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

Marcel Ramos Marcel.Ramos at roswellpark.org
Tue Mar 20 18:03:54 CET 2018

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

Here is the wercker.yml that I used:

>> wercker build --docker-local

box: bioconductor/devel_core2

    - 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



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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