As you've probably found the message comes from CMLAtom, and is one of the hardcoded validation rules for CML (these would be better done with an XPath-type tool like Schematron, but that's irrelevant).
The error makes no sense! My guess would be that it's picked up the wrong version of some library. I haven't used Java recently - my suggestion would be to see if it is true with other Java versions. If I understand it right, the error occurs in the repository tests when building the system. P. On Sun, Jul 11, 2021 at 6:43 PM Egon Willighagen <egon.willigha...@gmail.com> wrote: > > > On Sun, Jul 11, 2021 at 7:29 PM Peter Murray-Rust <pm...@cam.ac.uk> wrote: > >> I imagine I wrote this code but don't have it on my machine at present. >> Can you give a pointer to the Github repo and I'll have a look - but I'm >> not very optimistic I can help. >> > > https://github.com/BlueObelisk/cmlxom > > >> Would love to see some projects that use CMLXom - it has a lot of >> potential still. >> > > Well, this is why I am working on it. The CDK is using it, and as a > consequence Bacting (*) is too. The current CMLXOM has some dependency > versions with security issues. > > I found a workaround for the failing test, to use cml:cml instead of > cml:atom. The problem is that it remembers a Stack that does not go with > the CML String being parsed. Hence my suspicion of some concurrency. The > problem basically is the global variables in CMLNodeFactory. > > So, with the code base also compiling in GitHub, I will move on next > weekend with updating the pom.xml to prepare for releases via Sonatype for > Maven Central. > > Egon > > -- > This year I am stepping down as co-Editor-in-Chief of the Journal of > Cheminformatics, because of a conflict of interest with Springer Nature. > See https://twitter.com/egonwillighagen/status/1403299501947899907 > > ----- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> > / @egonw <https://scholar.social/@egonw> > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: https://www.zotero.org/egonw > ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> > ImpactStory: https://impactstory.org/u/egonwillighagen > -- "I always retain copyright in my papers, and nothing in any contract I sign with any publisher will override that fact. You should do the same". Peter Murray-Rust Reader Emeritus in Molecular Informatics Yusuf Hamied Department of Chemistry University of Cambridge CB2 1EW, UK +44-1223-336432
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