Split dependency building and pkg checking on travis

[sgibb]

Currently our CI fails on travis because the hard runtime limit for jobs
is 50 minutes and installing all dependencies of MSnbase takes a lot of
more time.

This commit introduces multiple changes:

• Use 2 cores for package building/installation.
• Split building of dependencies and package checking into different
  jobs which allows us to use 2x50 minutes. The build job builds all dependencies and create a cache which is used by the check job.
• Automatically deploy of pkgdown based documentation to github pages the master branch.

@lgatto if you want to use the automatic deployment you have to create a Personal Access Token with the public_repo scope/permission and register it in the travis' settings with the name GITHUB_PAT

We could create even more jobs to reduce the check time a little bit (currently after cache building it takes ~ 35 min to run travis but using three check jobs ("examples", "vignettes", "test") we could go down to ~ 25 min:

2 jobs (build + check, current PR)

5 jobs (build + 3 check + codecov) (the codecov job failed because I accidentally used rscript instead of Rscript)

@lgatto If you wish I could easily extend this PR to the version with 5 jobs.

BTW:

• I add skip_on_travis() to tests/testthat/test_MSmap.R on my forked repository because downloading files from AnnotationHub always failed (maybe we should consider it to add it here, too).
• MSnbase needs more than 250 packages to build. Maybe we could remove a few, e.g. shiny is just used for one function (could selectFeatureData move to pRolocGUI?), same for XML which is just used by .isCentroidedFromFile and mzID both could be replaced by mzR/xml2 (the latter is downloaded anyway by other dependencies), affy/affyio just for MAplot, gplots just for heatmap.2 in the vignette, ... it is somehow connected to speed up package load time #201 but would just improve the build time. Should we open an issue and try to remove some build dependencies or just keep status quo?

[lgatto]

Great, thanks @sgibb. I have created a PAT and added it to the travis setting.
I wouldn't mind 5 jobs, if you are happy to do it and think it's worth it.

I would prefer to keep all tests, as much as possible.

I will need to check if .isCentroidedFromFile is still needed, but migrating it to xml2 would be good anyway. But not sure about mzID - I think it is important to verify some id data validity against mzR But I indeed think that we could re-implement (nicer) MAplots to get rid of affy. We still need a dependency to plot the heatmap in the vignette though.

But yes, let's open a issue to keep track of the dependencies and try to reduce them.

[sgibb]

I added skip_on_travis to tests/testthat/test_MSmap.R. Somehow AnnotationHub could not download the file (even when the VM on travis has internet access). Sometimes it is working, e.g.: https://travis-ci.org/sgibb/MSnbase/builds/444428390
But I rerun this last job multiple times without a single success (we just need a single successful download because the ~/.AnnotationHub is cached, too).

You can simply revert it with git revert 7b7c32d6293e13d281c85e18b7867df0386f46fc.

IMHO this could be merged to master now.

Please note: I recognized that pkgdown::build_site fails because of:

<simpleError in add_classes_to_exports(ns = nsenv, package = package, exports = exports,     nsInfo = nsInfo): in ‘MSnbase’ methods for export not found: reduce>
There were 50 or more warnings (use warnings() to see the first 50)
Error in add_classes_to_exports(ns = nsenv, package = package, exports = exports,  : 
  in ‘MSnbase’ methods for export not found: reduce

I am not sure how to solve this (without exporting reduce, seems to be related to pkgload

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[lgatto]

Thanks!

[lgatto]

@sgibb - is the pkgdown site build and deployed automatically, in the end?

[sgibb]

If the build of the master branch is successful, travis updates the gh-pages branch automatically (it works: https://github.com/lgatto/MSnbase/tree/gh-pages). But I guess you use the doc/ directory instead the gh-pages branch for the pkgdown site. So currently the automatically build site isn't visible.

There are two solutions:

1. You use the gh-pages branch for the github pages website, remove the doc/ directory from master (that would also remove the need for branch-specific .gitignore files).
2. Or I set the target_branch in .travis.yml to master but I was afraid that it could destroy our git history.

For https://github.com/sgibb/topdownr/ I use the first option.

[lgatto]

OK, thanks. I'll think about migrating to solution 1 above.

[lgatto]

I think the automatic deploy to gh-pages is a nice option. I modified the settings to use the gh-pages branch, but http://lgatto.github.io/MSnbase/ throws a 404 error. Not sure if it's only a matter of time, or did I miss something, @sgibb.

[lgatto]

All good now, it is live. I will apply the same strategy for my other packages. Thanks again @sgibb!

[sgibb]

I can't see a 404 but the regular pkgdown site. I guess it was just a matter of waiting for the next push from travis.