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

On 6/9/20 06:57, Martin Morgan wrote: I wrote a small gist

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

Martin, i think this is a very good solution, with your script one identifies automatically the broken dependencies and then the installation via git avoid having to clone the corresponding repos. i tried it on another package with broken dependencies right now and it works very well:

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

I wrote a small gist https://gist.github.com/mtmorgan/21e18991c6ebdb388e8828bcc0fe72f6 that queries for broken dependencies. Using two packages that have been mentioned recently on this mailing list > tbl <- deps_broken(c("EnrichmentBrowser", "GenomicScores")) > tbl # A tibble: 1 x 5

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

On 6/8/20 19:20, Hervé Pagès wrote: On 6/5/20 07:52, Martin Morgan wrote: 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! This makes a lot of

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

On 6/5/20 07:52, Martin Morgan wrote: 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! This makes a lot of sense for release but for devel maybe

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] 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

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

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

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

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

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

[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