Re: [Bioc-devel] is it possible to disable i386 builds on bioconductor

kResults/3.12/bioc-LATEST/ChemmineOB/ > > Cheers, > H. > > > On 3/17/21 10:23 AM, Thomas Girke wrote: > > Awesome, thanks! > > > > On Tue, Mar 16, 2021 at 11:40 PM Hervé Pagès > <mailto:hpages.on.git...@gmail.com>> wrote: > > > > Hi T

Re: [Bioc-devel] is it possible to disable i386 builds on bioconductor

iding openbabel3 for Ubuntu 18.04. Will take a > > look ASAP. > > > > @Thomas: Yes, the Ubuntu 18.04 builds are only used for the BioC 3.12 > > builds (release). BioC 3.13 and further BioC releases are/will be using > > Ubuntu >= 20.04. > > > > Best, > > H.

Re: [Bioc-devel] is it possible to disable i386 builds on bioconductor

> let us know and we will do that. The best thing would be to be able to > > use a .deb package for this. The easiest the procedure, the more > > likely people that are still using Ubuntu 18.04 will be able to > > install ChemmineOB. > > > > Best, > > H. > > > &

Re: [Bioc-devel] is it possible to disable i386 builds on bioconductor

in isolation. > > Thanks > > Kevin > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > ___ > Bioc-devel@r-projec

Re: [Bioc-devel] Additional developer

log in > to BiocCredentials and activate your account. > > Best, > > Nitesh > > > On Dec 17, 2018, at 9:53 PM, Thomas Girke wrote: > > > > Dear Nitesh, > > > > Could you please add a new developer to my BioC packages systemPipeR and > > systemP

[Bioc-devel] Additional developer

Dear Nitesh, Could you please add a new developer to my BioC packages systemPipeR and systemPipeRdata to provide commit/push access for the corresponding git repositories on git.bioconductor.org. The person's name is Daniela Cassol (new postdoc in my group) and her email is danicas...@gmail.com.

Re: [Bioc-devel] ShortRead::countLines integer overflow with large fastq files

Great thanks! Thomas On Wed, Feb 21, 2018 at 3:11 AM Martin Morgan <martin.mor...@roswellpark.org> wrote: > Thanks Thomas, countLines() in ShortRead 1.37.3 and later) will return > numeric() rather than integer() and hence support large files. > > Martin > > On 02/20/201

[Bioc-devel] ShortRead::countLines integer overflow with large fastq files

Dear Martin, countLines in ShrotRead returns the line counts as integers which appears to create problems with large FASTQ files (>536.8 Mio lines) due to R's integer limit (2^31-1). When the integer limit is reached/exceeded it seems that countLines returns negative values not reflecting the

Re: [Bioc-devel] Duplicate commit error on and off

8 > > > Give me a thumbs up and I’ll go ahead. > > > On Oct 5, 2017, at 11:03 AM, Thomas Girke <thomas.gi...@ucr.edu> wrote: > > > > Hi Nitesh, > > > > If the reset to #c84c7b5f is the best option then let's do this. > > > > Just wondering,

Re: [Bioc-devel] Duplicate commit error on and off

at:"%h %ad %an (%cn) %s" --date-order --date=iso After duplicated commit pairs have been identified, one can check with diff or vimdiff whether their content is identical: git --no-pager show > zzz1 git --no-pager show > zzz2 vimdiff zzz1 zzz2 Thomas On Fri, Sep 8, 2017 at 9:16

Re: [Bioc-devel] Duplicate commit error on and off

oks code, which we have since fixed. I’m glad to have made the shift to > Git, and hope the community enjoys it. > > Best Regards, > > Nitesh > > > > On Sep 8, 2017, at 2:59 PM, Thomas Girke <thomas.gi...@ucr.edu> wrote: > > > > Dear Martin and Nitesh, >

Re: [Bioc-devel] Duplicate commit error on and off

; Cherry-picking (into the official Bioconductor branch) rather than merging? > > I know it'll get hairy here, and maybe no easy or complete or simple > solution... maybe seeing the steps required for alternative solutions > would make the branch swap solution more palatable :) > >

Re: [Bioc-devel] Duplicate commit error on and off

ersion: 2.28.0 -Date: 2016-11-30 +Version: 2.28.1 +Date: 2017-6-30 Author: Y. Eddie Cao, Kevin Horan, Tyler Backman, Thomas Girke Maintainer: Thomas Girke <thomas.gi...@ucr.edu> Description: ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its la

Re: [Bioc-devel] Need for file-based handling of meta-data

Great thanks. I will add some ideas later this week or next week. Thomas On Wed, Jun 29, 2016 at 12:44 PM Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 06/29/2016 03:42 PM, Thomas Girke wrote: > > Yes, a "readSummarizedExperiment" would be a "mo

Re: [Bioc-devel] Need for file-based handling of meta-data

ify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > On 06/29/2016 01:57 PM, Thomas Girke wrote: > > Hi Vince and Martin, > > > > It was great seeing you at the Bioc conference, and thanks for all your > > time organizing

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

> > Hervé Pagès > > > Sent: Monday, October 26, 2015 12:39 PM > > > To: Thomas Girke <thomas.gi...@ucr.edu>; Arora, Sonali > > > <sar...@fredhutch.org>; bioc-devel@r-project.org > > > Subject: Re: [Bioc-devel] system

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

is extremely useful. Thomas On Mon, Oct 26, 2015 at 10:38 AM Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Thomas, > > On 10/25/2015 01:06 PM, Thomas Girke wrote: > > I fixed this in systemPipeR versions 1.4.3/1.5.3. The reason for this > error > > was that the tx_type

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

is generated from a GFF. Thanks, Thomas On Fri, Oct 23, 2015 at 12:49:09AM +, Thomas Girke wrote: > Thanks. Good to know. I have never tried this with an txdb instance > from makeTxDbFromUCSC(). Will fix this over the weekend. > Thomas > > > > On Thu, Oct 22, 2015 at

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

Thanks. Good to know. I have never tried this with an txdb instance from makeTxDbFromUCSC(). Will fix this over the weekend. Thomas On Thu, Oct 22, 2015 at 5:39 PM Arora, Sonali wrote: > Hi Thomas, > > I get the following error when I try to obtain the feature types using

[Bioc-devel] BiocStyle and R markdown

A simple formatting issue: Since support for table of contents in R markdown vignettes has become available, it seems like an amazing solution for many online documentation needs in the future. What would help me to fully to adopt to it, is a solution to get rid of the bullets in a numbered

Re: [Bioc-devel] BiocStyle and R markdown

template file. I am planning on doing some pull request along those lines soon; I have been testing Rmd - HTML extensively for a course I am developing, but I am also new to the knitr+markdown thing so I am still experimenting. Kasper On Wed, Jul 29, 2015 at 4:44 PM, Thomas Girke thomas.gi

Re: [Bioc-devel] BiocParallel-devel error

out the futile.logger package which looks promising for logging at both the system and user levels. We're also exploring more interactive debugging when an error is thrown. Valerie On 11/19/14 19:48, Thomas Girke wrote: Hi Valerie, Michel and others, Finally, I freed up some

Re: [Bioc-devel] BiocParallel-devel error

BiocParallel? Again sorry for the unnecessary noise. Thomas On Tue, Sep 23, 2014 at 06:59:11PM -0700, Thomas Girke wrote: Hi Valerie, Thanks for looking into this. Yes, if I include the bogus 'MYR' in *.tmpl then I am getting the same error in R-release as well. To double-check whether

[Bioc-devel] Faculty Position in Computational Systems Biology at UC Riverside

University of California, Riverside AP Recruit job link: https://aprecruit.ucr.edu/apply/JPF00230 POSITION We are seeking an Assistant Professor in the field of Computational Systems Biology. Research should be in systems biology, using computational approaches or a combination of both