Re: [Bioc-devel] build errors

Interesting. I'm glad you sorted it out and thanks for checking in a fix. If you run into problems with git there is some good documentation here: http://www.bioconductor.org/developers/how-to/git/ Valerie On 04/20/2018 02:55 PM, Karl Stamm wrote: Fixed. You were right about R 3.5. They've

Re: [Bioc-devel] build errors

I'm out for the next few days so will look into this more next week. I should mention this week we updated to the release candidate of R 3.5.0 on all release and devel build machines. Today rgsepd is broken on all 3 platforms which may point to a change in R itself. Are you using R 3.5.0 for

Re: [Bioc-devel] Bioc 3.7 build failed for GenvisR package

Hi Zach, The build report for today is not helpful because GenVisR failed on all platforms due to a biomaRt failure. Because that failure is intermittent, I just tried to build the package again on tokay2 and there were no problems (vignette or otherwise). Let's give this another day or two.

[Bioc-devel] DMRcaller build error

Hi everyone, I am the maintainer of DMRcaller. I did an update yesterday and on the build report today, the package failed with the error. Error: processing vignette 'DMRcaller.Rnw' failed with diagnostics: methylationProfile needs to be a GRangesList Execution halted On my machine (MacOS

Re: [Bioc-devel] package build error probably due to Biomart unavailability

There is this page http://bioconductor.org/developers/how-to/web-query/ That suggests some try catch loops to at least try and fail gracefully Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo,

Re: [Bioc-devel] TIMEOUT on package MEAL

Hi Lori, I made some changes to the MEAL vignettes and now MEAL successfully passes tests on Linux and Windows (build time: 1854 and 1613 seconds respectively). However, it still times out in OSX. Should I try to reduce the building time in merida2? Thanks, Carlos Ruiz El 13/04/2018 a las

Re: [Bioc-devel] Suggested edits to support site posting guide

May I also suggested when you are satisfied with user feedback and alterations to create a pull request for the website repository https://github.com/Bioconductor/bioconductor.org Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics &

Re: [Bioc-devel] Subsetting Multiple platform build/check report

This little post I wrote a while back might be of interest to folks who want a computable version of the build report, filterable using R tools. https://seandavi.github.io/post/2017/11/a-computable-bioconductor-build-report/ Sean On Fri, Apr 20, 2018 at 5:34 AM Mike Smith

Re: [Bioc-devel] Subsetting Multiple platform build/check report

I do something similar and have a local 'dashboard' page populated with the build status shields pulled from the package landing pages e.g. http://bioconductor.org/shields/build/devel/bioc/biomaRt.svg Then I can glance at that to see if anything isn't green. Mike On 20 April 2018 at 10:06,

Re: [Bioc-devel] Subsetting Multiple platform build/check report

Steffen, my hackish solution is to have links on my homepage to all the build pages I am interested in (www.hansenlab.org/software). Best, Kasper On Thu, Apr 19, 2018 at 3:33 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > It's not obvious or easy to test, and not meant cynically,

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

Hi Lluis, We (or at least I) had not considered linking the profile in the credentials app with the profile in the Support Site and currently they are not aware of each other. The email in DESCRIPTION was used to get some emails for the credentials app but it is not the case that an email

Re: [Bioc-devel] Web App for SSH keys

Hi Valerie, Thanks for the reply and the doc changes ^^. I added a few short replies below. Best, Leo On Thu, Apr 19, 2018 at 4:49 PM, Obenchain, Valerie wrote: > Hi Leo, > > Great feedback, thanks. > > On 04/19/2018 08:04 AM, Leonardo Collado Torres wrote: >

Re: [Bioc-devel] Web App for SSH keys

This looks great Valerie, congrats to all of those involved in making the web app! I hope that it leads to less questions/confusion. Here are some minor comments, mostly about including some links/docs. * Under the which packages we have access to, I noticed that it's not showing the

Re: [Bioc-devel] Web App for SSH keys

Hi Leo, Great feedback, thanks. On 04/19/2018 08:04 AM, Leonardo Collado Torres wrote: This looks great Valerie, congrats to all of those involved in making the web app! I hope that it leads to less questions/confusion. Here are some minor comments, mostly about including some links/docs. *