Hi Hervé, Very helpful :) thanks for looking into this. Best, Sergi
Missatge de Hervé Pagès <hpages.on.git...@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 <guangchuan...@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@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel