Re: RFS: cdk 1.4.9-1
Hi Niels,
On Wed, May 23, 2012 at 2:45 PM, Niels Thykier <niels@thykier.net> wrote:
> I "just" read the diff between our current version (1.2.10) and the RFS
> version 1.4.9. Actually, thanks you just made me realize that it FTBFS
> when built twice in a row!
Ah, right! Yes, from 1.2 to 1.4 there are API changes...
Please do provide me details about build fails... part of it is prob
Debian specific, but some perhaps also CDK specific... the latter I
like to hear about :)
> Anyhow, it is quite possible that I saw false positives as I just read
> the diff once without considering new interfaces/super classes and
> whether the methods were "defined internal" (despite being public).
> Anyhow, to mention examples:
>
> PartialFilledStructureMerger:
> -public IAtomContainer generate() throws CDKException
> +public IAtomContainer generate(IAtomContainerSet atomContainers)
> throws CDKException
>
> SmilesParser:
> -private IAtom assembleAtom(String s) throws InvalidSmilesException
> +private IAtom assembleAtom(String s, IAtom lastNode, boolean
> bondExists) throws InvalidSmilesException
>
> CDKSourceCodeWriter*:
> -public void writeAtomContainer(IAtomContainer molecule)
> throws Exception {
> +private void writeAtomContainer(IAtomContainer molecule)
> throws Exception {
>From 1.2 to 1.4 that actually makes sense...
> IChemObjectBuilder lost a lof interface methods and it does not extend
> any other interface that could have gained those methods.
Yes, this one has seen a major rewrite in 1.4.
> These are examples of what I found;
Thanx for the detail!
> they may (or may not) be an issue.
> I also noticed now that some of the files disappearing appears to
> auto-generated JJTree or so? Anyway, with the clean rule not working my
> diff is currently a bit tainted.
Yes, some source code files are generated indeed.
>>> Have you (build-)tested the reverse dependencies of cdk?
>>
>> I do not think there are any reverse dependencies... ? I wish there
>> were, and I hope Bioclipse will be one of those; but at this moment I
>> cannot think of any... I cannot find right now where to find that rev
>> dep info...
>
> For reverse dependencies (not including build-depends) I notice at least
> 3 (potentional) rdeps in Debian:
>
> $ apt-cache rdepends libcdk-java
> libcdk-java
> Reverse Depends:
> debichem-cheminformatics
> science-chemistry
> python-cinfony
>
> Actually, the first two turns out to be meta-packages, but
> python-cinfony appears to be a genuine reverse dependency.
Stupid of me to forget about Cinfony!
Cinfony 1.1 should work fine with CDK 1.4.x:
http://baoilleach.blogspot.com/2011/12/cinfony-11-released.html
That post tells about a compile against 1.4.5, but as said, within
1.4.x there are no API changes (or very minor ones).
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
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