[Bioc-devel] EXTERNAL: Question about Wercker continuous integration

[Kevin RUE]

Hi Marcel,

Thanks for the reply. I tried your `wercker.yml` file (exactly as is), and
still got the same issue:

* creating vignettes ... ERROR
Error: processing vignette 'MyPackage-vignette.Rmd' failed with diagnostics:
package ‘backports’ was installed by an R version with different internals;
it needs to be reinstalled for use with this R version
Execution halted
Error: Command failed (1)
In addition: Warning message:
`cleanup` is deprecated
Execution halted
Check Failed, dumping logs
find: ‘./*.Rcheck’: No such file or directory
failed: Check Failed

I'll leave it be for now, and see if I can get it to work with the new
release in April.

Also, did my email really arrive as  "EXTERNAL" to the bioc-devel mailing
list? That would be odd, I sent it from my bioc-devel registered email
address :/

Kind regards,
Kevin

On Tue, Mar 20, 2018 at 5:03 PM, Marcel Ramos <Marcel.Ramos at roswellpark.org>
wrote:

> Hi Kevin,
>
> Being that I am unable to fully reproduce the issue, I can only say that
> I have been successful in running the steps in the Wercker build for a
> different package.
>
> Please do a *clean* pull of the Bioconductor image from docker hub by
> removing any stale images
> first.
>
> Here is the wercker.yml that I used:
>
> >> wercker build --docker-local
>
> box: bioconductor/devel_core2
>
> build:
>   steps:
>     - script:
>         name: Install devtools
>         code: R -e "install.packages('devtools')"
>     - jimhester/r-dependencies:
>         cran_dependencies: backports
>     - jimhester/r-check
>     - jimhester/r-coverage
>
>
> *Note:*I removed the r-lint step because it was having some issues with
> xml.
>
>
> Regards,
>
> Marcel
>
>
> On 03/16/2018 07:53 AM, Kevin RUE wrote:
> > Dear all,
> >
> > I'm usually a big Travis CI fan, but I'm having a go at Wercker, using
> the
> > bioconductor/devel_core2 docker (I have also tried the rocker 'parent'
> ones
> > without further success).
> > I am running into the following issue:
> >
> > [...]
> > * creating vignettes ... ERROR
> > Error: processing vignette 'NewPackage-vignette.Rmd' failed with
> > diagnostics:
> > package ‘backports’ was installed by an R version with different
> internals;
> > it needs to be reinstalled for use with this R version
> > Execution halted
> > Error: Command failed (1)
> > In addition: Warning message:
> > `cleanup` is deprecated
> > Execution halted
> > Check Failed, dumping logs
> > find: ‘./*.Rcheck’: No such file or directory
> > failed: Check Failed
> >
> > I've tried adding a task that re-installs the `backports` package from
> > source (CRAN), but I still get the same error.
> >
> > My wercker.yml looks like:
> > box: bioconductor/devel_core2
> > build:
> >     steps:
> >         - script:
> >             name: Install devtools
> >             code: R -e "install.packages('devtools')"
> >         - script:
> >             name: Install backports
> >             code: R -e "install.packages('backports')"
> >         - jimhester/r-dependencies
> >         - jimhester/r-check
> >         - jimhester/r-lint
> >         - jimhester/r-coverage
> >
> >
> >
> > Any help/advice/experience with Wercker would be greatly appreciated!
> >
> > Best wishes,
> > Kevin
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or...{{dropped:4}}
>
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