Helge Hecht

Thanks for the quick reply! I'm currently also looking into the `devtools::check()` command but there are quite some other issues apparently - I will try to clean that up and...

By now I am at a point where `devtools::test()`, `devtools::check()` and `tools::testInstalledPackage('xMSannotator') all work, but `covr::package_coverage()` still fails the tests - any hints?

Yes, the most recent commit in which I changed the tests is here: https://github.com/hechth/recetox-xMSannotator/commit/71b585437ce3b3e2d43876b7c8434feb38871437. On my machine it now all passes, also the codecov works since I altered the test...

@jimhester I'm again at a point where `devtools::test(...)` and even `devtools::check(...)` pass, but the tests using `tools::testInstalledPackage(...)` fail - do you know someone who maybe has a better insight into...

@jimhester you need to fetch the test data (it is quite something, so we moved it to a different [repo](https://gitlab.ics.muni.cz/umsa/umsa-files/-/tree/master/testdata/recetox-xMSannotator) (should be publicly readable, just copy the content of the...

@dewittpe the tests in the project I mentioned above also involved comparisons of rather large files stored as .rds on disk, so there seems to be something in common.

@bgruening Indeed! I'm using a normal list, so the `inchi` format how it is called. Some example data is attached. [inchi.zip](https://github.com/bgruening/galaxytools/files/7970845/inchi.zip)

I tried using 2 columns separated with `,`, that didn't change anything on the specific history (https://umsa.cerit-sc.cz/u/hechth/h/compound-convert-test).

Nope - tried adding a column manually, using tabs, commas, the Galaxy tool, but always the same - no index in the output and invalid data gets dropped silently.

I explicitly want the inchi, since I want to compute smiles from inchi. I also don't get why indexing is possible with SMILES and not with inchi? They're both just...