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

[Kern, Lori]

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 using r-project.org> on behalf of CHEN Ying <chen_ying using gis.a-star.edu.sg>
Sent: Wednesday, February 23, 2022 6:40 AM
To: sergi sayols puig <sergisayolspuig using gmail.com>
Cc: bioc-devel using r-project.org <bioc-devel using 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 using gmail.com>
Sent: Tuesday, 22 February 2022 5:38 pm
To: CHEN Ying <chen_ying using gis.a-star.edu.sg>
Cc: bioc-devel using r-project.org <bioc-devel using 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 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
> This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://secure-web.cisco.com/160cddQU7Wl8jNei-eWMr11o56-gDDBOU-L__dH8ND6ivCy7ucerdfvRP5iUEHYetATEci0ALiO8mL2M4gtLAw3VhIpskFEyzgoJaDSylJXP4avovf7qsE8ds9wBMWMsJqwTWUoqCRah6xg-cfmnihYmlBedh8OPEqwZQh0jhxzLsubujnaIoem8LlxYVKK9-ioFDIUPRAca70ozBjrU_wWXeGd_ZDsZvt6ed9fMwEV22Lbl5xkdeQ8tYjNM5AdzxNYIZCJl41VCVdFFgmt3zrRzyQmsWXh9mYN2jz4tzbkOR_0VruqtBEkXCpAGMmkL6/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://secure-web.cisco.com/160cddQU7Wl8jNei-eWMr11o56-gDDBOU-L__dH8ND6ivCy7ucerdfvRP5iUEHYetATEci0ALiO8mL2M4gtLAw3VhIpskFEyzgoJaDSylJXP4avovf7qsE8ds9wBMWMsJqwTWUoqCRah6xg-cfmnihYmlBedh8OPEqwZQh0jhxzLsubujnaIoem8LlxYVKK9-ioFDIUPRAca70ozBjrU_wWXeGd_ZDsZvt6ed9fMwEV22Lbl5xkdeQ8tYjNM5AdzxNYIZCJl41VCVdFFgmt3zrRzyQmsWXh9mYN2jz4tzbkOR_0VruqtBEkXCpAGMmkL6/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel



This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]