[Bioc-devel] Recreating nebbiolo1's build environment

[Hervé Pagès]

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