[Bioc-devel] Can't reproduce the build errors with same system and R version

sergi sayols puig @erg|@@yo|@pu|g @end|ng |rom gm@||@com
Tue Feb 22 10:38:11 CET 2022

Hi Ying,
with regard to reproducing the build environment used in
Bioconductor's build machines, I've been quite successful using
Bioconductor's docker image.
Here's an example to create the build environment and building the
rrvgo package in it:

* pull docker image
    $ docker pull bioconductor/bioconductor_docker:devel
* open a 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 latetr
is required to build 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 >
* and build as described in the build report:
    # R_ENVIRON_USER=Renviron.bioc R CMD build --keep-empty-dirs
--no-resave-data rrvgo

Hope this helps.


Missatge de CHEN Ying <chen_ying using gis.a-star.edu.sg> del dia dl., 21 de
febr. 2022 a les 3:31:

> Hi Bioc-devel team,
> I am trying to debug the build error of the bambu development branch, and the report suggested a problem in loading data from the ExperimentHub package. With the same ubuntu system and R version, I can't seem to reproduce the errors on my laptop. Could someone help me with this? The build error has been there for quite some time. Do I need to re-upload the data?
> Thank you
> Regards,
> Ying
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