[Bioc-devel] Recreating nebbiolo1's build environment

[sergi sayols puig]

Hi Hervé,
Very helpful :) thanks for looking into this.

Best,
Sergi

Missatge de Hervé Pagès <hpages.on.github using gmail.com> del dia dt., 11
de gen. 2022 a les 17:59:

>
> Today's results for rrvgo:
>
>    https://bioconductor.org/checkResults/3.15/bioc-LATEST/rrvgo/
>
> The vignette error is gone. There are still some errors but they are
> different (org.Pf.plasmo.db was deprecated in BioC 3.14 and got removed
> from BioC 3.15).
>
> H.
>
>
> On 11/01/2022 09:28, Hervé Pagès wrote:
> > Hi Sergi,
> >
> > I can't reproduce this on my laptop either (Ubuntu 21.10) or on
> > nebbiolo1.
> >
> > And it looks like the build results for rrvgo will look fine on all
> > platform today (report not available yet).
> >
> > I suspect that the error was coming from a package that rrvgo depends
> > on and that it's been fixed now.
> >
> > I strongly suspect  GOSemSim:
> >
> >   commit 93e084381b6f73209da09b6564db7a30516e9b99 (HEAD -> master,
> > origin/master, origin/HEAD)
> >   Author: Guangchuang Yu <guangchuangyu using gmail.com>
> >   Date:   Mon Jan 10 10:12:55 2022 +0800
> >
> >     fixed #36 for returning NULL when it should be the input object
> >
> > Cheers,
> >
> > H.
> >
> >
> > On 11/01/2022 02:21, sergi sayols puig wrote:
> >> Dear all,
> >> Our package rrvgo has recently started to fail when building for BioC
> >> 3.15 (devel branch).
> >>
> >> I'm trying to replicate the build environment as in nebbiolo1 in order
> >> to reproduce the issue locally, with little success so far. I'm
> >> following carefully the instructions provided in the build report, but
> >> I must be missing something because I can build the package
> >> successfully.
> >>
> >> I tried both compiling R from source (snapshot
> >> R-devel_2022-01-05_r81451.tar.gz) + installing the devel version of
> >> Bioconductor, and also using the docker image of
> >> bioconductor_docker:devel. Here I provide the steps I followed to
> >> build from within the container, using vanilla .libPaths():
> >>
> >> * pull docker image
> >>      $ docker pull bioconductor/bioconductor_docker:devel
> >> * open shell in the running container:
> >>      $ docker exec -it bioconductor/bioconductor_docker:devel /bin/bash
> >> * install package + dependencies (within the container):
> >>      # R
> >>      R> install.packages("BiocManager")
> >>      R> BiocManager::install(version='devel')
> >>      R> BiocManager::install(c("rrvgo", "org.Hs.eg.db"))   # the second
> >> is required in the vignette
> >>      R> q()
> >> * clone the devel branch of the package:
> >>      # git clone https://git.bioconductor.org/packages/rrvgo
> >> * get nebbiolo1's .Renviron:
> >>      # wget -qO-
> >> http://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc >
> >> Renviron.bioc
> >> * and build as described in the build report:
> >>      # R_ENVIRON_USER=Renviron.bioc R CMD build --keep-empty-dirs
> >> --no-resave-data rrvgo
> >>
> >> This will successfully build the tarball of the package, without
> >> complains.
> >> Does anyone have any idea what I could possibly do to troubleshoot
> >> the error?
> >>
> >> Thanks a lot in advance!
> >>
> >> Best wishes,
> >> Sergi
> >>
> >> _______________________________________________
> >> Bioc-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>