Fix make check warnings

[dlm]

From Personal email from @jisuk1

So it seems like CRAN doesn't want Makefile and misc in the submission. For the submission, I can manually exclude them and submit, but for later maybe it would be better to reorganize file structure something like
r-tda: top level

• TDA: put all the things to be submitted there
• Makefiles
• misc

so that on the submission we can just build package from TDA directory and submit it to CRAN. How do you think?

[dlm]

Thank you for updating by hand for the release. I don't think we need to refactor the repo for future releases though. We can use the .Rbuildignore to tell the build command what files to ignore.

I can't test until we get the memory_fix brach merged, but, I will push a PR with a proposed fix (and if I can figure out how, add make check to the automated testing on travis.

[jkim82133]

I merged memory_fix branch, so could you check whether this will work?