travis build fails

[sgibb]

I fixed some dependencies on travis. Now all build dependencies build successfully. But building MSnbase fails with the following error:

Quitting from lines 188-193 (benchmarking.Rmd) 
Error: processing vignette 'benchmarking.Rmd' failed with diagnostics:
setting worker timeout:
  error reading from connection
Execution halted

https://travis-ci.org/lgatto/MSnbase/builds/183582212#L6627-L6631

Removing benchmarking.Rmd results in

Quitting from lines 903-910 (MSnbase-demo.Rnw) 
Error: processing vignette 'MSnbase-demo.Rnw' failed with diagnostics:
setting worker timeout:
  error reading from connection
Execution halted

Both chunks contain quantify calls but I don't think that is the reason for the error.

Any other ideas?

[lgatto]

Everything builds/checks fine locally. I guess it might be something related to parallel code on the travis server.

[jorainer]

Sounds like a BiocParallel error message. I sometimes get these messages on my mac too - eventually you could try:

options(bphost = "localhost")
library(BiocParallel)
register(MulticoreParam())

or alternatively use SnowParam by default - I don't know what the default on linux machines is.

[lgatto]

Or just use SerialParams(), but I would prefer to first see if we can't address it on the travis side.

[sgibb]

@lgatto Should we ask the r-travis folks about the parallel problem? Is there a environment variable we could use to use SerialParams() on travis and MulticoreParams() everywhere else?

BTW: sry for removing the texlive packages, I thought all of these packages where present in texlive-extra-font etc. (but ubuntu 12.04 is very old ...)

[lgatto]

I haven't had time to follow up, but yes, I think we need to check with r-travis folks. Please, go ahead if you have time.

[lgatto]

See travis-ci/travis-ci#7052

[lgatto]

It's a miracle, it builds!

Important config to avoid timeouts:

  - | 
    R CMD build .
    travis_wait 30 R CMD check MSnbase*tar.gz

and

after_success:
  - travis_wait 20 Rscript -e 'covr::codecov()'

But using serial processing. See this issue.

[sgibb]

travis claims that MSnbase could be build successfully (we get a green badge) but in fact it fails with exactly the same error, e.g. https://travis-ci.org/lgatto/MSnbase/builds/200311060

$ R CMD build .
travis_wait 30 R CMD check MSnbase*tar.gz
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘MSnbase’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Quitting from lines 187-192 (benchmarking.Rmd) 
Error: processing vignette 'benchmarking.Rmd' failed with diagnostics:
setting worker timeout:
  error reading from connection

Execution halted

Still running (1 of 30): R CMD check MSnbase*tar.gz

The command R CMD check MSnbase*tar.gz exited with 0.

The script should not exit with exit code 0

[lgatto]

I have cleaned the cache and restart a build - let's see how it goes.

[sgibb]

@lgatto did you close this issue intentionally? While showing a green badge and returning exit code 0, travis still fails to build MSnbase with exactly the same error as above: https://travis-ci.org/lgatto/MSnbase/builds/224609389

Quitting from lines 187-192 (benchmarking.Rmd) 
Error: processing vignette 'benchmarking.Rmd' failed with diagnostics:
setting worker timeout:
  error reading from connection

[lgatto]

This works again now. Just for the record, it only works with dist:precise, otherwise building R runs out of time.