Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

Hi Lori, Excellent solution. I will update my profile. Thank you! (I should have guessed bioc would have a mechanism for this) > On Jun 5, 2020, at 10:16 AM, Shepherd, Lori > wrote: > > Paul > > - On the support site, you can edit your profile and put package names as > watchedtags.

Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

Paul - On the support site, you can edit your profile and put package names as watchedtags. When a person posts to the support site and tags with the package name you would then be emailed. This assumes they tag the post correctly but also an option Lori Shepherd Bioconductor Core

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

Vince, thanks for the suggestions, i've taken the serializing route and submitted the fix. cheers, robert. On 05/06/2020 17:28, Vincent Carey wrote: > > > On Fri, Jun 5, 2020 at 10:24 AM Robert Castelo > wrote: > > hi Vince, > > no worries, i've been

Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

Thanks, Spencer. Sorry I missed the support posting - there’s no automatic forwarding from there to maintainers. I’ll take a look at this later today, then post back to the support list, and we will get a fix in. Thank you for pointing out the problem! - Paul > On Jun 5, 2020, at 9:46 AM,

Re: [Bioc-devel] Bioconductor package tidybulk

Thanks Lori, your email finally made me understand the relationship between my repo and Bioc repo. I have to admit that I was not familiar of remote vs. upstream. Now, I have pushed everything to RELEASE_3_11. But the tests did not trigger. I will push to develop as well early next week. Best

[Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

Hi, I've identified a few missing PWMs from the MotifDb package and would like to help get them added. I posted on the support page but have not received a response after 10 days, so messaging here instead (link to forum post: https://support.bioconductor.org/p/131312/). Full details can be

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

no, the build system should only propagate packages that have passed build and check -- the goal is to make the life of the user easier and more reliable, us developers have to sweat the details! Usually there is a single package that has changed and causes problems, and like in the present

[Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

hi, my package GenomicScores is not building, see: http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html apparently, it is breaking in the following lines of its vignette: library(gwascat) data(ebicat37) which in the report from the bioc build machine

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

I am really sorry about the situation with gwascat and will try to straighten it out today. On Fri, Jun 5, 2020 at 6:27 AM Robert Castelo wrote: > hi, > > my package GenomicScores is not building, see: > > >

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

never thought about it this way, but how can the system install something that does not build? how should *i* install something that does not build to reproduce the error? sorry if these are very naive questions!! robert. On 05/06/2020 13:34, Martin Morgan wrote: The build system installs

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

The build system installs the version of gwascat that is available from git checkout (anticipating that this will propagate). gwascat installs, but fails to pass check -- it is likely broken https://bioconductor.org/checkResults/devel/bioc-LATEST/gwascat/ in a way that causes your package to

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

R CMD INSTALL or install.packages("foo", repos = NULL) on a clone of the repository. A build might fail because the examples or vignette fail to build, whereas for installation the only requirement is that the package is syntactically correct. Martin On 6/5/20, 7:58 AM, "Robert Castelo"

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

Thanks Martin, i wasn't aware about that fact. i've cloned the gwascat repo and been able to directly install from the directory and reproduce the error. in this case, this was easy because it involved just one package but with multiple broken package dependencies, i'd have to manually clone

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

hi Vince, no worries, i've been finally able to reproduce the error in my computer and i'm afraid i'm probably using a deprecated dataset from 'gwascat', concretely the one that was stored as gwascat/data/ebicat37.rda what would be the replacement for the following kind of operation?

Re: [Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

On Fri, Jun 5, 2020 at 10:24 AM Robert Castelo wrote: > hi Vince, > > no worries, i've been finally able to reproduce the error in my computer > and i'm afraid i'm probably using a deprecated dataset from 'gwascat', > concretely the one that was stored as > > gwascat/data/ebicat37.rda > > what