commit: 937e76f417b041cc5fb9a9bb92d1849846420c3d Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc> AuthorDate: Fri Oct 2 17:38:21 2020 +0000 Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc> CommitDate: Fri Oct 2 17:38:21 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=937e76f4
sci-mathematics/tisean sci-biology/DisEMBL drop dead packages Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc> sci-biology/DisEMBL/DisEMBL-1.4.ebuild | 35 - sci-biology/DisEMBL/metadata.xml | 12 - .../tisean/files/tisean-3.0.1-backport.patch | 752 --------------------- .../tisean/files/tisean-3.0.1-gentoo.patch | 57 -- sci-mathematics/tisean/metadata.xml | 11 - sci-mathematics/tisean/tisean-3.0.1.ebuild | 45 -- 6 files changed, 912 deletions(-) diff --git a/sci-biology/DisEMBL/DisEMBL-1.4.ebuild b/sci-biology/DisEMBL/DisEMBL-1.4.ebuild deleted file mode 100644 index 712766d33..000000000 --- a/sci-biology/DisEMBL/DisEMBL-1.4.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit toolchain-funcs - -DESCRIPTION="Intrinsic Protein Disorder Prediction" -HOMEPAGE="http://dis.embl.de"; -SRC_URI="http://dis.embl.de/${P}.tgz"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -# The smoothing function sav_gol.c cannot be re-distributed but can be downloaded from TISEAN. -# http://www.mpipks-dresden.mpg.de/~tisean/ - -DEPEND="sci-mathematics/tisean" -RDEPEND="${DEPEND} - sci-biology/biopython" - -src_prepare(){ - sed -e 's@/usr/local/bin/@ /usr/bin/env @' -i DisEMBL.py || die -} - -src_compile(){ - $(tc-getCC) ${CFLAGS} ${LDFLAGS} disembl.c -o disembl -} - -src_install(){ - dobin DisEMBL.py disembl - dodoc INSTALL CHANGELOG -} diff --git a/sci-biology/DisEMBL/metadata.xml b/sci-biology/DisEMBL/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/DisEMBL/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch b/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch deleted file mode 100644 index dc86d1f16..000000000 --- a/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch +++ /dev/null @@ -1,752 +0,0 @@ -From 377911cf0ba30428e8e6095162ac9d63689838b8 Mon Sep 17 00:00:00 2001 -From: Rainer Hegger <[email protected]> -Date: Thu, 16 Apr 2015 15:49:31 +0200 -Subject: [PATCH] Collected changes over the last years - ---- - configure | 22 +++++----- - docs/docs_c/corr.html | 5 +++ - docs/docs_c/lfo-ar.html | 2 +- - docs/docs_c/lyap_spec.html | 4 +- - docs/tutorial/ex1.html | 2 +- - docs/tutorial/ex2.html | 10 ++--- - docs/tutorial/ex3.html | 2 +- - source_c/corr.c | 28 +++++++++--- - source_c/false_nearest.c | 10 ++++- - source_c/histogram.c | 55 +++++++++++++++--------- - source_c/lzo-run.c | 2 +- - source_c/mem_spec.c | 5 ++- - source_c/mutual.c | 105 +++++++++++++++++++++++++++++---------------- - source_c/polynom.c | 7 ++- - source_c/polynomp.c | 2 +- - source_c/xcor.c | 2 +- - source_f/cluster.f | 3 +- - 17 files changed, 172 insertions(+), 94 deletions(-) - -diff --git a/configure b/configure -index c27cf28..095e16d 100755 ---- a/configure -+++ b/configure -@@ -35,17 +35,17 @@ verbose= - x_includes=NONE - x_libraries=NONE - bindir='bin' --sbindir='${exec_prefix}/sbin' --libexecdir='${exec_prefix}/libexec' --datadir='${prefix}/share' --sysconfdir='${prefix}/etc' --sharedstatedir='${prefix}/com' --localstatedir='${prefix}/var' --libdir='${exec_prefix}/lib' --includedir='${prefix}/include' -+sbindir='sbin' -+libexecdir='libexec' -+datadir='share' -+sysconfdir='etc' -+sharedstatedir='com' -+localstatedir='var' -+libdir='lib' -+includedir='include' - oldincludedir='/usr/include' --infodir='${prefix}/info' --mandir='${prefix}/man' -+infodir='info' -+mandir='man' - - # Initialize some other variables. - subdirs= -@@ -1020,7 +1020,7 @@ fi - - - --for fff in "$FC" f77 g77 "f77 +U77" "f77 -q -f -B108 -lU77"; do -+for fff in "$FC" f77 g77 gfortran "f77 +U77" "f77 -q -f -B108 -lU77"; do - if test -z "$fff"; then - continue - fi -diff --git a/docs/docs_c/corr.html b/docs/docs_c/corr.html -index 8b2eb8c..f2aa4f2 100644 ---- a/docs/docs_c/corr.html -+++ b/docs/docs_c/corr.html -@@ -57,6 +57,11 @@ <h2 align=center>Usage:</h2> - <td>100 - </tr> - <tr> -+<th>-s# -+<td>calculate the correlation only every #-th step -+<td>1 -+</tr> -+<tr> - <th>-n - <td>don't use normalization to standard deviation - <td>not set -diff --git a/docs/docs_c/lfo-ar.html b/docs/docs_c/lfo-ar.html -index 59263b6..11a9b4e 100644 ---- a/docs/docs_c/lfo-ar.html -+++ b/docs/docs_c/lfo-ar.html -@@ -117,7 +117,7 @@ <h2 align=center>Description of the Output:</h2> - The output consists of 5 columns for each neighborhood size:</b> - <ul> - <li> neighborhood size (units of the data) --<li> relative forecast error ((forecast error)/(variance of the data)) -+<li> relative forecast error ((forecast error)/(standard deviation of data)) - <li> fraction of points for which neighbors were found for this neighborhood - size - <li> average number of neighbors found per point -diff --git a/docs/docs_c/lyap_spec.html b/docs/docs_c/lyap_spec.html -index ab67d84..189482a 100644 ---- a/docs/docs_c/lyap_spec.html -+++ b/docs/docs_c/lyap_spec.html -@@ -58,7 +58,9 @@ <h2 align=center>Usage:</h2> - --> - <tr> - <th>-r# --<td>minimal neighborhood size -+<td>minimal neighborhood size. This option dominates -k. This means -+ that if -r is set and more than -k neighbors are found, the number -+ of neighbors will not be reduced to the value given with -k. - <td>not set - </tr> - <tr> -diff --git a/docs/tutorial/ex1.html b/docs/tutorial/ex1.html -index e77be7b..660811b 100644 ---- a/docs/tutorial/ex1.html -+++ b/docs/tutorial/ex1.html -@@ -146,7 +146,7 @@ - variable <font color=blue>x </font> of the logistic equation for - various parameter values (e.g.: <font color=green> - gnuplot> plot '< henon -B0 -A2 -l10000 | histogram -b100' with --hist</font>). When a sufficiently long transient has been -+histeps</font>). When a sufficiently long transient has been - discarded, such a histogram is the approximation to the invaraint - measure on the bins of the histogram. Verify numerically:<br> - <ul> -diff --git a/docs/tutorial/ex2.html b/docs/tutorial/ex2.html -index 5324a15..a0fbb11 100644 ---- a/docs/tutorial/ex2.html -+++ b/docs/tutorial/ex2.html -@@ -82,7 +82,7 @@ - the two histograms, you thus should shift the one with respect to the - other by the mean value of the data:<br> - <font color=green> --set data style histep<br> -+set style data histep<br> - plot '< histogram amplitude.dat' u ($1-.146):2,'< histogram - ar.dat' </font> - <br>Result: The data sets are differnt: the distribution of <font -@@ -95,7 +95,7 @@ - <a href="../docs_f/spectrum.html">spectrum</a>) of both of them:<br> - <font color=red> corr amplitude.dat -D500 -o<br> - corr ar.dat -D500 -o</font><br> --<font color=green>set data style lines</font><br> -+<font color=green>set style data lines</font><br> - <font color=green> plot 'ar.dat.cor','amplitude.dat.cor'</font><br> - <font color=red>spectrum amplitude.dat -o<br> - spectrum ar.dat -o</font><br> -@@ -150,7 +150,7 @@ - <ul> - <li> compute the false nearest neighbour statistics - (<a href="../docs_c/false_nearest.html">false_nearest</a>):<br> --<font color=red> false_nearest amplitude.dat -M8 -d8 -o -+<font color=red> false_nearest amplitude.dat -M1,8 -d8 -o - -t200 -f5 </font><br> - Study the output, <font color=blue>amplitude.dat.fnn</font>, and - observe the invariance of the result (namely that the embedding dimension -@@ -158,9 +158,9 @@ - <br><br> - - <li> Use the zeorth-order predictor --(<a href="../docs_c/zeroth.html">zeroth</a>) -+(<a href="../docs_c/lzo-test.html">zeroth</a>) - on amplitude.dat and on ar.dat.<br> --<font color=red> zeroth amplitude.dat -m1,4 -d8 -o -+<font color=red> lzo-test amplitude.dat -m1,4 -d8 -o - -s250<br> - zeroth ar.dat -m1,4 -d8 -o - -s250</font><br> -diff --git a/docs/tutorial/ex3.html b/docs/tutorial/ex3.html -index 91735dd..2894689 100644 ---- a/docs/tutorial/ex3.html -+++ b/docs/tutorial/ex3.html -@@ -196,7 +196,7 @@ - <font color=red> ll-ar optimal.dat -d10 -m3 -i2000 -s1 -o</font>,<br> - and compare the results:<br> - <font color=green> --set data style linespoints<br> -+set style data linespoints<br> - plot 'whatisit.dat.ll', 'whatisit.dat.ll' u 1:3,'optimal.dat.ll', - 'optimal.dat.ll' u 1:3</font><br> - <br> -diff --git a/source_c/corr.c b/source_c/corr.c -index 06da07a..4c79b9a 100644 ---- a/source_c/corr.c -+++ b/source_c/corr.c -@@ -30,7 +30,7 @@ - char *format,*outfile=NULL,stout=1,normalize=1; - unsigned int column=1; - unsigned int verbosity=0xff; --unsigned long tau=100,length=ULONG_MAX,exclude=0; -+unsigned long tau=100,step=1,length=ULONG_MAX,exclude=0; - double *array; - double av,var; - char *infile=NULL; -@@ -48,6 +48,8 @@ void show_options(char *progname) - fprintf(stderr,"\t-x # of lines to be ignored [default 0]\n"); - fprintf(stderr,"\t-c column to read [default is 1]\n"); - fprintf(stderr,"\t-D corrlength [default is 100]\n"); -+ fprintf(stderr,"\t-s # calculate the correlation only every #-th step " -+ "[default is 1]\n"); - fprintf(stderr,"\t-n don\'t normalize to the variance" - " of the data [not set]\n"); - fprintf(stderr,"\t-o output_file [default is 'datafile'.cor; no -o" -@@ -72,6 +74,8 @@ void scan_options(int argc,char **argv) - sscanf(out,"%u",&column); - if ((out=check_option(argv,argc,'D','u')) != NULL) - sscanf(out,"%lu",&tau); -+ if ((out=check_option(argv,argc,'s','u')) != NULL) -+ sscanf(out,"%lu",&step); - if ((out=check_option(argv,argc,'n','n')) != NULL) - normalize=0; - if ((out=check_option(argv,argc,'V','u')) != NULL) -@@ -88,16 +92,17 @@ double corr(long i) - long j; - double c=0.0; - -- for (j=0;j<(length-i);j++) -+ for (j=0;j<(length-i);j++) { - c += array[j]*array[j+i]; -+ } - -- return c/(length-i); -+ return c/(double)(length-i); - } - - int main(int argc,char** argv) - { -- char stdi=0; -- long i; -+ char stdi=0,done=0; -+ unsigned long i; - FILE *fout=NULL; - - if (scan_help(argc,argv)) -@@ -157,14 +162,25 @@ int main(int argc,char** argv) - else - var=1.0; - -- for (i=0;i<=tau;i++) -+ for (i=0;i<=tau;i += step) - if (!stout) { - fprintf(fout,"%ld %e\n",i,corr(i)/var); - fflush(fout); -+ if (i == tau) done=1; - } - else { - fprintf(stdout,"%ld %e\n",i,corr(i)/var); - fflush(stdout); -+ if (i == tau) done=1; -+ } -+ if (!done) -+ if (!stout) { -+ fprintf(fout,"%ld %e\n",tau,corr(tau)/var); -+ fflush(fout); -+ } -+ else { -+ fprintf(stdout,"%ld %e\n",tau,corr(tau)/var); -+ fflush(stdout); - } - if (!stout) - fclose(fout); -diff --git a/source_c/false_nearest.c b/source_c/false_nearest.c -index f8a16e9..f5eed04 100644 ---- a/source_c/false_nearest.c -+++ b/source_c/false_nearest.c -@@ -21,6 +21,7 @@ - /*Changes: - 12/10/05: It's multivariate now - 12/16/05: Scaled <eps> and sigma(eps) -+ 03/08/09: delay was missing in delay embedding of univariate case - */ - - #include <stdio.h> -@@ -37,7 +38,7 @@ char *infile=NULL; - char stdo=1,dimset=0; - char *column=NULL; - unsigned long length=ULONG_MAX,exclude=0,theiler=0; --unsigned int delay=1,maxdim=5,minemb=1; -+unsigned int delay=1,maxdim=6,minemb=1; - unsigned int comp=1,maxemb=5; - unsigned int verbosity=0xff; - double rt=2.0; -@@ -226,6 +227,11 @@ int main(int argc,char **argv) - series=(double**)get_multi_series(infile,&length,exclude,&comp,column, - dimset,verbosity); - -+ if ((maxemb*delay+1) >= length) { -+ fprintf(stderr,"Not enough points!\n"); -+ exit(FALSE_NEAREST_NOT_ENOUGH_POINTS); -+ } -+ - for (i=0;i<comp;i++) { - rescale_data(series[i],length,&min,&ind_inter); - variance(series[i],length,&av,&ind_var); -@@ -259,7 +265,7 @@ int main(int argc,char **argv) - for (i=0;i<maxdim;i++) { - if (comp == 1) { - vcomp[i]=0; -- vemb[i]=i; -+ vemb[i]=i*delay; - } - else { - vcomp[i]=i%comp; -diff --git a/source_c/histogram.c b/source_c/histogram.c -index 6ab9f02..a45576d 100644 ---- a/source_c/histogram.c -+++ b/source_c/histogram.c -@@ -17,10 +17,8 @@ - * along with TISEAN; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - */ --/*Author: Rainer Hegger. Last modified Dec 6, 2005*/ --/*Changes: -- 12/06/05: shift output x value to center of interval --*/ -+/*Author: Rainer Hegger. Last modified May 16, 2014*/ -+ - #include <math.h> - #include <limits.h> - #include <stdio.h> -@@ -28,7 +26,7 @@ - #include <string.h> - #include "routines/tsa.h" - --#define WID_STR "Makes a histogram of the data" -+#define WID_STR "Creates a histogram of a onedimensional dataset" - - unsigned long length=ULONG_MAX; - unsigned long base=50; -@@ -36,15 +34,10 @@ unsigned long exclude=0; - unsigned int column=1; - unsigned int verbosity=0xff; - double size; --char my_stdout=1,gotsize=0; -+char my_stdout=1,gotsize=0,density=0; - char *outfile=NULL; - char *infile=NULL; - --double *series; --double average,var; --double min,max; --long *box; -- - void show_options(char *progname) - { - what_i_do(progname,WID_STR); -@@ -57,6 +50,8 @@ void show_options(char *progname) - fprintf(stderr,"\t-x # of lines to ignore [default %ld]\n",exclude); - fprintf(stderr,"\t-c column to read [default %d]\n",column); - fprintf(stderr,"\t-b # of intervals [default %ld]\n",base); -+ fprintf(stderr,"\t-D output densities not relative frequencies" -+ " [default not set]\n"); - fprintf(stderr,"\t-o output file [default 'datafile'.dat ;" - " If no -o is given: stdout]\n"); - fprintf(stderr,"\t-V verbosity level [default 1]\n\t\t" -@@ -80,6 +75,8 @@ void scan_options(int n,char **str) - sscanf(out,"%lu",&base); - if ((out=check_option(str,n,'V','u')) != NULL) - sscanf(out,"%u",&verbosity); -+ if ((out=check_option(str,n,'D','n')) != NULL) -+ density=1; - if ((out=check_option(str,n,'o','o')) != NULL) { - my_stdout=0; - if (strlen(out) > 0) -@@ -92,6 +89,10 @@ int main(int argc,char **argv) - char stdi=0; - unsigned long i,j; - double x,norm,size=1.0,size2=1.0; -+ double min,max; -+ double *series; -+ double average,var; -+ long *box; - FILE *fout; - - if (scan_help(argc,argv)) -@@ -123,24 +124,36 @@ int main(int argc,char **argv) - - series=(double*)get_series(infile,&length,exclude,column,verbosity); - variance(series,length,&average,&var); -- rescale_data(series,length,&min,&max); -- -- -+ -+ min=max=series[0]; -+ for (i=1;i<length;i++) { -+ if (series[i] < min) min=series[i]; -+ else if (series[i] > max) max=series[i]; -+ } -+ max -= min; -+ -+ for (i=0;i<length;i++) -+ series[i]=(series[i]-min); -+ - if (base > 0) { - check_alloc(box=(long*)malloc(sizeof(long)*base)); - for (i=0;i<base;i++) - box[i]=0; - size=1./base; -- size2=size/2.0; -+ size2=(1.0-size/2.0)*max; - for (i=0;i<length;i++) { -- if (series[i] > (1.0-size2)) -- series[i]=1.0-size2; -- j=(long)(series[i]*base); -+ if (series[i] > size2) -+ series[i]=size2; -+ j=(long)(series[i]*base/max); - box[j]++; - } - } - -- norm=1.0/(double)length; -+ if (!density) -+ norm=1.0/(double)length; -+ else -+ norm=1.0/(double)length*(double)base/max; -+ - if (!my_stdout) { - fout=fopen(outfile,"w"); - if (verbosity&VER_INPUT) -@@ -150,7 +163,7 @@ int main(int argc,char **argv) - fprintf(fout,"#standard deviation= %e\n",var); - for (i=0;i<base;i++) { - x=(double)(i*size); -- fprintf(fout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm); -+ fprintf(fout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm); - } - fclose(fout); - } -@@ -162,7 +175,7 @@ int main(int argc,char **argv) - fprintf(stdout,"#standard deviation= %e\n",var); - for (i=0;i<base;i++) { - x=(double)(i*size); -- fprintf(stdout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm); -+ fprintf(stdout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm); - fflush(stdout); - } - } -diff --git a/source_c/lzo-run.c b/source_c/lzo-run.c -index 5393e9f..bc54fb5 100644 ---- a/source_c/lzo-run.c -+++ b/source_c/lzo-run.c -@@ -49,7 +49,7 @@ unsigned int MINN=50; - unsigned int **indexes; - unsigned long LENGTH=ULONG_MAX,FLENGTH=1000,exclude=0; - unsigned long seed=0x9074325L; --double EPS0=1.e-3,EPSF=1.2,Q=10.0; -+double EPS0=1.e-3,EPSF=1.2,Q=0.0; - - double **mat,*vec,*hsum,*newav; - -diff --git a/source_c/mem_spec.c b/source_c/mem_spec.c -index a38fcfd..9821488 100644 ---- a/source_c/mem_spec.c -+++ b/source_c/mem_spec.c -@@ -22,6 +22,7 @@ - Feb 19, 2007: changed meaning of -f flag and added -P flag to be - consistent with spectrum - Dec 5, 2006: Seg fault when poles > length; -+ Mar 15, 2007: normalization now the same as in spectrum - */ - #include <stdio.h> - #include <string.h> -@@ -216,7 +217,7 @@ int main(int argc,char **argv) - fdt=i/(2.0*out); - pow_spec=powcoef(fdt,cof); - fprintf(fout,"%e %e\n",fdt*samplingrate, -- pm/pow_spec/sqrt((double)length)); -+ pm/pow_spec/(double)length); - fflush(fout); - } - fclose(fout); -@@ -233,7 +234,7 @@ int main(int argc,char **argv) - fdt=i/(2.0*out); - pow_spec=powcoef(fdt,cof); - fprintf(stdout,"%e %e\n",fdt*samplingrate, -- pm/pow_spec/*/sqrt((double)length)*/); -+ pm/pow_spec/(double)length); - } - } - -diff --git a/source_c/mutual.c b/source_c/mutual.c -index fbea470..0496e92 100644 ---- a/source_c/mutual.c -+++ b/source_c/mutual.c -@@ -17,7 +17,7 @@ - * along with TISEAN; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - */ --/*Author: Rainer Hegger. Last modified, Sep 20, 2000 */ -+/*Author: Rainer Hegger. Last modified, Jul 13, 2010 */ - #include <stdio.h> - #include <stdlib.h> - #include <math.h> -@@ -26,16 +26,17 @@ - #include "routines/tsa.h" - - #define WID_STR "Estimates the time delayed mutual information\n\t\ --of the data set" -+of one or two data columns" - - --char *file_out=NULL,stout=1; -+char *file_out=NULL,stout=1,dimset=0; - char *infile=NULL; - unsigned long length=ULONG_MAX,exclude=0; --unsigned int column=1; -+unsigned int dim=1; - unsigned int verbosity=0xff; - long partitions=16,corrlength=20; --long *array,*h1,*h11,**h2; -+long **array,*h1,*h11,**h2; -+char *column=NULL; - - void show_options(char *progname) - { -@@ -48,7 +49,7 @@ void show_options(char *progname) - " means stdin\n"); - fprintf(stderr,"\t-l # of points to be used [Default is all]\n"); - fprintf(stderr,"\t-x # of lines to be ignored [Default is 0]\n"); -- fprintf(stderr,"\t-c column to read [Default is 1]\n"); -+ fprintf(stderr,"\t-c columns to read [Default is 1]\n"); - fprintf(stderr,"\t-b # of boxes [Default is 16]\n"); - fprintf(stderr,"\t-D max. time delay [Default is 20]\n"); - fprintf(stderr,"\t-o output file [-o without name means 'datafile'.mut;" -@@ -69,8 +70,8 @@ void scan_options(int n,char** in) - sscanf(out,"%lu",&length); - if ((out=check_option(in,n,'x','u')) != NULL) - sscanf(out,"%lu",&exclude); -- if ((out=check_option(in,n,'c','u')) != NULL) -- sscanf(out,"%u",&column); -+ if ((out=check_option(in,n,'c','s')) != NULL) -+ column=out; - if ((out=check_option(in,n,'b','u')) != NULL) - sscanf(out,"%lu",&partitions); - if ((out=check_option(in,n,'D','u')) != NULL) -@@ -86,7 +87,7 @@ void scan_options(int n,char** in) - - double make_cond_entropy(long t) - { -- long i,j,hi,hii,count=0; -+ long i,j,hi,hii,count=0,start,stop; - double hpi,hpj,pij,cond_ent=0.0,norm; - - for (i=0;i<partitions;i++) { -@@ -94,15 +95,23 @@ double make_cond_entropy(long t) - for (j=0;j<partitions;j++) - h2[i][j]=0; - } -- for (i=0;i<length;i++) -- if (i >= t) { -- hii=array[i]; -- hi=array[i-t]; -- h1[hi]++; -- h11[hii]++; -- h2[hi][hii]++; -- count++; -- } -+ if (t < 0) { -+ start=0; -+ stop=length+t; -+ } -+ else { -+ start=t; -+ stop=length; -+ } -+ -+ for (i=start;i<stop;i++) { -+ hii=array[0][i]; -+ hi=array[1][i+t]; -+ h1[hi]++; -+ h11[hii]++; -+ h2[hi][hii]++; -+ count++; -+ } - - norm=1.0/(double)count; - cond_ent=0.0; -@@ -127,8 +136,8 @@ double make_cond_entropy(long t) - int main(int argc,char** argv) - { - char stdi=0; -- long tau,i; -- double *series,min,interval,shannon; -+ long tau,i,j; -+ double **series,min1,min2,interval1,interval2,shannon,condent; - FILE *file; - - if (scan_help(argc,argv)) -@@ -140,7 +149,7 @@ int main(int argc,char** argv) - what_i_do(argv[0],WID_STR); - #endif - -- infile=search_datafile(argc,argv,&column,verbosity); -+ infile=search_datafile(argc,argv,NULL,verbosity); - if (infile == NULL) - stdi=1; - -@@ -158,20 +167,44 @@ int main(int argc,char** argv) - if (!stout) - test_outfile(file_out); - -- series=(double*)get_series(infile,&length,exclude,column,verbosity); -- rescale_data(series,length,&min,&interval); -+ if (column == NULL) { -+ series=(double**)get_multi_series(infile,&length,exclude,&dim,"", -+ dimset,verbosity); -+ } -+ else { -+ series=(double**)get_multi_series(infile,&length,exclude,&dim,column, -+ dimset,verbosity); -+ } - - check_alloc(h1=(long *)malloc(sizeof(long)*partitions)); - check_alloc(h11=(long *)malloc(sizeof(long)*partitions)); - check_alloc(h2=(long **)malloc(sizeof(long *)*partitions)); - for (i=0;i<partitions;i++) - check_alloc(h2[i]=(long *)malloc(sizeof(long)*partitions)); -- check_alloc(array=(long *)malloc(sizeof(long)*length)); -- for (i=0;i<length;i++) -- if (series[i] < 1.0) -- array[i]=(long)(series[i]*(double)partitions); -- else -- array[i]=partitions-1; -+ check_alloc(array=(long **)malloc(sizeof(long*)*2)); -+ check_alloc(array[0]=(long *)malloc(sizeof(long)*length)); -+ check_alloc(array[1]=(long *)malloc(sizeof(long)*length)); -+ if (dim == 1) { -+ rescale_data(series[0],length,&min1,&interval1); -+ for (i=0;i<length;i++) -+ if (series[0][i] < 1.0) -+ array[0][i]=array[1][i]=(long)(series[0][i]*(double)partitions); -+ else -+ array[0][i]=array[1][i]=partitions-1; -+ free(series[0]); -+ } -+ else { -+ rescale_data(series[0],length,&min1,&interval1); -+ rescale_data(series[1],length,&min2,&interval2); -+ for (j=0;j<2;j++) { -+ for (i=0;i<length;i++) -+ if (series[j][i] < 1.0) -+ array[j][i]=(long)(series[j][i]*(double)partitions); -+ else -+ array[j][i]=partitions-1; -+ free(series[j]); -+ } -+ } - free(series); - - shannon=make_cond_entropy(0); -@@ -182,10 +215,9 @@ int main(int argc,char** argv) - file=fopen(file_out,"w"); - if (verbosity&VER_INPUT) - fprintf(stderr,"Opened %s for writing\n",file_out); -- fprintf(file,"#shannon= %e\n",shannon); -- fprintf(file,"%d %e\n",0,shannon); -- for (tau=1;tau<=corrlength;tau++) { -- fprintf(file,"%ld %e\n",tau,make_cond_entropy(tau)); -+ for (tau=-corrlength;tau<=corrlength;tau++) { -+ condent=make_cond_entropy(tau); -+ fprintf(file,"%ld %e %e\n",tau,condent,condent/log((double)partitions)); - fflush(file); - } - fclose(file); -@@ -193,10 +225,9 @@ int main(int argc,char** argv) - else { - if (verbosity&VER_INPUT) - fprintf(stderr,"Writing to stdout\n"); -- fprintf(stdout,"#shannon= %e\n",shannon); -- fprintf(stdout,"%d %e\n",0,shannon); -- for (tau=1;tau<=corrlength;tau++) { -- fprintf(stdout,"%ld %e\n",tau,make_cond_entropy(tau)); -+ for (tau=-corrlength;tau<=corrlength;tau++) { -+ condent=make_cond_entropy(tau); -+ fprintf(stdout,"%ld %e %e\n",tau,condent,condent/log((double)partitions)); - fflush(stdout); - } - } -diff --git a/source_c/polynom.c b/source_c/polynom.c -index bc57ba8..6448f49 100644 ---- a/source_c/polynom.c -+++ b/source_c/polynom.c -@@ -20,6 +20,8 @@ - /*Author: Rainer Hegger*/ - /* Changes: - 6/30/2006: Norm of the errors was wrong -+ 6/5/2008: Norm was still wrong. Now its given as an absolute value in -+ units of the data - */ - #include <stdio.h> - #include <stdlib.h> -@@ -265,6 +267,7 @@ int main(int argc,char **argv) - - series=(double*)get_series(infile,&LENGTH,exclude,COLUMN,verbosity); - variance(series,LENGTH,&av,&std_dev); -+ - for (i=0;i<LENGTH;i++) - series[i] /= std_dev; - -@@ -307,11 +310,11 @@ int main(int argc,char **argv) - - in_error=make_error((unsigned long)0,INSAMPLE); - -- fprintf(file,"#average insample error= %e\n",sqrt(in_error)); -+ fprintf(file,"#average insample error= %e\n",sqrt(in_error)*std_dev); - - if (INSAMPLE < LENGTH) { - out_error=make_error(INSAMPLE,LENGTH); -- fprintf(file,"#average out of sample error= %e\n",sqrt(out_error)); -+ fprintf(file,"#average out of sample error= %e\n",sqrt(out_error)*std_dev); - } - - if (CAST) -diff --git a/source_c/polynomp.c b/source_c/polynomp.c -index 6021e19..5b32e58 100644 ---- a/source_c/polynomp.c -+++ b/source_c/polynomp.c -@@ -239,7 +239,7 @@ int main(int argc,char **argv) - fclose(file); - - dummy=(double**)get_multi_series(parin,&plength,0LU, -- &dim,"",(char)"1",verbosity); -+ &dim,"",1,verbosity); - - check_alloc(order=(unsigned int**)malloc(sizeof(int*)*plength)); - for (i=0;i<plength;i++) { -diff --git a/source_c/xcor.c b/source_c/xcor.c -index ec1ed7f..8f50609 100644 ---- a/source_c/xcor.c -+++ b/source_c/xcor.c -@@ -30,7 +30,7 @@ given as two columns of one file." - - char *columns=NULL,*outfile=NULL,stout=1; - unsigned long length=ULONG_MAX,exclude=0; --long tau=100; -+unsigned long tau=100; - unsigned int verbosity=0xff; - double *array1,*array2; - char *infile=NULL; -diff --git a/source_f/cluster.f b/source_f/cluster.f -index 61357ff..d564fc7 100644 ---- a/source_f/cluster.f -+++ b/source_f/cluster.f -@@ -47,7 +47,8 @@ - d(i,j)=dij - np=max(i,j,np) - goto 1 -- 999 if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np -+c 999 if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np -+ 999 if(iv_io(iverb).eq.1) write(0,*) "matrix size ", np - dmean=0 - nd=0 - do 20 i=1,np diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch b/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch deleted file mode 100644 index 7f80f6276..000000000 --- a/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch +++ /dev/null @@ -1,57 +0,0 @@ -diff --git a/Makefile.in b/Makefile.in -index c1f3e0c..60f9720 100644 ---- a/Makefile.in -+++ b/Makefile.in -@@ -9,8 +9,8 @@ HAVE_NR = @HAVE_NR@ - - all: - @head -20 README -- -if test -n "${FC}"; then (cd source_f && $(MAKE) $@); fi -- -if test -n "${CC}"; then (cd source_c && $(MAKE) $@); fi -+ $(MAKE) -C source_f $@ -+ $(MAKE) -C source_c $@ - - install: do_install missing - @echo "******************************************************************" -diff --git a/source_c/Makefile.in b/source_c/Makefile.in -index 1ab10e4..2efb803 100644 ---- a/source_c/Makefile.in -+++ b/source_c/Makefile.in -@@ -23,10 +23,10 @@ LOADLIBS = routines/libddtsa.a -lm - all: $(ALL) - - routines/libddtsa.a: -- (cd routines && $(MAKE)) -+ $(MAKE) -C routines - - $(ALL): routines/libddtsa.a *.c -- -$(CC) $(CFLAGS) $(COPTS) -o $@ [email protected] $(LOADLIBS) -+ -$(CC) $(LDFLAGS) $(CFLAGS) $(COPTS) -o $@ [email protected] $(LOADLIBS) - - install: all - -for bin in $(ALL); do $(INSTALL) $$bin $(BINDIR); done -diff --git a/source_f/Makefile.in b/source_f/Makefile.in -index 6525b72..e45eea7 100644 ---- a/source_f/Makefile.in -+++ b/source_f/Makefile.in -@@ -37,17 +37,17 @@ istdio.o: istdio_temp.f - $(FC) $(FFLAGS) -c istdio.f -o istdio.o - - $(BINS): libtsa.a libsla.a *.f -- -$(FC) $(FFLAGS) -o $@ [email protected] $(LOADLIBES) $(LDFLAGS) -+ -$(FC) $(LDFLAGS) $(FFLAGS) -o $@ [email protected] $(LOADLIBES) - - libtsa.a: $(INC) - $(AR) $(ARFLAGS) libtsa.a $? - $(RANLIB) libtsa.a - - libsla.a: slatec/*.f -- (cd slatec && $(MAKE)) -+ $(MAKE) -C slatec - - Randomize: libtsa.a libsla.a -- -(cd randomize && $(MAKE)) -+ $(MAKE) -C randomize - - clean: - @rm -f istdio.f diff --git a/sci-mathematics/tisean/metadata.xml b/sci-mathematics/tisean/metadata.xml deleted file mode 100644 index 02d26ebf3..000000000 --- a/sci-mathematics/tisean/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Justin Lecher (jlec)</name> - </maintainer> - <upstream> - <remote-id type="github">heggus/Tisean</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/tisean/tisean-3.0.1.ebuild b/sci-mathematics/tisean/tisean-3.0.1.ebuild deleted file mode 100644 index f43138ee6..000000000 --- a/sci-mathematics/tisean/tisean-3.0.1.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -MY_P="Tisean_${PV}" - -DESCRIPTION="Time series analytics with theory of non-liner deterministic dynamical systems" -HOMEPAGE=" - https://github.com/heggus/Tisean - http://www.mpipks-dresden.mpg.de/%7Etisean/Tisean_3.0.1/index.html"; -SRC_URI="http://www.mpipks-dresden.mpg.de/~tisean/TISEAN_3.0.1.tar.gz"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - tc-export FC CC - epatch \ - "${FILESDIR}"/${P}-gentoo.patch \ - "${FILESDIR}"/${P}-backport.patch -} - -src_configure() { - econf \ - --prefix="${ED}/usr" -} - -src_install() { - # TODO: fix file collisions with: - # media-gfx/graphviz: /usr/bin/cluster - # media-gfx/imagemagick: /usr/bin/compare - dodir /usr/bin - default -} - -pkg_postinst() { - optfeature "plotting support" sci-visualization/gnuplot -}
