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

[Kevin RUE]

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  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.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 

Re: [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
> >
> 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 

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

[Kevin RUE]

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 
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 mailing list
> > 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
>

[[alternative HTML version deleted]]

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

[Marcel Ramos]

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 mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



This email message may contain legally privileged and/or...{{dropped:4}}

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