Re: [Bioc-devel] check fails on arch 'i386'

Many thanks Kasper, this would be much appreciated. Best, Tim On 18/10/19 12:58 am, Kasper Daniel Hansen wrote: I see these packages may have something to do with mini. There is a a (very old, nothing new) issue with the annotation objects in minfi where loading them uses a _lot_ of ram. For a

Re: [Bioc-devel] Citation not updating

Hi David, It took me a while to figure this out but at the root of the problem is the non-conformance of your CITATION file. The problem is that it contains a call to packageVersion() which is not allowed in CITATION files. Here is what the "CITATION files" section of the "Writing R

Re: [Bioc-devel] Error with compiling Rhtslib

You're using R-devel, whereas Bioconductor is using R-3.6.x for both our release and devel branches. Consequently, you're being required to compile from source, rather than using the pre-built binaries. For this reason, your system needs to have the necessary libraries and their headers; this

Re: [Bioc-devel] Error with compiling Rhtslib

This isn't a bioc-devel question. This listserv is intended for people with package development questions, not general problems, which should be asked on the support site. And when I Google 'lzma.h' (which you could do as well), one of the answers is

[Bioc-devel] Error with compiling Rhtslib

Hi, It looks like Rhtslib can not be compiled for R_devel and the main error message says: cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found Please see details below: > BiocManager::install("Rhtslib") Bioconductor version 3.10 (BiocManager 1.30.8), R Under development (unstable)

Re: [Bioc-devel] Unable to reproduce chimeraviz 3.10 build failure

Thank you for the help. I'm still unable to reproduce the error. I'm working from the docker image bioconductor/devel_core2 (the latest version at the time of writing). Opening the R session I see this: ``` R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation

[Bioc-devel] Error in OmnipathR package

Dear all, The package OmnipathR has returned an error when running R CMD check in windows. https://bioconductor.org/checkResults/3.10/bioc-LATEST/OmnipathR/tokay1-checksrc.html No issues detected in Linux/MAC. It seems that the tests/examples run significantly slower in Windows. Could you

Re: [Bioc-devel] package has been cleaned for large data files and needs to be reset.

I believe we have reset it. Please really look at the documentation http://bioconductor.org/developers/how-to/git/ If you set up remotes to be linked to Bioc, please always remember to pull from bioc before making changes git pull upstream master # make changes # push to both git push #

[Bioc-devel] Might be worth following thread on R mailing lists

Hi I spotted this thread on the R-mailing list and thought it might be worth following as it might impact Bioc-Tidyverse users Aedin Message: 5 Date: Thu, 17 Oct 2019 10:28:45 +0100 From: Jocelyn Ireson-Paine To:r-h...@r-project.org Subject: [R] Surprisingly large amount of memory used by

Re: [Bioc-devel] caught segfault when compiling ensembldb

It's hard to tell from the stack trace, but is this reproducible in a new R (devel) session with loadNamespace("ensembldb") ? And did you actually install new packages in R-devel, or only re-use packages installed in an earlier version of R? If the latter, then definitely you'll want to

Re: [Bioc-devel] caught segfault when compiling ensembldb

A preliminary insight is that it looks like you're using R-devel (aka R-4.0), whereas at the moment (until the next Bioconductor release in a couple of weeks...) the 'supported' devel version of Bioconductor uses R-3.6.*. Martin On 10/17/19, 10:10 AM, "Bioc-devel on behalf of Zhu, Jack

[Bioc-devel] caught segfault when compiling ensembldb

Dear all, I have encountered a very frustrating 'memory not mapped' problem when compiling ensembldb package: >BiocManager::install("ensembldb", ask = FALSE) Bioconductor version 3.10 (BiocManager 1.30.8), R Under development (unstable) (2019-10-15 r77295) Installing package(s) 'ensembldb'

Re: [Bioc-devel] check fails on arch 'i386'

I see these packages may have something to do with mini. There is a a (very old, nothing new) issue with the annotation objects in minfi where loading them uses a _lot_ of ram. For a long time I couldn't understand it, but now I get it. I should really fix this, and probably _very_soon. It won't

Re: [Bioc-devel] plyranges group_by

Thank you Michael, In attach the example file, since I noticed you were unable to download it from gitlab. Will continue the discussion there, then :-) Aditya From: Michael Lawrence [lawrence.mich...@gene.com] Sent: Thursday, October 17, 2019 11:45 AM To:

Re: [Bioc-devel] package has been cleaned for large data files and needs to be reset.

Dear Lori, dear Bioconductor team, I have re-cleaned the repository, could you please run the tests again and reset the upstream? Thank you very much for the support. Best regards, Jelena Čuklina. On 16 Oct 2019, 16:01 +0200, Shepherd, Lori , wrote: Hi Jelena, I was running some checks on

Re: [Bioc-devel] plyranges group_by

I replied on the support site. Let's move the discussion there. On Thu, Oct 17, 2019 at 1:24 AM Bhagwat, Aditya < aditya.bhag...@mpi-bn.mpg.de> wrote: > Thank you Stuart and Michael for your feedback. > > Stuart, in response to your request for more context regarding my use > case, I have

Re: [Bioc-devel] Bioconductor Developers Forum - Thursday 17th October

Dear all, Just as a reminder, the next call is scheduled for today (Thursday 17th October) at 09:00 PDT/ 12:00 EDT / 18:00 CEST We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/528142528 (Meeting ID: 528 142 528) Best wishes, Mike On Thu, 10 Oct 2019 at

Re: [Bioc-devel] plyranges group_by

Thank you Stuart and Michael for your feedback. Stuart, in response to your request for more context regarding my use case, I have updated my recent BioC support post, now providing all use-case details. Michael, I didn't selfmatch yet, but Stuart's

Re: [Bioc-devel] check fails on arch 'i386'

Hi Hervé (and Reka), I am having much the same problem on tokay1 with DMRcate (https://bioconductor.org/checkResults/3.10/bioc-LATEST/DMRcate/tokay1-checksrc.html). I've gone through a number of iterations trying to minimise the amount of memory run by the examples (including your suggestions