[Bioc-devel] EXTERNAL: Question about Wercker continuous integration
Kevin RUE
kevinrue67 at gmail.com
Wed Mar 21 11:49:57 CET 2018
Thanks Marcel, it works!
After clearing the cache (Wercker > Project > Options > Cache > "Clear
cache" button), R CMD check now works perfectly on Wercker.
Indeed, I think I initially used an older box, and didn't realise that the
cached box was being fetched instead of downloading the more recent one.
Many many thanks for the time and headache saved!
Best wishes,
Kevin
On Tue, Mar 20, 2018 at 11:52 PM, Marcel Ramos <Marcel.Ramos at roswellpark.org
> wrote:
> 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> 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
>>
>>
>>
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