test case for pf-db2feather.gtdb.02 error problem

[GhadaNOUAIRIA]

pf-db2feather.gtdb.02.expect added
pf-db2feather.gtdb.02 target added to Makefile
pf-db2feather.gtdb.02.sqlite3 not added as sqlite3 extension is ignored in .gitignore (I can force git add but it is the same file from ~/dev/pfitmap-nextflow/gtdb.pf.db
Still working on a possible fix in pf-db2feather.r but haven't been successful yet

[erikrikarddaniel]

You must add the sqlite file; use git add -f. It's not incredibly large, I hope?

[GhadaNOUAIRIA]

I added pf-db2feather.02.sqlite3 now. The same error is replicated when using any old test case you have (like pf-db2feather.01.sqlite3

…

On Thu, 14 May 2020 at 13:59, Daniel Lundin ***@***.***> wrote: You must add the sqlite file; use git add -f. It's not incredibly large, I hope? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#25 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIWD25EICDPBWHHVHGUZGQLRRPMJHANCNFSM4NAQH4QA> .

-- Ghada NOUAÏRIA, PhD Department of Biophysics and Biochemistry Stockholm University Sweden

[erikrikarddaniel]

What do you mean with "The same error is replicated when using any old test case you have". They all pass for me.

[erikrikarddaniel]

When I run your new test case in your repo (dev branch) I get the following error:

INFO: 2020-05-14 15:43:14: pf-db2feather.r 1.9.2, connecting to pf-db2feather.gtdb.02.sqlite3
Error: no such table: accessions
Execution halted
make: *** [Makefile:148: pf-db2feather.gtdb.02] Error 1

To me, this suggests something went wrong with the upstream process, i.e. pf-classify.r. Moreover, it's not the same error as you mentioned before.

[erikrikarddaniel]

On closer inspection (using the "DB browser for SQLite" program, available in Ubuntu), there are no tables in the new sqlite file.