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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