[Bioc-devel] possible ld issues at palomino7

Hi Bioc team, my and several other packages (Rhtslib , bamsignals

Re: [Bioc-devel] groHMM package error

Hi, don't know much about it, but at least to a certain extent your errors might be connected to this . Best, Oleksii On Tue, 10 Dec 2024 at 22:32, Tulip Nandu wrote: > Hi, > I solved the error of decideTests() but now there is a w

Re: [Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

ith libstdcxx)). > But then it appeared that adding ~/miniforge3/lib to LD_LIBRARY_PATH > breaks dnf/yum ... > Now I reworked the way miniforge3/lib is exposed to the builder and it > should be OK again! > Thanks for reporting it! > > Martin > > On Thu, Oct 24, 2024 at 7:20

Re: [Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

Hi Martin, sorry to bother, but there's some other issue <https://bioconductor.org/checkResults/devel/bioc-LATEST/epialleleR/kunpeng2-buildsrc.html> now, possibly related to conda as well. Could you please have a look? Best, Oleksii On Wed, 23 Oct 2024 at 11:14, Oleksii

[Bioc-devel] Error on palomino8

Dear Bioc team, my package check fails on palomino8 only and I'm not sure how to approach it. Looks like the unit test task gets killed (or segfaults) - but unfortunately no usable message is shown. It migh

Re: [Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

Thanks very much! Oleksii On Wed, 23 Oct 2024 at 10:52, Martin Grigorov wrote: > Hi Oleksii, > > On Wed, Oct 23, 2024 at 9:47 AM Oleksii Nikolaienko < > oleksii.nikolaie...@gmail.com> wrote: > >> Hi Martin, >> could you please also install libz-dev or zli

Re: [Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

Hi Martin, could you please also install libz-dev or zlib1g-dev (not sure which one is needed)? - https://bioconductor.org/checkResults/devel/bioc-LATEST/epialleleR/kunpeng2-install.html Best, Oleksii On Wed, 23 Oct 2024 at 08:33, Martin Grigorov wrote: > Hi, > > The problem was missing rustc

Re: [Bioc-devel] pkgdown::build_site_github_pages fails with "Quarto articles require Bootstrap 5"

Thanks again for suggestions. Issue was on my side and I fixed it by adding _pkgdown.yml with usethis::use_pkgdown() Best, Oleksii On Thu, 10 Oct 2024 at 15:52, Oleksii Nikolaienko < oleksii.nikolaie...@gmail.com> wrote: > Thanks for the quick reply. > I do not have a ./pkg

Re: [Bioc-devel] pkgdown::build_site_github_pages fails with "Quarto articles require Bootstrap 5"

reason? Best, Oleksii On Thu, 10 Oct 2024 at 15:43, Louis Le Nézet wrote: > Hi, > > Did you add in your /mypackage/pkgdown/_pkgdown.yml: > > ```yml > template: > bootstrap: 5 > ``` > > Best, > Louis > > -Message d'origine- > De : Bio

[Bioc-devel] pkgdown::build_site_github_pages fails with "Quarto articles require Bootstrap 5"

I apologise if the reason for this error will be outside the scope of this list, but I'd appreciate it if someone can help me to identify it. >From today (more likely yesterday) check-bioc Github action that uses "bioconductor/bioconductor_docker:devel" container fails during pkgdown::build_site_gi

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

> Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ---------- > *From:* Bioc-devel on behalf of > Oleksii Nikolaienko > *Sent:* Thursday, Augus

[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] No cairo device on merida1

Dear Bioc team, my package is failing on merida1 with the message "svg: Cairo-based devices are not available for this platform". I didn't find relevant issues at https://github.com/Bioconductor/BBS, therefor

Re: [Bioc-devel] Omada package failing due to removed dependency

>> >> Roswell Park Comprehensive Cancer Center >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> -- >> *From:* Bioc-devel on behalf of >>

Re: [Bioc-devel] Omada package failing due to removed dependency

Hi, in this case maybe it's worth reaching out to the maintainer of clusterCrit. It was removed from CRAN because of (seems-to-be) minor warnings, which can be addressed by the clusterCrit developer in no time... Best, Oleksii On Thu, 29 Jun 2023 at 08:44, Sokratis Kariotis wrote: > Dear Biocon

Re: [Bioc-devel] RforProteomics: vignette error - cannot find the file(s)

Hi, I wonder if it's because the entire "vignettes/figures" is not pushed to Bioc git (it's included in your .gitignore). And the previous chunk does not re-create the figure. Best, Oleksii On Fri, 28 Apr 2023 at 15:24, Laurent Gatto wrote: > I am puzzled by this error: > > The vignette fails

Re: [Bioc-devel] Fwd: philr problems reported in the Multiple platform build/check report for BioC 3.17

Hi, looks like the latest commit to the relevant code in package mia has changed the arguments of makePhyloseqFromTreeSummarizedExperiment (makeP

Re: [Bioc-devel] Missing dependency errors on nebbiolo1 (Bioc 3.17)

Hi, maybe because BiocStyle is not listed as a dependency or suggested package in DESCRIPTION? More info here: https://github.com/Bioconductor/BBS/issues/248 Best, Oleksii On Tue, 4 Apr 2023 at 11:22, Rainer Johannes wrote: > Dear all, > > I'm continuing to see some strange dependency problems

[Bioc-devel] Warnings in "checking compiled code" of R CMD check

Hi all, it seems that the devel version of R CMD check has raised the level of messages in "checking compiled code" from NOTE to WARNING. My package contains entry points for abort, exit, stdout, stderr and s

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

I don't know if this has been mentioned, but the following pages are of an immense help: https://mac.r-project.org/ https://mac.r-project.org/openmp/ It is possible and quite easy to get a native M1 build of R with OpenMP support and no issues with Bioc packages. Best, Oleksii On Sun, 20 Feb 2022

[Bioc-devel] BiocCheck fails during Github action workflow

Hi, this question probably relates to Bioc docker images, thus asking here first. I am using biocthis GitHub action and I recently noticed that it started to fail with a BiocCheck message: "ERROR: dependencies ‘Genomi

Re: [Bioc-devel] printing GRanges fails

//bioconductor.org/developers/how-to/git/ > > Cheers, > H. > > > On 21/11/2021 07:28, Oleksii Nikolaienko wrote: > > Hi, > > devel branch of my package (ramr) cannot be built due to an error which I > > don't understand. Package has sample data of cla

[Bioc-devel] printing GRanges fails

;) [1] "GenomicRanges" > ramr.data GRanges object with 3000 ranges and 100 metadata columns: Error: C stack usage 7954616 is too close to the limit This object seems to be ok in the release branch. Could anyone advise me on further steps, please? Best regards, Oleksii Nikolaie

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

wonder if this can be fixed. Best regards, Oleksii Nikolaienko [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] SplicingFactory: problem with release bugfix build

Hi Endre, I guess it's because it hasn't been built yet. I'm also waiting for the build, but it looks like it happens once in three days, is that correct? Best, Oleksii On Fri, 25 Jun 2021 at 22:56, Endre Sebestyen wrote: > Hi all, > > I fixed some bugs in our package SplicingFactory, both for

Re: [Bioc-devel] C++ parallel computing

() or reduceByFile() might be relevant. > > I am not totally current (others on this list probably know more) but I > don't think openMP is supported on MacOS ( > https://mac.r-project.org/openmp/) so would be a poor choice at the C > level if cross-platform utility were important.

Re: [Bioc-devel] %outside% on GRanges

ot;Vector" > query="IntegerRangesList", subject="IntegerRangesList" > query="Vector", subject="missing" > query="Vector", subject="Vector" > > So far as I can tell there is no code in GenomicRanges to make this happen

[Bioc-devel] %outside% on GRanges

; IRanges::`%outside%`(ranges(a), ranges(b)) [1] FALSE It is correct and intuitive, but %outside% does not seem to be defined or included in help pages of the GenomicRanges library. Can I rely on such behaviour of %outside% in the future? Best, Oleks

Re: [Bioc-devel] C++ parallel computing

ht be worth outlining in a bit more detail what your task is and how > (not too much detail!) you've tried to implement this in Rsamtools. > > Martin Morgan > > On 5/24/21, 10:01 AM, "Bioc-devel on behalf of Oleksii Nikolaienko" < > bioc-devel-boun...@r-proj

[Bioc-devel] C++ parallel computing

y Big Sur/ARM64, but I wouldn't want to drop its support anyway. (On the actual task: loading and specific processing of very large BAM files, ideally significantly faster than by means of Rsamtools as a backend) Best, Oleksii Nikolaienko [[alterna

Re: [Bioc-devel] non-subsettable GRanges object

; > recently because of some minor refactoring of the rbind() method for > > DataFrame objects that I made a few days ago in S4Vectors. > > > > I'm working on a fix and will let you know when it's ready. > > > > Cheers, > > H. > > > > > > On

[Bioc-devel] non-subsettable GRanges object

Dear Bioc team, my package has started to fail during the build check ( http://bioconductor.org/checkResults/devel/bioc-LATEST/ramr/). I tried to figure out why and it appears that I somehow make GRanges object non-subsettable. Could anyone from "GenomicRanges" developers look at my issue and advis