Fix 1013

[LeilyR]

inspired by #1013

[LeilyR]

Hi @dpryan79, sorry to bother you. Could you please have a look at this. I think it needs to be fixed under account. Let me know if there anything I can do for it. Thanks a lot!

[dpryan79]

@LeilyR I'll see what I can do

[LeilyR]

@dpryan79 Thanks a lot

[LeilyR]

Just to let you know, this pc2 value changes frequently between those two numbers, sometime is 1.2325951644078315e-32 some other time is 2.49319462166397e-32. I have seen both of them.

[dpryan79]

Yeah, I think it depends on the CPU that gets used.

[dpryan79]

@LeilyR can you check computeMatrixOperations locally? It's running rbind and I have no clue why it's immediately throwing an error.

[LeilyR]

@dpryan79 I have already tried it locally and it fails there too. I was also really confused, since it says it cannot find the info command. with the updated galaxy version also master branch fails for this test, Though I could get to run the 3.4.3 version locally with no issue. 3.4.3 is the latest version before introducing dataRange. What I do not understand is that if that is the problem why rbind test passes. Also info used to pass before we change the galaxy version. I will have a look at it again, but if you also have any opinion I would be happy to hear. Again thank a million for looking into it.

[dpryan79]

I mean on the command line, does it run properly there with computeMatrixOperations rbind ...? The data is under galaxy/wrapper/test-data.

[LeilyR]

I see ok thanks , i will check

[LeilyR]

Hi @dpryan79 , I got to fix the galaxy issues. However there is an issue with the tests running under your account. The error is:
Error: Theadd-pathcommand is disabled. Please upgrade to using Environment Files or opt into unsecure command execution by setting theACTIONS_ALLOW_UNSECURE_COMMANDSenvironment variable totrue. For more information see: https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/
Could you please update this? Do you think I should merge my PR despite those failures?

[dpryan79]

The azure tests are all green so it's safe to merge. I'll see if I can get the environment variable set properly. Otherwise I'll just update the nodejs stuff, which should get migrated to the deeptools repo so others can update it more easily.

[dpryan79]

It only fails on the annoying plotPCA test. Long-term we might just remove that, since it results only in false positive errors.

[LeilyR]

thanks a lot @dpryan79 ! I will merge it then :)