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

I had a look at the downloaded data from the hub and it looks like there might have been a bad file download.  I have reset the cache on nebbiolo1.  Let's see if it clears up over the next 2 days otherwise we can follow up with assistance debugging.

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of CHEN Ying <chen_ying at gis.a-star.edu.sg>
Sent: Wednesday, February 23, 2022 6:40 AM
To: sergi sayols puig <sergisayolspuig at gmail.com>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Can't reproduce the build errors with same system and R version

Hi Sergi,

Thank you so much for your help! The docker image solution is very useful. I am able to get it run. However, I still can't reproduce the errors, which to me look like a ExperimentHub connection issue.

Thanks a lot anyways!!
Regards,
Ying


________________________________
From: sergi sayols puig <sergisayolspuig at gmail.com>
Sent: Tuesday, 22 February 2022 5:38 pm
To: CHEN Ying <chen_ying at gis.a-star.edu.sg>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Can't reproduce the build errors with same system and R version

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://secure-web.cisco.com/1j3I9olTt5f0WTOwBiDaa_qk0tQv_3JWPoYWTIWLbVwH7dNX3eEKu6lCSUvU3CD4zgiod_sTOzpamY7w6HAPyBpqTS7NVr6gRo9Wq-GcE9kWsnSc129W8D8TcsoGyIf4DEQIs7arOeF1YMUgqjXaJqUOwmgYn0zjRClgCY-cEaY7QHLag670QC1LVZNJ0EabTuL8oGlxfDWprLxoLp0kDRUqsZieFBJJacM0T3dTk_PTWACkX5sRLJBQqVdsKvd20Uqi-ElcpVQIx0OADh-Yg5gbSu3TI1bhUhYHDt2fqjBALy3nKW4Oib15hXs7gjTaF/https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2Frrvgo
* get nebbiolo1's .Renviron:
    # wget -qO-
http://secure-web.cisco.com/1ZcHL7ar03hb6LyJ18L3hutm5VKAna5fZP1WgvcIHkFGq0uOxaEcej0kixKYzyuniW2C02zlW3199R8dVSTBg3xhsh7FsZFD9YldGmtjK7riTRRHhVEtFcWJvYRb4n_ioVxwcJ1EnOEQM4mGggeZ9DMSqsxYpAm4UUkvI0Mf2ydu8Me5cfJAdQ6P_Oan3Ci0mrRJhW-vrfhHZuZhDbzOcVWtxORa8C4JdWGiVeGjXxML1aaaBI8SMSk-c0Nf7choTT4Lj1Fm7FQgR3yP2S_zsmGF-ntWdO4kKo7GchMCmW0Z4ev02UNkM5VS4FJKr41rP/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FRenviron.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
```

Hope this helps.

Cheers,
Sergi

Missatge de CHEN Ying <chen_ying at 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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