[Bioc-devel] Recreating nebbiolo1's build environment

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Tue Jan 11 18:28:51 CET 2022

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



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
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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