[Bioc-devel] Fwd: [Bioconductor/Contributions] GIGSEA (#720)

Hi Everyone, My package just passed the check, without errors or warnings. I am pretty new to Bioconductor. May I ask whether this is done? or anything else I need to do for releasing my package? Any help would be much appreciated. Best Shijia -- Forwarded message -- From:

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

On 04/18/2018 02:45 PM, Vincent Carey wrote: On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan > wrote: On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote: Dear Martin, On Fri, 06-April-2018, at

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

yes, the [] is a habit i need to break. ok, we'll get by. On Wed, Apr 18, 2018 at 3:09 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > > > On 04/18/2018 02:45 PM, Vincent Carey wrote: > >> >> >> On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan < >> martin.mor...@roswellpark.org

Re: [Bioc-devel] GateFinder: Windows Server Error

Hi Lori, Thanks for your assistance and helping me understand how to change the supported platforms on a package, it's much appreciated. When might I know whether these changes had the desired affect? Is there a way to have it checked directly or will I have to wait for another set of tests to be

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > > > On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote: > >> >> Dear Martin, >> >> On Fri, 06-April-2018, at 18:59:00, Martin Morgan < >> martin.mor...@roswellpark.org> wrote: >> >>> On 04/06/2018 10:44 AM,

Re: [Bioc-devel] incompatibility between logo for build et the version and success of compilation

This page http://bioconductor.org/packages/3.7/bioc/html/coMET.html gets updated when there is a successful build and once the package propagates on our system as determined by the latest build report. It can be a little delayed behind the successful post here:

Re: [Bioc-devel] incompatibility between logo for build et the version and success of compilation

Great, thanks Lori. From: Shepherd, Lori Sent: 18 April 2018 17:46:24 To: Martin, Tiphaine; bioc-devel@r-project.org Subject: Re: incompatibility between logo for build et the version and success of compilation This page

[Bioc-devel] incompatibility between logo for build et the version and success of compilation

Hi, I updated the dev version of my package, http://bioconductor.org/packages/3.7/bioc/html/coMET.html if I am looking the webpage, it seems that my build fails and I can install only the version 11.3. however, if i am looking at the different compilations, everything is ok for the version

Re: [Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2

Also FWIW changing things like (there are a number of these changes) sum(unlist(lapply(data, length)))/1e+06 to sum(lengths(data)) / 1e6 actually has measurable effect on the speed of your code. Martin On 04/18/2018 10:47 AM, Carmen M. Livi wrote: Dear Martin Morgan, ok, I will

Re: [Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2

Dear Martin Morgan, ok, I will switch back to parallel then. Thank you very much for your reply. Kind regards, Carmen On 18/04/2018 15:30, Martin Morgan wrote: I'm sorry not to respond to your first email. This is a problem in BiocParallel that I am working on. In your particular case, where

Re: [Bioc-devel] Can not push to bioconductor! please help me!

Dear BioMedR Maintainer I'm sorry that you never responded to our many earlier emails and notifications. I recommend checking your email systems to make sure emails from Bioconductor and RoswellPark are not being blocked or spammed. To address your first point: Your github repository is not

Re: [Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2

I'm sorry not to respond to your first email. This is a problem in BiocParallel that I am working on. In your particular case, where you are relying on a third-party package that uses parallel::mclapply, I think you should revert to using that. Martin On 04/18/2018 09:22 AM, Carmen M. Livi

[Bioc-devel] ‘SOCKcluster’ cluster error with bplapply() under merida2

Hi all, I was using parallel::mclapply() but have been encouraged to substitute it with BiocParallel::bplapply(). BiocParallel::bplapply(data,     BPPARAM = BiocParallel::MulticoreParam(workers =x ),     FUN  =...) I never had problems with the code. Now the package got accepted and

Re: [Bioc-devel] Transition from Google Sheet to Web App

This transition will start at 9am EST today. We'll post back when it's done. Valerie On 04/17/2018 10:27 AM, Obenchain, Valerie wrote: Hi developers, Tomorrow we are bringing a web app online to help with the management of SSH keys. The app will replace the Google Sheet currently used to add

Re: [Bioc-devel] GateFinder: Windows Server Error

Yes this is possible. If you add the file to the top level of your package ".BBSoptions" with the entry "UnsupportedPlatforms: win32" Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New

Re: [Bioc-devel] Can not push to bioconductor! please help me!

Dear sir, Thank you for your letter. Firstly, Actually, I don't know why does the content in GitHub and Bioconductor are not the same when the package was firstly releaed in bioconductor? In the GitHub we have removed the error file since the first release. Then, the tips of the