 4.3). See https://contributions.bioconductor.org/use-devel.html#use-devel For SingleCellSignalR, the dependence on SIMLR seems problematic. SIMLR is in an error state on the devel branch. One could see that even in the

Re: [Bioc-devel] CTCF annotation package's vignette not updating

Maybe I am wrong Mikhail but I think you have about 6 months to enhance the documentation of your package in 3.16. On Sun, Oct 30, 2022 at 7:54 PM Mikhail Dozmorov wrote: > Hello, > I'm trying to update documentation for the >

Re: [Bioc-devel] Increase version of system dependency?

My suggestion is that your interfaces to python be mediated with the basilisk package. Please contact me off line if you need assistance; see BiocSklearn for an example; I am sure there are others. On Tue, Oct 18, 2022 at 12:31 PM Sarvesh Nikumbh wrote: > Hi bioc team, > > My package seqArchR

Re: [Bioc-devel] Version number trouble

Hi Mirko -- the devel branch has an odd y in x.y.z stvjc@stvjc-XPS-13-9300:~/BIOC_SOURCES$ cd BindingSiteFinder stvjc@stvjc-XPS-13-9300:~/BIOC_SOURCES/BindingSiteFinder$ grep Version DE* Version: 1.3.0 stvjc@stvjc-XPS-13-9300:~/BIOC_SOURCES/BindingSiteFinder$ git fetch --all Fetching origin The

Re: [Bioc-devel] CITEViz Package Submission Not Building Inbox

Hi Garth. I can see 0.99.4 ... Your package has not been subjected to pre-check yet because of the needs interop label. I will add comments on the issue for your package. I think pre-check will pass soon and then it will be ingested for build and review later this week. On Sun, Oct 9, 2022 at

Re: [Bioc-devel] Mac ARM64 binaries available

We are not running check on ARM platform at this time. If you want to provide a link to the package/error you are having trouble with I will have a look on my machine. If you are passing on the other platforms there will be no consequences for remaining in the bioc ecosystem. On Tue, Oct 4,

Re: [Bioc-devel] [External] Re: error in bioconductor package DSS

> > git cherry-pick master > > git push > > > > Is this what I should do? > > > > *From: *"Wu, Hao" > *Date: *Friday, September 30, 2022 at 6:08 PM > *To: *Vincent Carey > *Cc: *"bioc-devel@r-project.org" , Harry Feng < &g

Re: [Bioc-devel] error in bioconductor package DSS

I don't think you are looking at the RELEASE_3_15 branch, but that is where the error is occurring. On Fri, Sep 30, 2022 at 6:03 PM Wu, Hao wrote: > Hello, > > I recently received an email regarding an error for DSS: >

Re: [Bioc-devel] groHMM package error check report error

There are .o and .so files in /src in the repo. These should not be present in any source package. Please remove them. On Sat, Sep 24, 2022 at 6:58 AM Tulip Nandu wrote: > Hi, > > I received the following email, > "According to the Multiple platform build/check report for BioC 3.16, > the

[Bioc-devel] apps for overviews of adverse bioc package building events

some code has been written and put in a shiny app to help drill down to those packages in the BIoc build system that are exhibiting errors or warning at various stages of the install/build/check process https://vjcitn.shinyapps.io/biocPkgState316/ https://vjcitn.shinyapps.io/biocPkgState315/

[Bioc-devel] Fwd: Package fails to install

I forgot to reply all. Here is my initial response. -- Forwarded message - From: Vincent Carey Date: Wed, Jul 27, 2022 at 8:20 AM Subject: Re: [Bioc-devel] Package fails to install To: Alemu Takele On Wed, Jul 27, 2022 at 8:13 AM Alemu Takele wrote: > Hi the Bioconduc

Re: [Bioc-devel] Bioconductor install instructions for M1-based Mac

Thanks Gordon, I agree that some documentation should be added. While we are not in a position to provide binaries for M1 at this time, anyone who has prepared their M1-oriented version of R to install packages from source can install Bioconductor packages. I will respond on the support site,

Re: [Bioc-devel] Git recognizes me but denies access

How are we doing with this? Can destiny be maintained? Do we need more git assistance? I am told the package is not passing check in 3.14. On Thu, Nov 18, 2021 at 4:24 AM Philipp A. wrote: > My addresses are phil.ange...@gmail.com (not philipp) and > flying-sh...@web.de. > > I’ll add a key as

Re: [Bioc-devel] MAGMA executable

I didn't find an obvious licensing statement at the magma site. I did see note that standard copyright applies; the MAGMA binaries and source code may not be distributed or modified) the licensing situation would affect my advice on this process, but others may have other more specific advice

Re: [Bioc-devel] [External] Memory error from sesame build

It seems noteworthy that this is occurring only for the i386 build on windows. i've had no luck reproducing the error with * sessionInfo() R version 4.1.2 RC (2021-10-25 r81110) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 10 x64 (build 19043) Matrix products: default

Re: [Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

; > >CHRONOS > > > > debCAM > > > >esATAC > > > >gaggle > > > >Onassis > > > >ReQON > > > >RGMQL > > > >rmelting > > > >sarks > > > >SELEX > > >

Re: [Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

That should be fixable. The build system needs to have a correct setting for JAVA_HOME. But you have clearly nonportable code in .onLoad in paxtoolsr.R -- system("which java") ... this should not be necessary at all, just import rJava. On Mon, Oct 18, 2021 at 12:29 PM Augustin Luna wrote: > I

Re: [Bioc-devel] Best Practices for Renaming S4 Slots

if changes to a class require so much work, it incentives > developers to simply ditch old S4 classes and reimplement them in a new > package. Doesn’t that go against the spirit of reuse that is supposed to be > encouraged by adoption of S4 classes? > > TL;DR – IMO API = interface; imple

Re: [Bioc-devel] Best Practices for Renaming S4 Slots

I will defer to Herve about all details, but I would say that this level of change control is implied by the "no changes to package API without an interval of deprecation spanning at least one release". See https://bioconductor.org/developers/how-to/deprecation/ That text mentions that removal

[Bioc-devel] Recent contribution processing

Contribution processing has encountered some technical difficulties. We expect normal operations to resume Monday. Contributors of new packages should hold steady; moderation and review will resume ASAP. -- The information in this e-mail is intended only for the ...{{dropped:18}}

Re: [Bioc-devel] Issues with package size

It seems to me the reason for the large vignette size is that you have significant DT::datatable rendering capabilities within your vignettes, and the tables are large. I would propose that you use subsets of the table content for the vignettes, and direct the reader who wants to search the

Re: [Bioc-devel] BrowserViz build test times out, checks for web browser availability, apparently needs update

Sorry for delay in responding Paul. I had a look at BrowserViz and ran into > PORT_RANGE <- 12111:12120 > if(BrowserViz::webBrowserAvailableForTesting()){ +bvApp <- BrowserViz(browserFile=browserVizBrowserFile, quiet=TRUE) +data <- list(lowercase=letters, uppercase=LETTERS) +

Re: [Bioc-devel] Changing package names

Please reconsider. The names of your packages enter components of a metadata collection that must be manually altered by our core development staff to accommodate package name changes. While it is easy to change names of entities in programs and local file systems, our package ingestion, review,

Re: [Bioc-devel] Large data frames in inst/extdata

If the data frames are outcomes of experiments (wet lab or computational) use ExperimentHub If annotation, use AnnotationHub Submission instructions for these Hub contributions are available at, e.g.,

Re: [Bioc-devel] Could anyone help me to fix it?

see entry 16 here https://bioconductor.org/developers/how-to/git/faq/ On Wed, Jul 28, 2021 at 6:32 AM Guo Kai wrote: > Hi, > I git an error: > Load key "/Users/bioguo/.ssh/id_rsa.pub": bad permissions > g...@git.bioconductor.org : Permission > denied

Re: [Bioc-devel] pre-receive hook declined

hi you can't update 3.12 3.x is frozen when 3.(x+1) becomes release perhaps the error message can be clarified On Tue, Jul 27, 2021 at 3:44 PM Clay Wright wrote: > Hi, > > I am now encountering the following similar error trying to push a bugfix > to my package. Does my account also need a

Re: [Bioc-devel] MOFA2 build error

It's good that it works on the other platforms. We will look at this failure closely. On Mon, Jul 26, 2021 at 2:35 AM Britta Velten wrote: > Dear all, > > We are currently experiencing a build error in the dev version of MOFA2 on > merida1. > >

Re: [Bioc-devel] Getting ready for package submission, running into a couple of errors/warnings that I can't figure out

On Mon, Jul 12, 2021 at 5:58 PM Wight, Andrew E. < andrewe_wi...@dfci.harvard.edu> wrote: > Good evening all - I'm getting my first package ready for submission to > Bioconductor, and I'm running into a couple of errors/warnings when I run R > CMD CHECK or BiocCheck. All of my current

Re: [Bioc-devel] Package did not update after push

Your changes are present in Bioconductor git. The next available build report should reflect their effects. On Mon, Jul 5, 2021 at 7:49 AM Fabricio de Almeida < fabricio_almeidasi...@hotmail.com> wrote: > Hi, all. > > I pushed a simple bug fix to my package BioNERO on Friday, but the Bioc >

Re: [Bioc-devel] Build error

Thanks for your note. I had a look at your vignette and found devtools::install_github('christophergandrud/repmis') That's not permitted. repmis is on CRAN and seems synced with the github repo, so please take this out. You also have a download event in the vignette. > source_data("

Re: [Bioc-devel] pre-receive hook declined

are you using wvictor14 On Wed, Jun 30, 2021 at 1:41 PM Victor Yuan wrote: > Hi I cannot seem to push to the remote g...@git.bioconductor.org: > packages/GSE159526 > > I get a "pre-receive hook declined" error: > > > $ git push upstream master > Enumerating objects: 21, done. > Counting

Re: [Bioc-devel] Build report page is not updated, DOI leads nowhere

On Sat, Jun 26, 2021 at 6:18 PM Oleksii Nikolaienko < oleksii.nikolaie...@gmail.com> wrote: > Dear Bioc team, > I recently pushed changes to the release branch and was waiting for > http://bioconductor.org/checkResults/release/bioc-LATEST/ramr/ page to > reflect them. Strangely, this page does

Re: [Bioc-devel] pairwiseAlignment strings too long?

On Fri, Jun 18, 2021 at 5:06 AM csmatyi via Bioc-devel < bioc-devel@r-project.org> wrote: > Hello, > > I am trying to align two sequences, in DNAString format using the R > command pairwiseAlignment. > I keep getting this error: > > pairwiseAlignment(si,sj) > Error in

Re: [Bioc-devel] bug fix push to Release 3.13 not working for wpm package

Notice that the pull date for https://bioconductor.org/checkResults/3.13/bioc-LATEST/ is 6/15. Your pushes to RELEASE_3_13 are sound and on my platform vers 1.2.1 of your package checks out fine in release. We have reduced the frequency of build/check in release branch as most sources there do

Re: [Bioc-devel] Need Information about Sheep

Dear Salsabeel Yousuf, Please use support.bioconductor.org for questions of this kind. In fact, the question was posed there five years ago: https://support.bioconductor.org/p/84686/#84690 I will add a comment to that support.bioconductor.org response to bring it up to date. Please check

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

mand-line R (ie started from bash shell) but not > in Rstudio but perhaps they have different ways of caching loaded MAE > objects? > Best,Shraddha > I neglected to mention that my transcript was developed in RStudio on Terra, with RStudio 1.4.1106, 2389bc24 > > On Wed, Jun

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

You are behind the release and should update. However, with a reasonably close instance I can't reproduce your error. I had a flaky download at one point; you might want to reconstitute your brca data. > brca = curatedTCGAData("BRCA", c("miRNASeqGene", "mRNAArray", "RPPAArray", >

Re: [Bioc-devel] Genomics Extension for SQLite seeking R/bioC co-maintainer

Thanks Mike, we're having a look. I haven't found much comparative benchmarking data by prowling around your site ... am I missing anything? The colab notebook is helpful. On Tue, Jun 1, 2021 at 5:07 AM Mike Lin wrote: > Dear all, > > I'm writing in hopes of recruiting an R/Bioconductor

Re: [Bioc-devel] About the size limitation of the package

On Wed, May 26, 2021 at 5:55 PM Stuart Lee wrote: > Hi You and Lori, > > Are fitted models in scope for ExperimentHub? I thought it was more for > data. Maybe there should be a ModelHub for developers to include trained > models from papers in their packages? > > @You: if that model has been

Re: [Bioc-devel] VariantAnnotation Installation Compile Error

On Sun, May 23, 2021 at 10:00 PM Dario Strbenac wrote: > Good day, > > I apparently have a valid Bioconductor package library but > VariantAnnotation won't install successfully. > > > valid() > [1] TRUE > > install("VariantAnnotation") > Bioconductor version 3.13 (BiocManager 1.30.15), R 4.1.0

Re: [Bioc-devel] VariantAnnotation Installation Compile Error

Thanks for the report. I just installed from source successfully with > sessionInfo() R version 4.1.0 Patched (2021-05-23 r80366) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04 LTS (fossa-melisa X20) Matrix products: default BLAS:

Re: [Bioc-devel] EnMCB reduce dependencies

IlluminaHumanMethylation450kanno.ilmn12.hg19 is primarily a collection of data.frames isn't it? I notice that the Illum...anno... package itself depends on minfi, which seems unnecessary. But perhaps Kasper will comment. On Fri, May 21, 2021 at 5:32 AM xin wwa wrote: > Dear Bioconductor team,

Re: [Bioc-devel] reproducing the BioC package error

On Wed, May 12, 2021 at 6:14 AM Venu Thatikonda wrote: > Hello all, > > I am trying to reproduce the build error of my package > > > https://master.bioconductor.org/checkResults/3.13/bioc-LATEST/ALPS/nebbiolo1-buildsrc.html > > As I understand, BioC 3.13 uses R 4.1. However, it seems R 4.1.0 is

[Bioc-devel] avoid updating BiocManager to 1.30.13; provisional fix available

A problem has been observed with the version of BiocManager currently available at CRAN. Do not upgrade to 1.30.13. If you have already done so, please use devtools::install_github("Bioconductor/BiocManager", ref="ghost-binary-repo" ) and restart R; this will provide BiocManager 1.30.13.1 If

Re: [Bioc-devel] Can't install Bioconductor 3.13 under Windows 10

This is a known problem and is being investigated. Thanks for the report. On Sat, May 8, 2021 at 8:18 AM Gordon K Smyth wrote: > I am currently unable to install any Bioconductor 3.13 packages using > BiocManager for Windows. Here is a sample R session using R 4.1.0beta for > Windows. Notice

Re: [Bioc-devel] R CMD CHECK warning -

I'd suggest that this topic be dealt with on the associated contribution issue. Please report sessionInfo() when discussing warnings. I will now make some comments on the contribution issue as I am trying to follow up your concerns. Thanks On Tue, Apr 27, 2021 at 3:07 AM alan murphy wrote:

Re: [Bioc-devel] biocLite not installing

Dear Dr Diaz: This email list is for development of software in Bioconductor. Questions about basic functionality should go to support.bioconductor.org -- please visit that site and make an account. For your specific question please note the message >

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

gt; if(all(moveres)) unlink(olddir, recursive=TRUE) > ah = AnnotationHub() # try again snapshotDate(): 2021-03-15 On Wed, Apr 7, 2021 at 12:03 PM Vincent Carey wrote: > For convenience here are relevant sections of the new vignette. Give it > a try and let us know. This is

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

For convenience here are relevant sections of the new vignette. Give it a try and let us know. This is "devel". 4Default Caching Location Update As of BiocFileCache version > 1.15.1, the default caching location has changed. The default cache is now controlled by the function

Re: [Bioc-devel] docker build failure when installing dependencies

note that diffcyt does not currently build at https://bioconductor.org/checkResults/3.13/bioc-LATEST/ -- its errors need to be repaired for your build to succeed On Tue, Mar 9, 2021 at 11:07 AM Reto Gerber via Bioc-devel < bioc-devel@r-project.org> wrote: > Dear all, > > I would like to

Re: [Bioc-devel] Moving minfi classes definition to a lighter package

i advocated pkgnet and included a png but email seems to have been rejected On Wed, Mar 3, 2021 at 7:29 AM Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > I am happy to engage in a discussion about this, although I'm not sure that > I am ultimately interested in having two

Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

My understanding is that we will not permit dependencies outside of Bioc or CRAN. If a repository is created that is at least as rigorous in package admission as CRAN, perhaps it needs to be considered. If there are details known about alternate repositories that we should learn about, please

Re: [Bioc-devel] Devel version of R for package development

On Tue, Feb 23, 2021 at 11:25 AM Matesi, Gregory < gregory.mat...@ucdenver.edu> wrote: > Hello all, > > I had a question about package development using the devel version of > bioconductor. We are encouraged to add dependence to the version of R that > is used by the devel branch of Bioconductor,

Re: [Bioc-devel] EWCE Bioconductor package

EWCE may need to be reviewed for reinclusion. I tried to check on R-devel with the repo you mentioned. Do you have a current personal repo that passes check with Bioc 3.13/R-devel? Quitting from lines 220-223 (EWCE.Rmd) Error: processing vignette 'EWCE.Rmd' failed with diagnostics: Invalid

Re: [Bioc-devel] EWCE Bioconductor package

Please disregard my note. As Lori has indicated formal review must proceed before reinclusion. On Thu, Feb 11, 2021 at 9:51 AM Vincent Carey wrote: > EWCE may need to be reviewed for reinclusion. I tried to check on R-devel > with the repo you mentioned. Do you > have a current pers

Re: [Bioc-devel] How to integrate code from a package not available on bioconductor

It is wise to be careful here. If we don't know the provenance of the code in github it might actually be someone else's. It reminds me of the Numerical Recipes events, in which folks redistributed proprietary code without permission. What repo are we talking about anyway? On Wed, Feb 10, 2021

Re: [Bioc-devel] How to integrate code from a package not available on bioconductor

On Wed, Feb 10, 2021 at 8:32 AM Kern, Lori wrote: > Have you reached out to the maintainer of the github package to see if > they would plan on submitting to CRAN or Bioconductor? > If they do not, you could see if they are okay with you including the > code in your package and then clearly

Re: [Bioc-devel] How to replace KEGG.db

I did a little work in this area, relieving GenomicRanges of dependency on KEGG.db. For your example, which does not run (?), I would suggest a) avoiding the use of the old environments like hgu95av2PATH2PROBE, replacing this with AnnotationDbi::select calls b) replace the KEGG.db invocations

Re: [Bioc-devel] Warnings about man pages for assignment operators on Windows builds

Hi Stephanie I see similar problems for GenomicFiles, so it is not a problem unique to your package. I was not able to generate this error with r79717 in Windows 10, so I conjecture that this will go away when the R-devel for windows is upgraded. Best regards Vince On Tue, Dec 29, 2020 at 1:58

Re: [Bioc-devel] Missing knitcitations package on devel for PharmacoGx

This problem has been recognized: https://github.com/cboettig/knitcitations/issues/107 In a few days it will likely clear. On Wed, Nov 25, 2020 at 10:26 PM Eeles, Christopher < christopher.ee...@uhnresearch.ca> wrote: > Hello Bioc community, > > I am the maintainer for PharmacoGx and have

[Bioc-devel] apologies

my email "topics sought ..." was not intended for this list, but i welcome direct contact from anyone who is interested in it -- The information in this e-mail is intended only for the ...{{dropped:18}} ___ Bioc-devel@r-project.org mailing list

[Bioc-devel] topics sought for bioc tab discussion dec 3 2020

Hi -- I know this is an inopportune moment for many but I just wanted to reach out to the TAB to ask for topics of interest. Mike Love and colleagues will be discussing *Hubs in the TAB talk section, but there is time for other concerns. We do plan to discuss handling .github/workflow folders in

Re: [Bioc-devel] RCurl on Windows

le error. Anyway, there isn't a current version on > Github (there is a two-year old version at github.com/cran/RCurl), so > there isn't a more interactive way to report the error. > > On Mon, Nov 23, 2020 at 12:20 PM Vincent Carey > wrote: > >> I reproduced the problem yo

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