cbroeckl / RAMClustR

Assigning precursor-product ion relationships in indiscriminant MS/MS data
MIT License
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suspected write problem in RAMClustR::write.msp #18

Closed martenson closed 3 years ago

martenson commented 3 years ago

As part of our wrapping of RAMClustR in Galaxy, we are routinely running a fairly basic test described below. After switching from 1.0.9 to 1.2.1 we are experiencing the following error:

Error in round(ramclustObj$clri[i], 2) : 
  non-numeric argument to mathematical function
Calls: store_output -> <Anonymous> -> paste0
Execution halted

Our store_output function calls the RAMClustR::write.msp here

@hechth suspects that new version of RAMClustR does not expect a parameter to be missing

The parameters of the test are here The input file is here

hechth commented 3 years ago

I did some follow-up and seems like x$clri is Null, therefore it can't be passed to the round(...) function.

The input data doesn't contain retention indices. I'll be happy to try to contribute a possible fix for this problem :).

martenson commented 3 years ago

@cbroeckl Could you please give us some feedback on this issue?

cbroeckl commented 3 years ago

@martenson My apologies - i need to figure out why i am not getting notifications! I will get this fixed shortly.

cbroeckl commented 3 years ago

@martenson I believe that this should pass your Galaxy check now. I also believe i figured out how to have Github notifiy when an issue is created or commented on. Win.

cbroeckl commented 3 years ago

@martenson @hechth - updated ramclustr is on its way to CRAN.

martenson commented 3 years ago

This is awesome! Many thanks @cbroeckl!

martenson commented 3 years ago

Seems to work as advertised. Many thanks!