Re: [Bioc-devel] Unexpected Build Failure for BulkSignalR

Thanks for your note. I don't know that bioc-devel is a great venue to discuss this event for a particular package. Nor am I completely clear on what platform-specific failures imply for package acceptance etc., but it seems to me the package is part of 3.21 and hence implicitly for 3.22. Finall

Re: [Bioc-devel] Issue Installing hugene10stv1cdf on R 4.4.2

please provide the full log of error events, esp. when you try to install from source. a typical problem is that the download time is too long and you get an incomplete package image. options(timeout=3600) might help. be sure to use a nearby mirror if possible. On Mon, Jan 13, 2025 at 7:16 AM Sa

Re: [Bioc-devel] Testing the srnadiff package with R CMD check takes lots of time

I tried running your tests (checked out from github repo at commit e580d52d7242693b79ec6b8483d68a65d6fb9e02 (HEAD -> master, origin/master, origin/HEAD) Author: Matthias Zytnicki Date: Mon Mar 6 21:35:41 2023 +0100 version bump and ran into some serious issues -- a very long stream of >

Re: [Bioc-devel] support.bioconductor.org very slow

Thanks to you both and sorry for the inconvenience, Gordon. We have been working on reducing cloud expenses in various directions. This has been important because of an across-the-board budget cut at NIH -- we lost 17% of our expected budget. I do not think there was an intentional reduction in

Re: [Bioc-devel] Error in SVMDO Package

On Sun, Aug 25, 2024 at 3:33 PM MUSTAFA ERHAN ÖZER via Bioc-devel < bioc-devel@r-project.org> wrote: > Good day, > > The recent Multiple platform build/check report for BioC 3.19 of SVMDO > package resulted in error for every platform. > > The error is " Error in `get_anno_data(ontology)`: ontolog

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 Pr

[R-pkg-devel] debugging R CMD build

https://bioconductor.org/checkResults/3.20/bioc-LATEST/velociraptor/nebbiolo2-buildsrc.html shows an error arising in R CMD build that cannot be reproduced in manual attempts with the vignette code that is triggering the error. "It works fine except in CMD build" (on linux). I have tried debuggi

Re: [Bioc-devel] Remote BigWig file access

an's lab from a few years ago > which was explicitly designed to replace bigwigs: > https://www.nature.com/articles/s43588-021-00085-0 > > All that said, we're pretty committed to bigwigs at this point given the > ~750,000 sequence runs we've encoded using them for reco

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 for

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, we

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 https://bioconductor.org/packages/release/bioc/vignettes/UniProt.ws/inst/doc/UniProt.ws.html

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 > respo

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 CYTB4

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: > > > https://github.com/klausju

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 v

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 buil

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 &g

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 at

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: x86_64-pc-linux-gn

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

7;t believe a different OrgDb is required. The OrgDb package is meant > to provide annotations for genes such as gene symbol or GO term, etc, which > are orthogonal to the sequence of the genome, so the current version should > suffice. > > -Original Message- > From: B

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 https://s3-us-west-2.amazonaws.com/human-pangenomics/inde

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/ > I

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 Windows/M

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

h every version of > tensorflow > >> = 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 exp

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

only 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. Ou

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 a

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': ‘...’ F

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 fea

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 http://con

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: > "the

Re: [Bioc-devel] rifiComparative

In RELEASE_3_17 branch your vignette has devtools::load_all(".") I don't know why that would be necessary. 1.0.0 in the RELEASE_3_17 branch does not have devtools in Suggests. On Sun, May 21, 2023 at 3:53 PM Loubna Youssar wrote: > Hello, > > I am the developer and maintainer of rifiComparat

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 questio

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 anythin

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 install

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 th

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 change

Re: [Bioc-devel] Large vignettes

oc rot are first-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 re

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 ARM64-bas

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 so

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 w

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 c

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

push-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 &

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: > Dea

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 method

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 i

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 rele

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 > https://bioconductor.org/packages/devel/data/annotation/html/CTCF.htm

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 t

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 c

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 2

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, 2022

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: > https://bioconductor.org/checkResults/3.15/bioc-LATEST/DSS/palomino3-buildsrc

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/ sta

[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, and

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 O

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 locale

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

d on Windows) > >BridgeDbR > > > >CHRONOS > > > >debCAM > > > >esATAC > > > >gaggle > > > >Onassis > > > >ReQON > > > >RGMQL > > > >rmelting > > > >sarks

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

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; implementat

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 may

[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 entire

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) +json.retu

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, c

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., https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHubData/inst/doc/ExperimentHu

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 (publickey)

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 simi

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. > > http://bioconductor.org/checkResults/devel/bioc-LA

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 troubleshoot

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 > page

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(" https://g

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 obj

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 not

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 .Call2("XStringSet_align_pair

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 not

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 there.

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", > "Methylation_m

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 co-mai

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 fitt

Re: [Rcpp-devel] efficient ingestion of "sparse csv"

On this theme, the following proved sufficient to ingest and convert sparse csv without column headers or row names: #include "RcppArmadillo.h" using namespace Rcpp; // [[Rcpp::depends(RcppArmadillo)]] // [[Rcpp::export]] List parse_sparse_csv_impl(SEXP fname) { using namespace Rcpp; std::strin

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 (2

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: /home/stvjc/R-4-1-dist/lib/R/lib/libRblas.s

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,

[R-SIG-Mac] tcltk on M1 mac?

I can't seem to get tcltk running with R on M1 machine. Homebrew tcltk seems to have wrong architecture; attempt to build from source does not help. Any hints appreciated. R version 4.1.0 RC (2021-05-10 r80283) -- "Camp Pontanezen" Copyright (C) 2021 The R Foundation for Statistical Computing

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 n

Re: [Rcpp-devel] efficient ingestion of "sparse csv"

Thanks Dirk, lots of useful information there. I wonder whether the sparse ingestion problem would best be solved with multiple passes -- it seems one would want to learn the dimensions and the number of nonzero elements per row to allocate the index vectors, and then populate them and the data ve

[Rcpp-devel] efficient ingestion of "sparse csv"

This problem has been discussed in various places but I don't see a clear solution. Certain applications are generating large comma-delimited files with mostly zero entries. The aim is to ingest efficiently, converting to sparse representation a record at a time. Presumably a triplet format woul

[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 y

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 th

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 > source("https://bioconductor.org/biocLite.

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