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

[Marcel Ramos]

Hi Kevin,

My hunch is that the image that you're working with is old. If you're
working with an
older image, you could run into that problem with different R versions
used to install 'backports'.

I would first ensure that I'm working with a clean image by stopping any
active containers, removing them, and then doing `docker rmi` to remove
the `bioconductor/devel_core2` image.

Pull a clean image from docker hub and run `wercker build` with your
`wercker.yml` file.

Any new changes made by your `yml` file can be saved to a different
image by doing
`docker commit`.
See:
https://stackoverflow.com/questions/26322247/docker-revert-changes-to-container

This allows you to preserve the `devel_core2` image as it was downloaded
and try again with
an updated 'wercker.yml' file.

PS. A correction to the `wecker.yml` file:

```
build:
  steps:
    - script:
        name: Install devtools
        code: R -e "install.packages(c('devtools', 'backports'))"
    - jimhester/r-dependencies
    - jimhester/r-check
    - jimhester/r-coverage
```

Also, the EXTERNAL tag is generated by the Roswell Park email system.


Best regards,

Marcel




On 03/20/2018 05:14 PM, Kevin RUE wrote:
> 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 <mailto: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]]
>     >
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