Recent r java issues

[trinker]

As of about a week ago my repo that contains java based r packages now errors and I am unsure of how to fix this. The repo utilizes the following .yml:

language: java

before_install:
  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
  - chmod 755 ./travis-tool.sh
  - ./travis-tool.sh bootstrap
install:
  - sh -e /etc/init.d/xvfb start
  - sudo R CMD javareconf
  - ./travis-tool.sh aptget_install r-cran-xml 
  - ./travis-tool.sh aptget_install r-cran-gplots
  - ./travis-tool.sh install_github hadley/devtools
  - ./travis-tool.sh install_github cboettig/knitcitations
  - ./travis-tool.sh install_deps
  - Rscript -e "source('http://bioconductor.org/biocLite.R');
      biocLite();
      biocLite('Rgraphviz')"
script: ./travis-tool.sh run_tests
notifications:
  email:
    on_success: change
    on_failure: change

env:
   global:
     - R_BUILD_ARGS="--compact-vignettes=gs+qpdf" 
     - R_BUILD_ARGS="--resave-data=best" 
     - DISPLAY=:99.0

But now errors with:

* installing the package to build vignettes
      -----------------------------------
ERROR: dependencies ‘openNLP’, ‘venneuler’, ‘xlsx’ are not available for package ‘qdap’
* removing ‘/tmp/RtmpmgnE7h/Rinst6c5c1aa1ec6d/qdap’
      -----------------------------------
ERROR: package installation failed
The command "./travis-tool.sh run_tests" exited with 1.
Done. Your build exited with 1.

The common link between these 3 packages is an rJava/java dependency. The package passes local CRAN checks.

[craigcitro]

this looks like some dependencies got changed out from under you... I'll give it a spin later tonight and see what I find.

[craigcitro]

OK, I fixed the rJava issue, but just hit a separate TeX-related problem that I've seen before:
https://travis-ci.org/craigcitro/qdap/builds/22349517
I'll have time to take another crack at it tonight, and hopefully I'll send a PR with the fix then.

[craigcitro]

OK, that run got to the point of hitting a TeX issue -- @trinker, is this something that looks familiar? (if not, i'll dig a little deeper.)

[trinker]

Thanks for taking the time to look at this. No this is new as well. That vignette has been a part of qdap since early March with no errors (and multiple commits and uploads to GitHub. The errors occurred beginning April 1st.

[craigcitro]

OK, so I've cleaned up all the issues you were seeing, and learned something useful in the process -- but there's still one thing I'm not 100% clear on.

• The build issues you were seeing were indeed that rJava was failing to install from source; switching that to a binary package pulled the right dependencies, so that worked fine.
• I added BOOTSTRAP_LATEX=1 to your .travis.yml, so that all the right TeX-related packages were installed.
• That was still causing trouble -- it turns out the default TeX packages in ubuntu 12.04 (which is what travis's images use) are really old, and there's a well-known collection of backports to solve exactly this problem. (I opened Switch to using a PPA for newer TeX packages? #113 to track possibly always using that when tex packages are requested.)

So, problem solved -- but I'm still totally stumped as to why this ever worked. My current hypothesis is that one of the other repos we use (possibly one of the PPAs?) had some newer packages, but has since removed them. As confirmation, builds that once passed are now failing (here and here) -- so something upstream from all of us changed.

[craigcitro]

(... hit Comment too soon ...)

I'm closing for now, but do open this again if you see weirdness pop up again.

[trinker]

Thank you kindly. This indeed did work. I must admit I chuckled a bit about this comment So, problem solved -- but I'm still totally stumped as to why this ever worked.

Thank you for taking the time to track this down and get me up and running again. I also opened an issue with Colin G. csgillespie/travis-examples#10 to reference this issue in case he feels it would be useful to update the examples he has there. It may not even be relevant but I am trying to connect the pieces in case it is.