From: Syed A. R. <s9...@go...> - 2009-12-19 09:55:53
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Hi, While compiling the cdk code I found these warnings in abundance for example org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:148: warning: [deprecation] org.openscience.cdk.qsar.model.R.V2M in org.openscience.cdk.qsar.model.R has been deprecated [javac] this.rmssd = V2M.VectorToMatrix(rmssd, ncase, npvar); [javac] ^ secondly [javac] /DebugAdductFormula.java:76: warning: [deprecation] setCharge(java.lang.Integer) in org.openscience.cdk.formula.AdductFormula has been deprecated [javac] public void setCharge(Integer charge) { lastly DebugAminoAcid.java:268: warning: [deprecation] getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in org.openscience.cdk.AtomContainer has been deprecated [javac] public double getBondOrderSum(IAtom atom) { Dr. Syed Asad Rahman Research Scientist s9...@go... |
From: Rajarshi G. <raj...@gm...> - 2009-12-19 14:45:39
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On Sat, Dec 19, 2009 at 4:55 AM, Syed Asad Rahman <s9...@go...>wrote: > Hi, > While compiling the cdk code I found these warnings in abundance for > example > > org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:148: warning: > [deprecation] org.openscience.cdk.qsar.model.R.V2M in > org.openscience.cdk.qsar.model.R has been deprecated > [javac] this.rmssd = V2M.VectorToMatrix(rmssd, ncase, npvar); > [javac] ^ > For the warnings of this type I think it might be useful to remove the model.R package from master. IMO, a statistics interface is not really core cheminformatics. Does anybody actually use classes in this pacakge? [javac] /DebugAdductFormula.java:76: warning: [deprecation] > setCharge(java.lang.Integer) in org.openscience.cdk.formula.AdductFormula > has been deprecated > [javac] public void setCharge(Integer charge) { > > lastly > > DebugAminoAcid.java:268: warning: [deprecation] > getBondOrderSum(org.openscience.cdk.interfaces.IAtom) in > org.openscience.cdk.AtomContainer has been deprecated > [javac] public double getBondOrderSum(IAtom atom) { > Yes, these should probably get cleaned up in master -- Rajarshi Guha NIH Chemical Genomics Center |
From: Egon W. <ego...@gm...> - 2009-12-28 14:20:55
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Rajarshi, On Sat, Dec 19, 2009 at 3:45 PM, Rajarshi Guha <raj...@gm...> wrote: > On Sat, Dec 19, 2009 at 4:55 AM, Syed Asad Rahman <s9...@go...> > wrote: >> While compiling the cdk code I found these warnings in abundance for >> example >> >> org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:148: warning: >> [deprecation] org.openscience.cdk.qsar.model.R.V2M in >> org.openscience.cdk.qsar.model.R has been deprecated >> [javac] this.rmssd = V2M.VectorToMatrix(rmssd, ncase, npvar); >> [javac] ^ > > For the warnings of this type I think it might be useful to remove the > model.R package from master. IMO, a statistics interface is not really core > cheminformatics. Does anybody actually use classes in this pacakge? What are these classes doing? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Rajarshi G. <raj...@gm...> - 2009-12-29 12:38:43
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On Mon, Dec 28, 2009 at 9:20 AM, Egon Willighagen < ego...@gm...> wrote: > Rajarshi, > > On Sat, Dec 19, 2009 at 3:45 PM, Rajarshi Guha <raj...@gm...> > wrote: > > On Sat, Dec 19, 2009 at 4:55 AM, Syed Asad Rahman <s9...@go... > > > > wrote: > >> While compiling the cdk code I found these warnings in abundance for > >> example > >> > >> org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java:148: > warning: > >> [deprecation] org.openscience.cdk.qsar.model.R.V2M in > >> org.openscience.cdk.qsar.model.R has been deprecated > >> [javac] this.rmssd = V2M.VectorToMatrix(rmssd, ncase, npvar); > >> [javac] ^ > > > > For the warnings of this type I think it might be useful to remove the > > model.R package from master. IMO, a statistics interface is not really > core > > cheminformatics. Does anybody actually use classes in this pacakge? > > What are these classes doing? > They're wrappers around the JRI and R functionality, so that for example building a PLS model is simply a matter of instantiating a CDK class, rather then having to know the details of the pls() method in R. Given that a new version of JRI and Rserve is used, which quite different from the current version used in the CDK, it'd likely require a good amount of effort to update things. -- Rajarshi Guha NIH Chemical Genomics Center |