mbWorkflow error (missing IUPAC Name)

[sneumann]

Issue by tsufz from Tuesday Oct 22, 2013 at 16:30 GMT Originally opened as https://github.com/sneumann/RMassBank/issues/24

---

I get this error while fetching data from CTS. Some first idea? If not, I could upload files for analysis.

mbWorkflow: Step 1. Gather info from CTS 4172: smiles 4175: smiles 4177: smiles 4183: smiles 4187: smiles 4193: smiles 4204: smiles 4206: smiles Error in which(unlist(lapply(infos$synonyms, function(s) s$type == "IUPAC Name (Preferred)"))) : argument to 'which' is not logical

[sneumann]

Comment by schymane from Wednesday Oct 23, 2013 at 07:42 GMT

---

4206: I don't see an obvious issue SMILES to InChIKey with Cactus: http://cactus.nci.nih.gov/chemical/structure/CC(C)CC1=CC=CC(C(O)=O)=C1C(O)=O/stdinchikey then check in CTS: http://cts.fiehnlab.ucdavis.edu/service/compound/WXVFMRKUWGIPRB-UHFFFAOYSA-N {"type":"IUPAC Name (Preferred)","name":"3-(2-methylpropyl)phthalic acid","score":0}

The file order tells us that 4216 should be next...

4216: http://cactus.nci.nih.gov/chemical/structure/OC1=CC=C2C=CC=CC2=C1N=NC1=CC=C(C=C1)S(O)(=O)=O/stdinchikey http://cts.fiehnlab.ucdavis.edu/service/compound/RDUJRVXKAIVTDH-UHFFFAOYSA-N and this doesn't appear to have an IUPAC Name (Preferred) present (using find via Firefox). In fact, no IUPAC entries at all :(

[sneumann]

Comment by sneumann from Monday Oct 28, 2013 at 14:12 GMT

---

Fixed by [april2013hackfest 9aa778f] Added test for empty CTS data in sneumann, should go into meowcat, should go into BioC

[ermueller]

Can't this be closed? Or am I missing sth.?

[sneumann]

Yes, 9aa778fa9f174457706552b8f8062c88d560e2c9 is in meowcat.

[schymane]

yes, this is now in as a warning message, not an error: Warning messages: 1: In gatherData(id) : Compound ID 3334: no IUPAC name could be identified.