fix R environment at Travis

[StrikerRUS]

While preparing #228 I've noticed that code coverage value was extremely small:

I've dig deeper and it turned out that all this time tests hadn't been run due to this function:

rgf/R-package/tests/testthat/test_package.R

Line 7 in f47000c

skip_test_if_no_module <- function(MODULE) { # MODULE is of type character string ( length(MODULE) >= 1 )

The reason was in that even after applying all my hotfixes in #208 scipy (or numpy) failed because of hard linking to conda's library, which conflicts with system-wide one. So, this PR solves this problem by installing PyPI versions of all packages.

While R CMD check is not verbose, but I needed any info why rgf module is not available, I managed to get useful logs by running Rscript -e 'testthat::test_dir("./tests")'.

In addition, even in this new clean environment and after improving the code coverage test_dir yields the following error/warning (I don't know what it is):

✔ | OK F W S | Context
Error in x[[method]](...) : attempt to apply non-function
Calls: <Anonymous> ... <Anonymous> -> o_apply -> lapply -> FUN -> <Anonymous>
══ Results ═════════════════════════════════════════════════════════════════════
OK:       0
Failed:   2
Warnings: 0
Skipped:  0
Execution halted
Warning: unknown option ‘--with-keep.parse.data’

My assumption is that RGF suffers from the following bug: r-lib/testthat#700 . Ping @mlampros for the future investigation.

[mlampros]

@StrikerRUS the attempt to apply non-function is a known issue when there is a problem with either the python configuration or when python packages are not installed properly. There are similar issues for packages that I ported from python like the fuzzywuzzyR package.

However, based on the web-link you've mentioned it seems that we should add

context("tests for RGF")

in the first line of the tests file so that this issue can be resolved.

[StrikerRUS]

Thank you for your prompt response, @mlampros !

Yeah, I've observed errors, that you've mentioned, before I switched to PyPI packages. With those errors the coverage was ~17% what indicates real problems.

However, the exact error message

Error in x[[method]](...) : attempt to apply non-function
Calls: <Anonymous> ... <Anonymous> -> o_apply -> lapply -> FUN -> <Anonymous>

didn't appeared in issue reports for your other packages and seems to be a different error. Also please note that the coverage is OK now with this PR. So, I'm a little bit confused... Have you ever got this error locally on your machine (by Rscript -e 'testthat::test_dir("./tests")', for instance)?

I tried to set contex as it suggested here but it didn't solve the issue. However, I think that context should be set anyway. Please create a PR for this.

[mlampros]

@StrikerRUS this error case is new to me. I don't know if it's related with the conda environment set-up. In all of my packages (Github repositories) I add the usual .travis.yml file. I don't know if the related testing documentation could be of any help here.
I'll open the PR as you suggested.

[mlampros]

I'll open a PR to address the error case : 'attempt to apply non-function

[fukatani]

Thanks!