sci-mathematics/tisean sci-biology/DisEMBL drop

dead packages

Signed-off-by: Aisha Tammy <gentoo@aisha.cc>

8 files changed, 0 insertions, 914 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/Manifest b/sci-biology/DisEMBL/Manifest
deleted file mode 100644
index 26eb31cda..000000000
--- a/sci-biology/DisEMBL/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST DisEMBL-1.4.tgz 626226 BLAKE2B 80cb7ead8239fae6bc46e2e422f953e34e7a017e5c1bc0d4994d142788fee8f882841e19c53c4805fb4def3529b71261b44194c17e8aec690682b778d616b3e6 SHA512 3544324b9456f03f021b5cfeaaf8c168aa9ddb1862383b746fb52e44579c9774f0e8cc8552fe50f8662ad7fee8d37c731244cde44c3ee09ce574aab1401cca2f
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>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-mathematics/tisean/Manifest b/sci-mathematics/tisean/Manifest
deleted file mode 100644
index 3139928c2..000000000
--- a/sci-mathematics/tisean/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST TISEAN_3.0.1.tar.gz 876454 BLAKE2B 5d1fb099fb28650d0a93b53ef52f332257ab87046f3ad4823c8c2b64e282ff681d839a193cec52a6a7b3934cdd1abaf5359e2954a501790f8fa06d61d49f41d9 SHA512 7c69f4189d0aeaadcd5d558f672bd2db0f4aa8d43bb390e54d283ae4a7a562446f909d46426da3de058c99ec54c84e8d7a69cec82a9b1772a946f5a7a5861f33
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 <hegger@theochem.uni-frankfurt.de>
-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&#62; plot '&#60; 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 '&#60; histogram amplitude.dat' u ($1-.146):2,'&#60; 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 $@ $@.c $(LOADLIBS)
-+	-$(CC) $(LDFLAGS) $(CFLAGS) $(COPTS) -o $@ $@.c $(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 $@ $@.f $(LOADLIBES) $(LDFLAGS)
-+	-$(FC) $(LDFLAGS) $(FFLAGS) -o $@ $@.f $(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))
-+	$(MAKE) -C randomize
- 
- clean:
- 	@rm -f istdio.f
diff --git a/sci-mathematics/tisean/metadata.xml b/sci-mathematics/tisean/metadata.xml
deleted file mode 100644
index 02d26ebf3..000000000
--- a/sci-mathematics/tisean/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-		<name>Justin Lecher (jlec)</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">heggus/Tisean</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-mathematics/tisean/tisean-3.0.1.ebuild b/sci-mathematics/tisean/tisean-3.0.1.ebuild
deleted file mode 100644
index f43138ee6..000000000
--- a/sci-mathematics/tisean/tisean-3.0.1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-MY_P="Tisean_${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
-}