Hi. Il 02/02/2015 10:31, Michael Crusoe ha scritto: > I am packaging the Trinity RNASeq assembler for Debian and it > (sadly) does use this old library. Can you restore > libcollections15-java to the archive?
Having a quick look at it, it seems to me that RNASeq uses collections just through the Jung library (just as geogebra does), which is not in Debian as well (and has a many-years-old RFP bug, #368931). Do you intend to package it? Take also into account that, apparently, RNASeq only uses very small parts of jung, and that jung appears to be dead since early 2010. Personally, I would suggest to do as I did with geogebra: put an embedded copy of the jung classes you need in your package, document this in d/README.source and patch them in order to use the new collections library (you can probably take a lot from Emmanuel's patch on geogebra). I also read in d/README.source from geogebra (that I wrote a long time ago) that there are parts of jung that are not free, so jung as a whole could not be packaged (I do not remember how extensively the non-free part are and what was the actual problem). Fortunately geogebra does not need the non-free parts, so I could embed just the classes that were needed. HTH. Regards, Giovanni. -- Giovanni Mascellani <giovanni.mascell...@sns.it> PhD Student - Scuola Normale Superiore, Pisa, Italy http://poisson.phc.unipi.it/~mascellani
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