get travis-ci to build and run models about example-models

[dmenne]

I have written a minimal test package for TravisCI and running vignette build; see

https://travis-ci.org/dmenne/rstanyaml/builds/75600644

Build of rstan stops at line 1566.

Out of memory as reported by many others. clang to the rescue?

travis-ci/travis-ci#1972

Looks like Travis open source version cannot handle rstan complexity. Too bad. Will give up.

lang__grammars__statement_2_grammar_inst.o
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c lang__grammars__statement_grammar_inst.cpp -o lang__grammars__statement_grammar_inst.o

g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.6/README.Bugs> for instructions.
make: *** [lang__grammars__statement_grammar_inst.o] Error 4
ERROR: compilation failed for package ‘rstan’

[dmenne]

I am currently working on a package to structure examples. I had played around with travisci, and it has great support for package, out of the box.

I suggest to make examples to package: in inst/extdata/vol1/rats etc, I keep the raw stan and data.R files with the same structure as before. All R-test files will be written as vignettes; these are automatically tested by travis build, and provide nice documentation.

If someone wants to play with the code, the vignettes can be run separately, no global rebuild needed.

You can put makefiles into the inst/extadata/volx files; those currently available do not run, and I gave up when trying to understand the directory structure, which is surprisingly different between the CmdStan installer and Github clone. Maybe you could provide one working example. I know that Bob want standalone tests.

So for pure CmdStan testing, a top level makefile refering to the sub-makefiles could be added.
I will make a separate github repository tomorrow so you can check the concept.

(Corrected: should be packages, not projects as had been written)

[syclik]

That would be great! I couldn't follow everything you said, but if you have
an idea of an implementation, that's better than what I've got.

On Wed, Aug 12, 2015 at 11:30 AM, Dieter Menne [email protected]
wrote:

I am currently working on a project to structure examples. I had played
around with travisci, and it has great support for projects, out of the
box. I suggest to make examples to projects: in inst/extdata/vol1/rats etc,
I keep the raw stan and data.R files with the same structure as before. All
R-test files will be written as vignettes; these are automatically tested
by travis build, and provide nice documentation.

If someone wants to play with the code, the vignettes can be run
separately, no global rebuild needed.

You can put makefiles into the inst/extadata/volx files; those currently
available do not run, and I gave up when trying to understand the directory
structure, which is surprisingly different between the CmdStan installer
and Github clone. Maybe you could provide one working example.

So for pure CmdStan testing, a top level makefile refering to the
sub-makefiles could be added.
I will make a separate github repository tomorrow so you can check the
concept.

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#26 (comment)
.

[dmenne]

See https://github.com/dmenne/bugsexamples and http://menne-biomed.de/uni/rats.html for a sample output vignette. Yaml not yet done, but hopefully coming soon. The CmdStan version is your homework assigment .-)

[dmenne]

https://travis-ci.org/dmenne/bugsexamples/builds

Working on yaml/rstan. This sometimes works, sometimes there is an error during rstan install. In one case vignette build (=lot of rstan) finished with ok, but there was an internal error not caught as such by Travis.
Running with multiple chains and/or cpu has been switched off.

I suspect there is some sort of timeout going on. Any other examples of vignette rstan builds around?