[Bioc-devel] Bioconductor Developers Forum - Thursday 16th July

Dear all, The next Bioconductor Developers' Forum is scheduled for Thursday 16th July at 09:00 PDT/ 12:00 EDT / 18:00 CEST Calendar invite available from https://bit.ly/3gCsFXO We will be using BlueJeans and the meeting can be joined via: https://bluejeans.com/114067881 (Meeting ID: 114 067 881)

Re: [Bioc-devel] Unable to replicate Windows build error on new package.

Your reviewer should be aware to ignore the error and will review your package shortly. Cheers Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] Unable to replicate Windows build error on new package.

Thanks, Do I need to bump the version or do anything to trigger a rebuild or just wait for review now? -Original Message-From: "Shepherd, Lori" To: Erik Christensen , bioc-devel@r-project.org Subject: Re: [Bioc-devel] Unable to replicate Windows build error on new package.Date: Mon,

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Fantastic - thankyou Herve! Aditya From: Hervé Pagès [hpa...@fredhutch.org] Sent: Tuesday, July 07, 2020 11:55 AM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel? On 7/7/20

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

On 7/7/20 02:50, Hervé Pagès wrote: On 7/7/20 02:46, Bhagwat, Aditya wrote: Thankyou Herve! I guess that means that I can pull the fix in a day or two, is that right? Yes, as soon as BSgenome 1.57.4 propagates, which should take between 24h and 48h. To be clear: BSgenome 1.57.4 will

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

On 7/7/20 02:46, Bhagwat, Aditya wrote: Thankyou Herve! I guess that means that I can pull the fix in a day or two, is that right? Yes, as soon as BSgenome 1.57.4 propagates, which should take between 24h and 48h. H. Aditya From: Hervé Pagès

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Thankyou Herve! I guess that means that I can pull the fix in a day or two, is that right? Aditya From: Hervé Pagès [hpa...@fredhutch.org] Sent: Tuesday, July 07, 2020 11:45 AM To: Bhagwat, Aditya; bioc-devel@r-project.org Subject: Re: [Bioc-devel]

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Hi Aditya, This change was not intended, sorry. Should be fixed in BSgenome 1.57.4. Cheers, H. On 7/7/20 01:53, Bhagwat, Aditya wrote: Sorry, my earlier email had a copy/paste error - corrected now From: Bioc-devel [bioc-devel-boun...@r-project.org] on

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Sorry, my earlier email had a copy/paste error - corrected now From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Tuesday, July 07, 2020 10:50 AM To: bioc-devel@r-project.org Subject: Re:

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

It's the BSgenome to GenomeDescription coercer that seems to be missing - is this on purpose? # bsgenomeName(BSgenomeObj) FAILS #--- bsname <- GenomeInfoDb::bsgenomeName(bsgenome) index_genome(bsgenome, indexedgenomesdir = tempdir()) Error in

[Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Dear bioc-devel, multicrispr is having an error on the bioc-devel build machines, caused by: unable to find an inherited method for function 'bsgenomeName' for signature '"BSgenome" This is a bit