[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,

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

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

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

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

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

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

[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

Re: [Bioc-devel] printing GRanges fails

ctor.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 class GRanges, but

[Bioc-devel] printing GRanges fails

] "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 Nikolaienko

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

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

t 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. If it were me, and again I &g

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

quot; > 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 > - it

[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

g 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-project.org on behalf of >

[Bioc-devel] C++ parallel computing

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 [[alternative HTML versi

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

ently 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 4/5/21 1:12 PM, Ole

[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