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-boun...@r-project.org> on behalf of CHEN Ying
<chen_y...@gis.a-star.edu.sg>
Sent: Wednesday, February 23, 2022 6:40 AM
To: sergi sayols puig <sergisayolsp...@gmail.com>
Cc: bioc-devel@r-project.org <bioc-devel@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 <sergisayolsp...@gmail.com>
Sent: Tuesday, 22 February 2022 5:38 pm
To: CHEN Ying <chen_y...@gis.a-star.edu.sg>
Cc: bioc-devel@r-project.org <bioc-devel@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_y...@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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