Attempts to fix the build timeout on Circle.

[hlapp]

More precisely, fix the deploy step timeout. The build actually succeeds, which presumably is why there wasn't any issue with the test on PR #143. The build with failed deploy step is here: https://circleci.com/gh/NESCent/popgenInfo/428

The odd thing here is that nobody changed the jquery copy, so it's not clear why this would be write-protected now if it wasn't before.

The integration test for this PR is somewhat bogus, because the failing step (deployment of rebuilt website) is not (and, until we create a development server, arguably cannot be) actually part of the tests conducted for a PR.

[zkamvar]

This seems to pass, so I'm going to merge it.

[zkamvar]

aaand, it doesn't work: https://circleci.com/gh/NESCent/popgenInfo/430

[zkamvar]

When I inspect the directories, all of the write permissions appear to be the same:

12:29:36~/Documents/popgenInfo (master)> ls -larth build/libs/highlight/
total 40
-rw-r--r--  1 zhian  staff   320B Mar  1 12:29 textmate.css
-rw-r--r--  1 zhian  staff    10K Mar  1 12:29 highlight.js
-rw-r--r--  1 zhian  staff   299B Mar  1 12:29 default.css
drwxr-xr-x  5 zhian  staff   170B Mar  1 12:29 ..
drwxr-xr-x  5 zhian  staff   170B Mar  1 12:29 .
12:29:45~/Documents/popgenInfo (master)> ls -larth use
total 136
-rw-r--r--   1 zhian  staff   3.1K Mar  1 12:29 startMicrosatellite.Rmd
-rw-r--r--   1 zhian  staff   5.6K Mar  1 12:29 StartSNP.Rmd
-rw-r--r--   1 zhian  staff     0B Mar  1 12:29 README.md
-rw-r--r--   1 zhian  staff   5.2K Mar  1 12:29 PopDiffSequenceData.Rmd
-rw-r--r--   1 zhian  staff   162B Mar  1 12:29 Makefile
-rw-r--r--   1 zhian  staff   1.3K Mar  1 12:29 LinksToResources.md
-rw-r--r--   1 zhian  staff   6.4K Mar  1 12:29 DifferentiationSNP.Rmd
-rw-r--r--   1 zhian  staff   9.2K Mar  1 12:29 2016-01-26-SNP-selection.Rmd
-rw-r--r--   1 zhian  staff    11K Mar  1 12:29 2015-12-15-microsatellite-differentiation.Rmd
-rw-r--r--   1 zhian  staff   5.9K Mar  1 12:29 2015-05-18-Dist-SNP.Rmd
drwxr-xr-x  38 zhian  staff   1.3K Mar  1 12:29 ..
drwxr-xr-x  12 zhian  staff   408B Mar  1 12:29 .

[hlapp]

Apparently the bootstrap and jQuery libraries have been updated for Rmarkdown/pandoc. The following is after issuing make deploy:

hlapp@host:~/popgenInfo$ ls -l build/libs/
total 24
drwxr-xr-x 6 hlapp adm  4096 Mar  1 19:55 bootstrap-3.3.1
drwxr-xr-x 6 root  root 4096 Mar  1 20:05 bootstrap-3.3.5
drwxr-xr-x 2 hlapp adm  4096 Mar  1 19:55 highlight
drwxr-xr-x 2 hlapp adm  4096 Mar  1 19:55 jquery-1.11.0
drwxr-xr-x 2 root  root 4096 Mar  1 20:05 jquery-1.11.3
drwxr-xr-x 2 root  root 4096 Mar  1 20:05 navigation-1.0
hlapp@host:~/popgenInfo$ 

The directories owned by root were newly created from within the Docker container, so must have come from running the rendering through Rmarkdown and pandoc.

@zkamvar: Is there any reason we need to keep anything under build/lib in the git repo if the rendering generates these anyway? If not, I can just delete the whole build/lib directory from within the container after the rendered site archive is created.

I should of course also look into controlling the userID under which the processes run within the container. I think newer versions of Docker allow this (unlike at the time of the hackathon).

[zkamvar]

@zkamvar: Is there any reason we need to keep anything under build/lib in the git repo if the rendering generates these anyway? If not, I can just delete the whole build/lib directory from within the container after the rendered site archive is created.

No, I don't think we need to keep anything under build/lib if Rmarkdown/pandoc is auto-generating it upon absence. I've created a branch that removes these.