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.ra...@roswellpark.org <mailto:marcel.ra...@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@r-project.org <mailto:Bioc-devel@r-project.org> > mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > > This email message may contain legally privileged > and/or...{{dropped:4}} > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing > list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > This email message may contain legally privileged and/or...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
