Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]
Hi Sune,
On Sun, Feb 22, 2015 at 06:12:55PM +0000, Sune Vuorela wrote:
> On 2015-02-22, Andreas Tille <andreas@an3as.eu> wrote:
> > I tried the stupid approach and simply replaced the affected files
> >
> > IAxis.java IHistogram*.java
> >
> > by the equally named files I found in SVN. But this was probably to
> > simple and did not build. I guess this approached needs somebody who
> > has some basic Java experience.
> >
> >> That leaves src/hep/aida/bin where I couldn't find correspondent files
> >> on freehep.org. That means you probably have to remove the whole
> >> directory and try to recompile colt. Every class that imports
> >> "hep.aida.bin" will need a patch or has to be excluded as well.
> >
> > I could imagine that this would work. Any volunteer?
>
> I do imagine it be easier for people to jump in if there was a git
> branch or similar with your not working stuff, and a quick introduction
> to how to attempt to build it.
OK, point taken. I moved the repository to
Vcs-Git: git://anonscm.debian.org/debian-med/colt.git
Respositories of Debian Med have ACLs set so any DD can commit. If you
are no DD and no member of Debian Med team I'd happily forward any
patches. When doing so I realised the changes commited by Tim Booth
that try to tackle the issue in a similar as suggested manner (I somehow
forgot this over time) but there are remaining issues brought up by
ftpmaster which are documented in the header of the patch:
https://anonscm.debian.org/cgit/debian-med/colt.git/tree/debian/patches/build_without_aida_interface_defs.patch
As far as I understand ftpmaster everything needs to be removed in
src/hep/aida (including bin and ref). I did not manage to remove
since it is used in the cern code:
$ grep -R hep\.aida\. | grep \.java:
src/cern/colt/matrix/bench/BenchmarkMatrix.java: hep.aida.bin.BinFunctions1D F = hep.aida.bin.BinFunctions1D.functions;
src/cern/colt/matrix/bench/BenchmarkMatrix.java: hep.aida.bin.BinFunction1D[] aggr = null; //{F.mean, F.median, F.sum};
src/cern/colt/matrix/bench/BenchmarkMatrix.java: hep.aida.bin.BinFunctions1D F = hep.aida.bin.BinFunctions1D.functions;
src/cern/colt/matrix/bench/BenchmarkMatrix.java: hep.aida.bin.BinFunction1D[] aggr = null; //{F.mean, F.median, F.sum};
src/cern/colt/matrix/doublealgo/Sorting.java: hep.aida.bin.BinFunctions1D.sum<br>
src/cern/colt/matrix/doublealgo/Sorting.java:DoubleMatrix2D sorted = quickSort(matrix,hep.aida.bin.BinFunctions1D.median);
src/cern/colt/matrix/doublealgo/Sorting.java://DoubleMatrix2D sorted = quickSort(matrix,hep.aida.bin.BinFunctions1D.sumOfLogarithms);
src/cern/colt/matrix/doublealgo/Sorting.java:public DoubleMatrix2D sort(DoubleMatrix2D matrix, hep.aida.bin.BinFunction1D aggregate) {
src/cern/colt/matrix/doublealgo/Sorting.java: hep.aida.bin.BinFunction1D[] func = {aggregate};
src/cern/colt/matrix/doublealgo/Sorting.java: A = sort.sort(A,hep.aida.bin.BinFunctions1D.median);
src/cern/colt/matrix/doublealgo/Sorting.java: //A = sort.sort(A,hep.aida.bin.BinFunctions1D.sumLog);
src/cern/colt/matrix/doublealgo/Sorting.java: hep.aida.bin.BinFunction1D[] funs = {hep.aida.bin.BinFunctions1D.median, hep.aida.bin.BinFunctions1D.sumLog, hep.aida.bin.BinFunctions1D.geometricMean};
src/cern/colt/matrix/doublealgo/Formatter.java: hep.aida.bin.BinFunctions1D F = hep.aida.bin.BinFunctions1D.functions; // alias<br>
src/cern/colt/matrix/doublealgo/Formatter.java: hep.aida.bin.BinFunction1D[] aggr = {F.mean, F.rms, F.quantile(0.25), F.median, F.quantile(0.75), F.stdDev, F.min, F.max};<br>
src/cern/colt/matrix/doublealgo/Formatter.java:hep.aida.bin.BinFunctions1D F = hep.aida.bin.BinFunctions1D.functions;
src/cern/colt/matrix/doublealgo/Formatter.java:hep.aida.bin.BinFunction1D[] aggr = {F.mean, F.rms, F.quantile(0.25), F.median,F.quantile(0.75), F.stdDev, F.min, F.max};
src/cern/colt/matrix/doublealgo/Formatter.java://hep.aida.bin.BinFunction1D[] aggr = {F.mean, F.median, F.sum};
src/cern/colt/matrix/doublealgo/Formatter.java:@see hep.aida.bin.BinFunction1D
src/cern/colt/matrix/doublealgo/Formatter.java:@see hep.aida.bin.BinFunctions1D
src/cern/colt/matrix/doublealgo/Formatter.java:public String toTitleString(DoubleMatrix2D matrix, String[] rowNames, String[] columnNames, String rowAxisName, String columnAxisName, String title, hep.aida.bin.BinFunction1D[] aggr) {
src/cern/colt/matrix/doublealgo/Formatter.java:@see hep.aida.bin.BinFunction1D
src/cern/colt/matrix/doublealgo/Formatter.java:@see hep.aida.bin.BinFunctions1D
src/cern/colt/matrix/doublealgo/Formatter.java:public String toTitleString(DoubleMatrix3D matrix, String[] sliceNames, String[] rowNames, String[] columnNames, String sliceAxisName, String rowAxisName, String columnAxisName, String title, hep.aida.bin.BinFunction1D[] aggr) {
src/cern/colt/matrix/doublealgo/Statistic.java:import hep.aida.bin.DynamicBin1D;
src/cern/colt/matrix/doublealgo/Statistic.java:Also see {@link cern.jet.stat} and {@link hep.aida.bin}, in particular {@link hep.aida.bin.DynamicBin1D}.
src/cern/colt/matrix/doublealgo/Statistic.java: * @see hep.aida.bin.BinFunction1D
src/cern/colt/matrix/doublealgo/Statistic.java: * @see hep.aida.bin.BinFunctions1D
src/cern/colt/matrix/doublealgo/Statistic.java:public static DoubleMatrix2D aggregate(DoubleMatrix2D matrix, hep.aida.bin.BinFunction1D[] aggr, DoubleMatrix2D result) {
src/cern/colt/matrix/doublealgo/Statistic.java:If you use hep.aida.ref.Converter.toString(histo) on the result, the OLAP cube of x-"column" vs. y-"column" , summing the weights "column" will be printed.
src/cern/colt/matrix/doublealgo/Statistic.java:public static hep.aida.IHistogram2D cube(DoubleMatrix1D x, DoubleMatrix1D y, DoubleMatrix1D weights) {
src/cern/colt/matrix/doublealgo/Statistic.java: hep.aida.IAxis xaxis = new hep.aida.ref.VariableAxis(distinct.elements());
src/cern/colt/matrix/doublealgo/Statistic.java: hep.aida.IAxis yaxis = new hep.aida.ref.VariableAxis(distinct.elements());
src/cern/colt/matrix/doublealgo/Statistic.java: hep.aida.IHistogram2D histo = new hep.aida.ref.Histogram2D("Cube",xaxis,yaxis);
src/cern/colt/matrix/doublealgo/Statistic.java:If you use hep.aida.ref.Converter.toString(histo) on the result, the OLAP cube of x-"column" vs. y-"column" vs. z-"column", summing the weights "column" will be printed.
src/cern/colt/matrix/doublealgo/Statistic.java:public static hep.aida.IHistogram3D cube(DoubleMatrix1D x, DoubleMatrix1D y, DoubleMatrix1D z, DoubleMatrix1D weights) {
src/cern/colt/matrix/doublealgo/Statistic.java: hep.aida.IAxis xaxis = new hep.aida.ref.VariableAxis(distinct.elements());
src/cern/colt/matrix/doublealgo/Statistic.java: hep.aida.IAxis yaxis = new hep.aida.ref.VariableAxis(distinct.elements());
src/cern/colt/matrix/doublealgo/Statistic.java: hep.aida.IAxis zaxis = new hep.aida.ref.VariableAxis(distinct.elements());
src/cern/colt/matrix/doublealgo/Statistic.java: hep.aida.IHistogram3D histo = new hep.aida.ref.Histogram3D("Cube",xaxis,yaxis,zaxis);
src/cern/colt/matrix/doublealgo/Statistic.java:public static hep.aida.IHistogram1D histogram(hep.aida.IHistogram1D histo, DoubleMatrix1D vector) {
src/cern/colt/matrix/doublealgo/Statistic.java:public static hep.aida.IHistogram2D histogram(hep.aida.IHistogram2D histo, DoubleMatrix1D x, DoubleMatrix1D y) {
src/cern/colt/matrix/doublealgo/Statistic.java:public static hep.aida.IHistogram2D histogram(hep.aida.IHistogram2D histo, DoubleMatrix1D x, DoubleMatrix1D y, DoubleMatrix1D weights) {
src/cern/colt/matrix/doublealgo/Statistic.java:public static hep.aida.IHistogram3D histogram(hep.aida.IHistogram3D histo, DoubleMatrix1D x, DoubleMatrix1D y, DoubleMatrix1D z, DoubleMatrix1D weights) {
src/cern/colt/matrix/impl/TestMatrix2D.java: hep.aida.bin.DynamicBin1D d1ynamicBin = cern.colt.matrix.doublealgo.Statistic.bin(d1Double);
src/cern/jet/random/Benchmark.java:hep.aida.bin.DynamicBin1D bin = new hep.aida.bin.DynamicBin1D();
src/cern/jet/random/Benchmark.java: hep.aida.bin.DynamicBin1D bin = new hep.aida.bin.DynamicBin1D();
src/cern/jet/random/Benchmark.java: hep.aida.bin.DynamicBin1D binA = new hep.aida.bin.DynamicBin1D();
src/cern/jet/random/Benchmark.java: hep.aida.bin.DynamicBin1D binB = new hep.aida.bin.DynamicBin1D();
src/cern/jet/stat/quantile/QuantileFinderFactory.java: * Also see {@link hep.aida.bin.QuantileBin1D}, demonstrating how this package can be used.
src/cern/jet/stat/quantile/DoubleQuantileFinder.java: * Also see {@link hep.aida.bin.QuantileBin1D}, demonstrating how this package can be used.
src/cern/jet/stat/quantile/Quantile1Test.java:import hep.aida.bin.DynamicBin1D;
src/cern/jet/stat/quantile/Quantile1Test.java:import hep.aida.bin.QuantileBin1D;
I'd be happy to provide more input if it helps solving the issue
finally.
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: