Re: [R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Dirk Eddelbuettel 


On 5 August 2019 at 00:13, Iñaki Ucar wrote:
| On Mon, 5 Aug 2019 at 00:08, Ben Bolker  wrote:
| >
| >
| >   Yeah, I might try that, or I might try installing the downstream
| > packages that are causing problems from Rutter's repo.
| 
| AFAICT from the build log, the packages that are causing problems are
| being installed precisely from Rutter's repo:
| 
| Get:7 http://ppa.launchpad.net/marutter/c2d4u/ubuntu xenial/main amd64
| r-cran-ps amd64 1.3.0-1cran1ppa0 [149 kB]
| Get:20 http://ppa.launchpad.net/marutter/c2d4u/ubuntu xenial/main
| amd64 r-cran-fansi amd64 0.4.0-1cran1ppa0 [133 kB]
| Get:42 http://ppa.launchpad.net/marutter/c2d4u/ubuntu xenial/main
| amd64 r-cran-scales amd64 1.0.0-1cran1ppa0 [422 kB]
| 
| but not from c2d4u3.5.

Yes, and that is the problem just like Josh said. We want '3.5' (or greater),
not '3.4'.  Ie in r-travis (which is what use for my packages) I have

BootstrapLinux() {
# Set up our CRAN mirror.
if [[ "${R_VERSION}" == "3.5" ]]; then
sudo add-apt-repository "deb ${CRAN}/bin/linux/ubuntu $(lsb_release 
-cs)-cran35/"
elif [[ "${R_VERSION}" == "3.4" ]]; then
sudo add-apt-repository "deb ${CRAN}/bin/linux/ubuntu $(lsb_release 
-cs)/"
fi
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 
E298A3A825C0D65DFD57CBB651716619E084DAB9

# Add marutter's c2d4u repository.
if [[ "${R_VERSION}" == "3.5" ]]; then
sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"
elif [[ "${R_VERSION}" == "3.4" ]]; then
sudo add-apt-repository -y "ppa:marutter/rrutter"
sudo add-apt-repository -y "ppa:marutter/c2d4u"
fi


Cf https://github.com/eddelbuettel/r-travis/blob/master/run.sh#L96-L112 

Dirk

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Re: [R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Ben Bolker 
  Thanks everyone!  Passes now.

On 2019-08-04 7:05 p.m., Dirk Eddelbuettel wrote:
> 
> On 5 August 2019 at 00:13, Iñaki Ucar wrote:
> | On Mon, 5 Aug 2019 at 00:08, Ben Bolker  wrote:
> | >
> | >
> | >   Yeah, I might try that, or I might try installing the downstream
> | > packages that are causing problems from Rutter's repo.
> | 
> | AFAICT from the build log, the packages that are causing problems are
> | being installed precisely from Rutter's repo:
> | 
> | Get:7 http://ppa.launchpad.net/marutter/c2d4u/ubuntu xenial/main amd64
> | r-cran-ps amd64 1.3.0-1cran1ppa0 [149 kB]
> | Get:20 http://ppa.launchpad.net/marutter/c2d4u/ubuntu xenial/main
> | amd64 r-cran-fansi amd64 0.4.0-1cran1ppa0 [133 kB]
> | Get:42 http://ppa.launchpad.net/marutter/c2d4u/ubuntu xenial/main
> | amd64 r-cran-scales amd64 1.0.0-1cran1ppa0 [422 kB]
> | 
> | but not from c2d4u3.5.
> 
> Yes, and that is the problem just like Josh said. We want '3.5' (or greater),
> not '3.4'.  Ie in r-travis (which is what use for my packages) I have
> 
> BootstrapLinux() {
> # Set up our CRAN mirror.
> if [[ "${R_VERSION}" == "3.5" ]]; then
> sudo add-apt-repository "deb ${CRAN}/bin/linux/ubuntu $(lsb_release 
> -cs)-cran35/"
> elif [[ "${R_VERSION}" == "3.4" ]]; then
> sudo add-apt-repository "deb ${CRAN}/bin/linux/ubuntu $(lsb_release 
> -cs)/"
> fi
> sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 
> E298A3A825C0D65DFD57CBB651716619E084DAB9
> 
> # Add marutter's c2d4u repository.
> if [[ "${R_VERSION}" == "3.5" ]]; then
> sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
> sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"
> elif [[ "${R_VERSION}" == "3.4" ]]; then
> sudo add-apt-repository -y "ppa:marutter/rrutter"
> sudo add-apt-repository -y "ppa:marutter/c2d4u"
> fi
> 
> 
> Cf https://github.com/eddelbuettel/r-travis/blob/master/run.sh#L96-L112 
> 
> Dirk

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Re: [R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Iñaki Ucar 
On Mon, 5 Aug 2019 at 00:08, Ben Bolker  wrote:
>
>
>   Yeah, I might try that, or I might try installing the downstream
> packages that are causing problems from Rutter's repo.

AFAICT from the build log, the packages that are causing problems are
being installed precisely from Rutter's repo:

Get:7 http://ppa.launchpad.net/marutter/c2d4u/ubuntu xenial/main amd64
r-cran-ps amd64 1.3.0-1cran1ppa0 [149 kB]
Get:20 http://ppa.launchpad.net/marutter/c2d4u/ubuntu xenial/main
amd64 r-cran-fansi amd64 0.4.0-1cran1ppa0 [133 kB]
Get:42 http://ppa.launchpad.net/marutter/c2d4u/ubuntu xenial/main
amd64 r-cran-scales amd64 1.0.0-1cran1ppa0 [422 kB]

but not from c2d4u3.5.

Iñaki

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Re: [R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Ben Bolker 



On 2019-08-04 6:08 p.m., Joshua Ulrich wrote:
> On Sun, Aug 4, 2019 at 4:54 PM Ben Bolker  wrote:
>>
>> On 2019-08-04 5:43 p.m., Iñaki Ucar wrote:
>>> On Sun, 4 Aug 2019 at 23:26, Ben Bolker  wrote:


   I'm having some trouble with travis builds of a package (local checks
 work fine) and hoping if I can get suggestions for diagnosis &
 troubleshooting ...

 The package is 'broom.mixed'; I hadn't changed it in a while, but
 recently got a minor pull request which seemed reasonable. I believe the
 problems I'm having now are dependency and/or caching problems, not
 actually related to the changes in the package.

 The failing build is here

 https://travis-ci.org/bbolker/broom.mixed/builds/567597217
>>>
>>> I see various "package x was installed by an R version with different
>>> internals; it needs to be reinstalled for use with this R version".
>>>
>>> Top of the page, right side, you should see More options > Caches. Try
>>> removing them and restart the build.
>>>
>>> Iñaki
>>
>>   I tried that already, thanks.  That's why I'm now suspecting it's some
>> kind of mismatch between the Rutter PPAs and the default (?) repos that
>> Travis uses.  It would be a little painful, but I could edit out the
>> rstan dependency and try the builds with and without Rutter's PPA to
>> test that hypothesis ...
>>
> Try changing:
> sudo add-apt-repository -y "ppa:marutter/rrutter"
> sudo add-apt-repository -y "ppa:marutter/c2d4u"
> to:
> sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
> sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"
> 
> The R C API changed between R-3.4.x and R-3.5.x, which created
> incompatibility in packages installed using different versions.  Any R
>> 3.6.x should use the "ppa:*3.5" PPAs.
> 
> 
>>   cheers
>> Ben Bolker
>>
>>

  Aha! That sounds like it might be the right answer.  I almost tried
it, but I thought that the non-specifically tagged PPA
(ppa:marutter/c2d4u) was *post*-3.5 instead of *pre*-3.5 (and that
therefore it wouldn't help since I'm building on r-release (3.6) and
r-devel (3.x) ...)

  cheers
Ben Bolker



>>
>>>
>>
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> 
>

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Re: [R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Joshua Ulrich 
On Sun, Aug 4, 2019 at 4:54 PM Ben Bolker  wrote:
>
> On 2019-08-04 5:43 p.m., Iñaki Ucar wrote:
> > On Sun, 4 Aug 2019 at 23:26, Ben Bolker  wrote:
> >>
> >>
> >>   I'm having some trouble with travis builds of a package (local checks
> >> work fine) and hoping if I can get suggestions for diagnosis &
> >> troubleshooting ...
> >>
> >> The package is 'broom.mixed'; I hadn't changed it in a while, but
> >> recently got a minor pull request which seemed reasonable. I believe the
> >> problems I'm having now are dependency and/or caching problems, not
> >> actually related to the changes in the package.
> >>
> >> The failing build is here
> >>
> >> https://travis-ci.org/bbolker/broom.mixed/builds/567597217
> >
> > I see various "package x was installed by an R version with different
> > internals; it needs to be reinstalled for use with this R version".
> >
> > Top of the page, right side, you should see More options > Caches. Try
> > removing them and restart the build.
> >
> > Iñaki
>
>   I tried that already, thanks.  That's why I'm now suspecting it's some
> kind of mismatch between the Rutter PPAs and the default (?) repos that
> Travis uses.  It would be a little painful, but I could edit out the
> rstan dependency and try the builds with and without Rutter's PPA to
> test that hypothesis ...
>
Try changing:
sudo add-apt-repository -y "ppa:marutter/rrutter"
sudo add-apt-repository -y "ppa:marutter/c2d4u"
to:
sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"

The R C API changed between R-3.4.x and R-3.5.x, which created
incompatibility in packages installed using different versions.  Any R
> 3.6.x should use the "ppa:*3.5" PPAs.


>   cheers
> Ben Bolker
>
>
>
> >
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-package-devel



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Re: [R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Ben Bolker 


  Yeah, I might try that, or I might try installing the downstream
packages that are causing problems from Rutter's repo.  (Right now I'm
checking whether I can get it to build on travis without Rutter's repo,
and with rstan/rstanarm removed from the Suggests: list ...

  thanks,
Ben Bolker


On 2019-08-04 6:05 p.m., Iñaki Ucar wrote:
> On Sun, 4 Aug 2019 at 23:45, Ben Bolker  wrote:
>>
>>   I tried that already, thanks.
> 
> Sorry, I should have read til the end of the email before posting.
> 
>> That's why I'm now suspecting it's some
>> kind of mismatch between the Rutter PPAs and the default (?) repos that
>> Travis uses.  It would be a little painful, but I could edit out the
>> rstan dependency and try the builds with and without Rutter's PPA to
>> test that hypothesis ...
> 
> Yes, it seems that Rutter's repo is causing the trouble. You could try
> to install those erroring packages from CRAN, i.e., by adding:
> 
> r_packages:
>   - scales
>   - ps
>   - fansi
> 
> to your travis file.
> 
> Iñaki
>

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Re: [R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Iñaki Ucar 
On Sun, 4 Aug 2019 at 23:45, Ben Bolker  wrote:
>
>   I tried that already, thanks.

Sorry, I should have read til the end of the email before posting.

> That's why I'm now suspecting it's some
> kind of mismatch between the Rutter PPAs and the default (?) repos that
> Travis uses.  It would be a little painful, but I could edit out the
> rstan dependency and try the builds with and without Rutter's PPA to
> test that hypothesis ...

Yes, it seems that Rutter's repo is causing the trouble. You could try
to install those erroring packages from CRAN, i.e., by adding:

r_packages:
  - scales
  - ps
  - fansi

to your travis file.

Iñaki

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Re: [R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Ben Bolker 



On 2019-08-04 5:43 p.m., Iñaki Ucar wrote:
> On Sun, 4 Aug 2019 at 23:26, Ben Bolker  wrote:
>>
>>
>>   I'm having some trouble with travis builds of a package (local checks
>> work fine) and hoping if I can get suggestions for diagnosis &
>> troubleshooting ...
>>
>> The package is 'broom.mixed'; I hadn't changed it in a while, but
>> recently got a minor pull request which seemed reasonable. I believe the
>> problems I'm having now are dependency and/or caching problems, not
>> actually related to the changes in the package.
>>
>> The failing build is here
>>
>> https://travis-ci.org/bbolker/broom.mixed/builds/567597217
> 
> I see various "package x was installed by an R version with different
> internals; it needs to be reinstalled for use with this R version".
> 
> Top of the page, right side, you should see More options > Caches. Try
> removing them and restart the build.
> 
> Iñaki

  I tried that already, thanks.  That's why I'm now suspecting it's some
kind of mismatch between the Rutter PPAs and the default (?) repos that
Travis uses.  It would be a little painful, but I could edit out the
rstan dependency and try the builds with and without Rutter's PPA to
test that hypothesis ...

  cheers
Ben Bolker



>

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Re: [R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Iñaki Ucar 
On Sun, 4 Aug 2019 at 23:26, Ben Bolker  wrote:
>
>
>   I'm having some trouble with travis builds of a package (local checks
> work fine) and hoping if I can get suggestions for diagnosis &
> troubleshooting ...
>
> The package is 'broom.mixed'; I hadn't changed it in a while, but
> recently got a minor pull request which seemed reasonable. I believe the
> problems I'm having now are dependency and/or caching problems, not
> actually related to the changes in the package.
>
> The failing build is here
>
> https://travis-ci.org/bbolker/broom.mixed/builds/567597217

I see various "package x was installed by an R version with different
internals; it needs to be reinstalled for use with this R version".

Top of the page, right side, you should see More options > Caches. Try
removing them and restart the build.

Iñaki

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[R-pkg-devel] help troubleshooting travis-ci issues?

2019-08-04 Thread Ben Bolker 


  I'm having some trouble with travis builds of a package (local checks
work fine) and hoping if I can get suggestions for diagnosis &
troubleshooting ...

The package is 'broom.mixed'; I hadn't changed it in a while, but
recently got a minor pull request which seemed reasonable. I believe the
problems I'm having now are dependency and/or caching problems, not
actually related to the changes in the package.

The failing build is here

https://travis-ci.org/bbolker/broom.mixed/builds/567597217

The initial tests of the PR failed, I think because rstan took too long
to compile.  So I added some code to install rstan binaries from a PPA
instead of compiling it on the spot:

https://github.com/bbolker/broom.mixed/blob/master/.travis.yml#L32-L34

(thanks to various resources Dirk Eddelbuettel has written).  I got more
errors (described below) that I thought were caused by package caching,
but clearing the Travis cache
 doesn't seem
to have helped; now I'm afraid that they're due to a mismatch between
the R configuration in Michael Rutter's cd24u repo and the configuration
on Travis ... ?

  Any suggestions for what to look at?

  My travis skills are definitely cargo-culty, so please be gentle if
you look at my .travis.yml file (feel free to suggest/explain improvements!)

   Ben Bolker

---

---
[installing ggstance, ggridges, lmerTest]
Error: package "scales" was installed by an R version with different
internals; it needs to be reinstalled for use with this R version
Execution halted

[installing htmlwidgets]
Failed with error: "there is no package called "shiny"

[running examples]
Error: package "fansi" was installed by an R version with different
internals; it needs to be reinstalled for use with this R version
Execution halted

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