Rectified Issue #11

[Aggarwal-Ayush]

Now aliases are mapped correctly whenever chromosome is specified even when the gene is correct on another chromosome.

[lwaldron]

Thanks @Aggarwal-Ayush! Could you take a look at the cause of the failed checks? And, would you add a unit test that confirms your fix is working, e.g. it could use code I posted on the issue #11

[Aggarwal-Ayush]

Yes, I'm looking into it. I'll add the unit tests after I determine the cause of the failed checks.

[Aggarwal-Ayush]

Hi @lwaldron! Somehow the hgnc.table in the package does not contain the column for chromosome now and I think that is what is causing the checks to fail. Could you please take a look at it?

[lwaldron]

yes, will do.

[lwaldron]

@Aggarwal-Ayush check your HGNChelper version - 0.8.1 in CRAN does not have the chromosome column, but the current version on GitHub (0.8.7) does (you can check yourself in the data/ folder). But it means that isn't the reason for your commit failing, since GHA installs and checks the current version from GitHub.

[Aggarwal-Ayush]

@lwaldron Yes, my mistake. I updated to the latest version from GitHub and then ran the test_checkGeneSymbols.R manually in RStudio. It is passing all the test except for the mouse test 2. In that, the correct symbol specified for "Cpamd8" is "Cpamd8" whereas for "cpamd8" it is "Mug2" and for "mug2" it is "Cpamd8 /// Mug2" while for "Mug2" it is "Mug2". Is this the expected behaviour?
Also, I've added the unit test for my current fix under "human test 3 - chromosome".

[lwaldron]

@shbrief can you say what is the correct behavior for this mouse test? While you're checking - can you check whether there is a chromosome column available with the mouse map download?

[shbrief]

@Aggarwal-Ayush I can't reproduce the error with the mouse test 2 - all tests were passed from my end. Is it possible that your mouse data file is corrupted? Are you using GitHub LFS?

@lwaldron From the latest download, I didn't see a chromosome column in the mouse map.

[lwaldron]

Alright, I merged the PR, which should make it a little easier to make sure everyone is testing the same version. I'll also bump the version number to 0.8.8 in a moment.

[lwaldron]

Note, I also don't see any failing mouse unit test in GHA: https://github.com/waldronlab/HGNChelper/runs/1733750433?check_suite_focus=true

[Aggarwal-Ayush]

Yes, that was an error on my part only. I fixed it in the last commit. This error is "undefined columns selected" which may be referring to one of my code line although I'm not sure because my latest commit was passing all the tests in Rstudio(latest verion).