1 |
commit: 937e76f417b041cc5fb9a9bb92d1849846420c3d |
2 |
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc> |
3 |
AuthorDate: Fri Oct 2 17:38:21 2020 +0000 |
4 |
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc> |
5 |
CommitDate: Fri Oct 2 17:38:21 2020 +0000 |
6 |
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=937e76f4 |
7 |
|
8 |
sci-mathematics/tisean sci-biology/DisEMBL drop |
9 |
|
10 |
dead packages |
11 |
|
12 |
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc> |
13 |
|
14 |
sci-biology/DisEMBL/DisEMBL-1.4.ebuild | 35 - |
15 |
sci-biology/DisEMBL/metadata.xml | 12 - |
16 |
.../tisean/files/tisean-3.0.1-backport.patch | 752 --------------------- |
17 |
.../tisean/files/tisean-3.0.1-gentoo.patch | 57 -- |
18 |
sci-mathematics/tisean/metadata.xml | 11 - |
19 |
sci-mathematics/tisean/tisean-3.0.1.ebuild | 45 -- |
20 |
6 files changed, 912 deletions(-) |
21 |
|
22 |
diff --git a/sci-biology/DisEMBL/DisEMBL-1.4.ebuild b/sci-biology/DisEMBL/DisEMBL-1.4.ebuild |
23 |
deleted file mode 100644 |
24 |
index 712766d33..000000000 |
25 |
--- a/sci-biology/DisEMBL/DisEMBL-1.4.ebuild |
26 |
+++ /dev/null |
27 |
@@ -1,35 +0,0 @@ |
28 |
-# Copyright 1999-2016 Gentoo Foundation |
29 |
-# Distributed under the terms of the GNU General Public License v2 |
30 |
- |
31 |
-EAPI=5 |
32 |
- |
33 |
-inherit toolchain-funcs |
34 |
- |
35 |
-DESCRIPTION="Intrinsic Protein Disorder Prediction" |
36 |
-HOMEPAGE="http://dis.embl.de" |
37 |
-SRC_URI="http://dis.embl.de/${P}.tgz" |
38 |
- |
39 |
-LICENSE="GPL-2" |
40 |
-SLOT="0" |
41 |
-KEYWORDS="~amd64" |
42 |
-IUSE="" |
43 |
- |
44 |
-# The smoothing function sav_gol.c cannot be re-distributed but can be downloaded from TISEAN. |
45 |
-# http://www.mpipks-dresden.mpg.de/~tisean/ |
46 |
- |
47 |
-DEPEND="sci-mathematics/tisean" |
48 |
-RDEPEND="${DEPEND} |
49 |
- sci-biology/biopython" |
50 |
- |
51 |
-src_prepare(){ |
52 |
- sed -e 's@/usr/local/bin/@ /usr/bin/env @' -i DisEMBL.py || die |
53 |
-} |
54 |
- |
55 |
-src_compile(){ |
56 |
- $(tc-getCC) ${CFLAGS} ${LDFLAGS} disembl.c -o disembl |
57 |
-} |
58 |
- |
59 |
-src_install(){ |
60 |
- dobin DisEMBL.py disembl |
61 |
- dodoc INSTALL CHANGELOG |
62 |
-} |
63 |
|
64 |
diff --git a/sci-biology/DisEMBL/metadata.xml b/sci-biology/DisEMBL/metadata.xml |
65 |
deleted file mode 100644 |
66 |
index 138cb7705..000000000 |
67 |
--- a/sci-biology/DisEMBL/metadata.xml |
68 |
+++ /dev/null |
69 |
@@ -1,12 +0,0 @@ |
70 |
-<?xml version="1.0" encoding="UTF-8"?> |
71 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
72 |
-<pkgmetadata> |
73 |
- <maintainer type="person"> |
74 |
- <email>mmokrejs@×××××××××××××××.cz</email> |
75 |
- <name>Martin Mokrejs</name> |
76 |
- </maintainer> |
77 |
- <maintainer type="project"> |
78 |
- <email>sci-biology@g.o</email> |
79 |
- <name>Gentoo Biology Project</name> |
80 |
- </maintainer> |
81 |
-</pkgmetadata> |
82 |
|
83 |
diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch b/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch |
84 |
deleted file mode 100644 |
85 |
index dc86d1f16..000000000 |
86 |
--- a/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch |
87 |
+++ /dev/null |
88 |
@@ -1,752 +0,0 @@ |
89 |
-From 377911cf0ba30428e8e6095162ac9d63689838b8 Mon Sep 17 00:00:00 2001 |
90 |
-From: Rainer Hegger <hegger@××××××××××××××××××××××.de> |
91 |
-Date: Thu, 16 Apr 2015 15:49:31 +0200 |
92 |
-Subject: [PATCH] Collected changes over the last years |
93 |
- |
94 |
---- |
95 |
- configure | 22 +++++----- |
96 |
- docs/docs_c/corr.html | 5 +++ |
97 |
- docs/docs_c/lfo-ar.html | 2 +- |
98 |
- docs/docs_c/lyap_spec.html | 4 +- |
99 |
- docs/tutorial/ex1.html | 2 +- |
100 |
- docs/tutorial/ex2.html | 10 ++--- |
101 |
- docs/tutorial/ex3.html | 2 +- |
102 |
- source_c/corr.c | 28 +++++++++--- |
103 |
- source_c/false_nearest.c | 10 ++++- |
104 |
- source_c/histogram.c | 55 +++++++++++++++--------- |
105 |
- source_c/lzo-run.c | 2 +- |
106 |
- source_c/mem_spec.c | 5 ++- |
107 |
- source_c/mutual.c | 105 +++++++++++++++++++++++++++++---------------- |
108 |
- source_c/polynom.c | 7 ++- |
109 |
- source_c/polynomp.c | 2 +- |
110 |
- source_c/xcor.c | 2 +- |
111 |
- source_f/cluster.f | 3 +- |
112 |
- 17 files changed, 172 insertions(+), 94 deletions(-) |
113 |
- |
114 |
-diff --git a/configure b/configure |
115 |
-index c27cf28..095e16d 100755 |
116 |
---- a/configure |
117 |
-+++ b/configure |
118 |
-@@ -35,17 +35,17 @@ verbose= |
119 |
- x_includes=NONE |
120 |
- x_libraries=NONE |
121 |
- bindir='bin' |
122 |
--sbindir='${exec_prefix}/sbin' |
123 |
--libexecdir='${exec_prefix}/libexec' |
124 |
--datadir='${prefix}/share' |
125 |
--sysconfdir='${prefix}/etc' |
126 |
--sharedstatedir='${prefix}/com' |
127 |
--localstatedir='${prefix}/var' |
128 |
--libdir='${exec_prefix}/lib' |
129 |
--includedir='${prefix}/include' |
130 |
-+sbindir='sbin' |
131 |
-+libexecdir='libexec' |
132 |
-+datadir='share' |
133 |
-+sysconfdir='etc' |
134 |
-+sharedstatedir='com' |
135 |
-+localstatedir='var' |
136 |
-+libdir='lib' |
137 |
-+includedir='include' |
138 |
- oldincludedir='/usr/include' |
139 |
--infodir='${prefix}/info' |
140 |
--mandir='${prefix}/man' |
141 |
-+infodir='info' |
142 |
-+mandir='man' |
143 |
- |
144 |
- # Initialize some other variables. |
145 |
- subdirs= |
146 |
-@@ -1020,7 +1020,7 @@ fi |
147 |
- |
148 |
- |
149 |
- |
150 |
--for fff in "$FC" f77 g77 "f77 +U77" "f77 -q -f -B108 -lU77"; do |
151 |
-+for fff in "$FC" f77 g77 gfortran "f77 +U77" "f77 -q -f -B108 -lU77"; do |
152 |
- if test -z "$fff"; then |
153 |
- continue |
154 |
- fi |
155 |
-diff --git a/docs/docs_c/corr.html b/docs/docs_c/corr.html |
156 |
-index 8b2eb8c..f2aa4f2 100644 |
157 |
---- a/docs/docs_c/corr.html |
158 |
-+++ b/docs/docs_c/corr.html |
159 |
-@@ -57,6 +57,11 @@ <h2 align=center>Usage:</h2> |
160 |
- <td>100 |
161 |
- </tr> |
162 |
- <tr> |
163 |
-+<th>-s# |
164 |
-+<td>calculate the correlation only every #-th step |
165 |
-+<td>1 |
166 |
-+</tr> |
167 |
-+<tr> |
168 |
- <th>-n |
169 |
- <td>don't use normalization to standard deviation |
170 |
- <td>not set |
171 |
-diff --git a/docs/docs_c/lfo-ar.html b/docs/docs_c/lfo-ar.html |
172 |
-index 59263b6..11a9b4e 100644 |
173 |
---- a/docs/docs_c/lfo-ar.html |
174 |
-+++ b/docs/docs_c/lfo-ar.html |
175 |
-@@ -117,7 +117,7 @@ <h2 align=center>Description of the Output:</h2> |
176 |
- The output consists of 5 columns for each neighborhood size:</b> |
177 |
- <ul> |
178 |
- <li> neighborhood size (units of the data) |
179 |
--<li> relative forecast error ((forecast error)/(variance of the data)) |
180 |
-+<li> relative forecast error ((forecast error)/(standard deviation of data)) |
181 |
- <li> fraction of points for which neighbors were found for this neighborhood |
182 |
- size |
183 |
- <li> average number of neighbors found per point |
184 |
-diff --git a/docs/docs_c/lyap_spec.html b/docs/docs_c/lyap_spec.html |
185 |
-index ab67d84..189482a 100644 |
186 |
---- a/docs/docs_c/lyap_spec.html |
187 |
-+++ b/docs/docs_c/lyap_spec.html |
188 |
-@@ -58,7 +58,9 @@ <h2 align=center>Usage:</h2> |
189 |
- --> |
190 |
- <tr> |
191 |
- <th>-r# |
192 |
--<td>minimal neighborhood size |
193 |
-+<td>minimal neighborhood size. This option dominates -k. This means |
194 |
-+ that if -r is set and more than -k neighbors are found, the number |
195 |
-+ of neighbors will not be reduced to the value given with -k. |
196 |
- <td>not set |
197 |
- </tr> |
198 |
- <tr> |
199 |
-diff --git a/docs/tutorial/ex1.html b/docs/tutorial/ex1.html |
200 |
-index e77be7b..660811b 100644 |
201 |
---- a/docs/tutorial/ex1.html |
202 |
-+++ b/docs/tutorial/ex1.html |
203 |
-@@ -146,7 +146,7 @@ |
204 |
- variable <font color=blue>x </font> of the logistic equation for |
205 |
- various parameter values (e.g.: <font color=green> |
206 |
- gnuplot> plot '< henon -B0 -A2 -l10000 | histogram -b100' with |
207 |
--hist</font>). When a sufficiently long transient has been |
208 |
-+histeps</font>). When a sufficiently long transient has been |
209 |
- discarded, such a histogram is the approximation to the invaraint |
210 |
- measure on the bins of the histogram. Verify numerically:<br> |
211 |
- <ul> |
212 |
-diff --git a/docs/tutorial/ex2.html b/docs/tutorial/ex2.html |
213 |
-index 5324a15..a0fbb11 100644 |
214 |
---- a/docs/tutorial/ex2.html |
215 |
-+++ b/docs/tutorial/ex2.html |
216 |
-@@ -82,7 +82,7 @@ |
217 |
- the two histograms, you thus should shift the one with respect to the |
218 |
- other by the mean value of the data:<br> |
219 |
- <font color=green> |
220 |
--set data style histep<br> |
221 |
-+set style data histep<br> |
222 |
- plot '< histogram amplitude.dat' u ($1-.146):2,'< histogram |
223 |
- ar.dat' </font> |
224 |
- <br>Result: The data sets are differnt: the distribution of <font |
225 |
-@@ -95,7 +95,7 @@ |
226 |
- <a href="../docs_f/spectrum.html">spectrum</a>) of both of them:<br> |
227 |
- <font color=red> corr amplitude.dat -D500 -o<br> |
228 |
- corr ar.dat -D500 -o</font><br> |
229 |
--<font color=green>set data style lines</font><br> |
230 |
-+<font color=green>set style data lines</font><br> |
231 |
- <font color=green> plot 'ar.dat.cor','amplitude.dat.cor'</font><br> |
232 |
- <font color=red>spectrum amplitude.dat -o<br> |
233 |
- spectrum ar.dat -o</font><br> |
234 |
-@@ -150,7 +150,7 @@ |
235 |
- <ul> |
236 |
- <li> compute the false nearest neighbour statistics |
237 |
- (<a href="../docs_c/false_nearest.html">false_nearest</a>):<br> |
238 |
--<font color=red> false_nearest amplitude.dat -M8 -d8 -o |
239 |
-+<font color=red> false_nearest amplitude.dat -M1,8 -d8 -o |
240 |
- -t200 -f5 </font><br> |
241 |
- Study the output, <font color=blue>amplitude.dat.fnn</font>, and |
242 |
- observe the invariance of the result (namely that the embedding dimension |
243 |
-@@ -158,9 +158,9 @@ |
244 |
- <br><br> |
245 |
- |
246 |
- <li> Use the zeorth-order predictor |
247 |
--(<a href="../docs_c/zeroth.html">zeroth</a>) |
248 |
-+(<a href="../docs_c/lzo-test.html">zeroth</a>) |
249 |
- on amplitude.dat and on ar.dat.<br> |
250 |
--<font color=red> zeroth amplitude.dat -m1,4 -d8 -o |
251 |
-+<font color=red> lzo-test amplitude.dat -m1,4 -d8 -o |
252 |
- -s250<br> |
253 |
- zeroth ar.dat -m1,4 -d8 -o |
254 |
- -s250</font><br> |
255 |
-diff --git a/docs/tutorial/ex3.html b/docs/tutorial/ex3.html |
256 |
-index 91735dd..2894689 100644 |
257 |
---- a/docs/tutorial/ex3.html |
258 |
-+++ b/docs/tutorial/ex3.html |
259 |
-@@ -196,7 +196,7 @@ |
260 |
- <font color=red> ll-ar optimal.dat -d10 -m3 -i2000 -s1 -o</font>,<br> |
261 |
- and compare the results:<br> |
262 |
- <font color=green> |
263 |
--set data style linespoints<br> |
264 |
-+set style data linespoints<br> |
265 |
- plot 'whatisit.dat.ll', 'whatisit.dat.ll' u 1:3,'optimal.dat.ll', |
266 |
- 'optimal.dat.ll' u 1:3</font><br> |
267 |
- <br> |
268 |
-diff --git a/source_c/corr.c b/source_c/corr.c |
269 |
-index 06da07a..4c79b9a 100644 |
270 |
---- a/source_c/corr.c |
271 |
-+++ b/source_c/corr.c |
272 |
-@@ -30,7 +30,7 @@ |
273 |
- char *format,*outfile=NULL,stout=1,normalize=1; |
274 |
- unsigned int column=1; |
275 |
- unsigned int verbosity=0xff; |
276 |
--unsigned long tau=100,length=ULONG_MAX,exclude=0; |
277 |
-+unsigned long tau=100,step=1,length=ULONG_MAX,exclude=0; |
278 |
- double *array; |
279 |
- double av,var; |
280 |
- char *infile=NULL; |
281 |
-@@ -48,6 +48,8 @@ void show_options(char *progname) |
282 |
- fprintf(stderr,"\t-x # of lines to be ignored [default 0]\n"); |
283 |
- fprintf(stderr,"\t-c column to read [default is 1]\n"); |
284 |
- fprintf(stderr,"\t-D corrlength [default is 100]\n"); |
285 |
-+ fprintf(stderr,"\t-s # calculate the correlation only every #-th step " |
286 |
-+ "[default is 1]\n"); |
287 |
- fprintf(stderr,"\t-n don\'t normalize to the variance" |
288 |
- " of the data [not set]\n"); |
289 |
- fprintf(stderr,"\t-o output_file [default is 'datafile'.cor; no -o" |
290 |
-@@ -72,6 +74,8 @@ void scan_options(int argc,char **argv) |
291 |
- sscanf(out,"%u",&column); |
292 |
- if ((out=check_option(argv,argc,'D','u')) != NULL) |
293 |
- sscanf(out,"%lu",&tau); |
294 |
-+ if ((out=check_option(argv,argc,'s','u')) != NULL) |
295 |
-+ sscanf(out,"%lu",&step); |
296 |
- if ((out=check_option(argv,argc,'n','n')) != NULL) |
297 |
- normalize=0; |
298 |
- if ((out=check_option(argv,argc,'V','u')) != NULL) |
299 |
-@@ -88,16 +92,17 @@ double corr(long i) |
300 |
- long j; |
301 |
- double c=0.0; |
302 |
- |
303 |
-- for (j=0;j<(length-i);j++) |
304 |
-+ for (j=0;j<(length-i);j++) { |
305 |
- c += array[j]*array[j+i]; |
306 |
-+ } |
307 |
- |
308 |
-- return c/(length-i); |
309 |
-+ return c/(double)(length-i); |
310 |
- } |
311 |
- |
312 |
- int main(int argc,char** argv) |
313 |
- { |
314 |
-- char stdi=0; |
315 |
-- long i; |
316 |
-+ char stdi=0,done=0; |
317 |
-+ unsigned long i; |
318 |
- FILE *fout=NULL; |
319 |
- |
320 |
- if (scan_help(argc,argv)) |
321 |
-@@ -157,14 +162,25 @@ int main(int argc,char** argv) |
322 |
- else |
323 |
- var=1.0; |
324 |
- |
325 |
-- for (i=0;i<=tau;i++) |
326 |
-+ for (i=0;i<=tau;i += step) |
327 |
- if (!stout) { |
328 |
- fprintf(fout,"%ld %e\n",i,corr(i)/var); |
329 |
- fflush(fout); |
330 |
-+ if (i == tau) done=1; |
331 |
- } |
332 |
- else { |
333 |
- fprintf(stdout,"%ld %e\n",i,corr(i)/var); |
334 |
- fflush(stdout); |
335 |
-+ if (i == tau) done=1; |
336 |
-+ } |
337 |
-+ if (!done) |
338 |
-+ if (!stout) { |
339 |
-+ fprintf(fout,"%ld %e\n",tau,corr(tau)/var); |
340 |
-+ fflush(fout); |
341 |
-+ } |
342 |
-+ else { |
343 |
-+ fprintf(stdout,"%ld %e\n",tau,corr(tau)/var); |
344 |
-+ fflush(stdout); |
345 |
- } |
346 |
- if (!stout) |
347 |
- fclose(fout); |
348 |
-diff --git a/source_c/false_nearest.c b/source_c/false_nearest.c |
349 |
-index f8a16e9..f5eed04 100644 |
350 |
---- a/source_c/false_nearest.c |
351 |
-+++ b/source_c/false_nearest.c |
352 |
-@@ -21,6 +21,7 @@ |
353 |
- /*Changes: |
354 |
- 12/10/05: It's multivariate now |
355 |
- 12/16/05: Scaled <eps> and sigma(eps) |
356 |
-+ 03/08/09: delay was missing in delay embedding of univariate case |
357 |
- */ |
358 |
- |
359 |
- #include <stdio.h> |
360 |
-@@ -37,7 +38,7 @@ char *infile=NULL; |
361 |
- char stdo=1,dimset=0; |
362 |
- char *column=NULL; |
363 |
- unsigned long length=ULONG_MAX,exclude=0,theiler=0; |
364 |
--unsigned int delay=1,maxdim=5,minemb=1; |
365 |
-+unsigned int delay=1,maxdim=6,minemb=1; |
366 |
- unsigned int comp=1,maxemb=5; |
367 |
- unsigned int verbosity=0xff; |
368 |
- double rt=2.0; |
369 |
-@@ -226,6 +227,11 @@ int main(int argc,char **argv) |
370 |
- series=(double**)get_multi_series(infile,&length,exclude,&comp,column, |
371 |
- dimset,verbosity); |
372 |
- |
373 |
-+ if ((maxemb*delay+1) >= length) { |
374 |
-+ fprintf(stderr,"Not enough points!\n"); |
375 |
-+ exit(FALSE_NEAREST_NOT_ENOUGH_POINTS); |
376 |
-+ } |
377 |
-+ |
378 |
- for (i=0;i<comp;i++) { |
379 |
- rescale_data(series[i],length,&min,&ind_inter); |
380 |
- variance(series[i],length,&av,&ind_var); |
381 |
-@@ -259,7 +265,7 @@ int main(int argc,char **argv) |
382 |
- for (i=0;i<maxdim;i++) { |
383 |
- if (comp == 1) { |
384 |
- vcomp[i]=0; |
385 |
-- vemb[i]=i; |
386 |
-+ vemb[i]=i*delay; |
387 |
- } |
388 |
- else { |
389 |
- vcomp[i]=i%comp; |
390 |
-diff --git a/source_c/histogram.c b/source_c/histogram.c |
391 |
-index 6ab9f02..a45576d 100644 |
392 |
---- a/source_c/histogram.c |
393 |
-+++ b/source_c/histogram.c |
394 |
-@@ -17,10 +17,8 @@ |
395 |
- * along with TISEAN; if not, write to the Free Software |
396 |
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA |
397 |
- */ |
398 |
--/*Author: Rainer Hegger. Last modified Dec 6, 2005*/ |
399 |
--/*Changes: |
400 |
-- 12/06/05: shift output x value to center of interval |
401 |
--*/ |
402 |
-+/*Author: Rainer Hegger. Last modified May 16, 2014*/ |
403 |
-+ |
404 |
- #include <math.h> |
405 |
- #include <limits.h> |
406 |
- #include <stdio.h> |
407 |
-@@ -28,7 +26,7 @@ |
408 |
- #include <string.h> |
409 |
- #include "routines/tsa.h" |
410 |
- |
411 |
--#define WID_STR "Makes a histogram of the data" |
412 |
-+#define WID_STR "Creates a histogram of a onedimensional dataset" |
413 |
- |
414 |
- unsigned long length=ULONG_MAX; |
415 |
- unsigned long base=50; |
416 |
-@@ -36,15 +34,10 @@ unsigned long exclude=0; |
417 |
- unsigned int column=1; |
418 |
- unsigned int verbosity=0xff; |
419 |
- double size; |
420 |
--char my_stdout=1,gotsize=0; |
421 |
-+char my_stdout=1,gotsize=0,density=0; |
422 |
- char *outfile=NULL; |
423 |
- char *infile=NULL; |
424 |
- |
425 |
--double *series; |
426 |
--double average,var; |
427 |
--double min,max; |
428 |
--long *box; |
429 |
-- |
430 |
- void show_options(char *progname) |
431 |
- { |
432 |
- what_i_do(progname,WID_STR); |
433 |
-@@ -57,6 +50,8 @@ void show_options(char *progname) |
434 |
- fprintf(stderr,"\t-x # of lines to ignore [default %ld]\n",exclude); |
435 |
- fprintf(stderr,"\t-c column to read [default %d]\n",column); |
436 |
- fprintf(stderr,"\t-b # of intervals [default %ld]\n",base); |
437 |
-+ fprintf(stderr,"\t-D output densities not relative frequencies" |
438 |
-+ " [default not set]\n"); |
439 |
- fprintf(stderr,"\t-o output file [default 'datafile'.dat ;" |
440 |
- " If no -o is given: stdout]\n"); |
441 |
- fprintf(stderr,"\t-V verbosity level [default 1]\n\t\t" |
442 |
-@@ -80,6 +75,8 @@ void scan_options(int n,char **str) |
443 |
- sscanf(out,"%lu",&base); |
444 |
- if ((out=check_option(str,n,'V','u')) != NULL) |
445 |
- sscanf(out,"%u",&verbosity); |
446 |
-+ if ((out=check_option(str,n,'D','n')) != NULL) |
447 |
-+ density=1; |
448 |
- if ((out=check_option(str,n,'o','o')) != NULL) { |
449 |
- my_stdout=0; |
450 |
- if (strlen(out) > 0) |
451 |
-@@ -92,6 +89,10 @@ int main(int argc,char **argv) |
452 |
- char stdi=0; |
453 |
- unsigned long i,j; |
454 |
- double x,norm,size=1.0,size2=1.0; |
455 |
-+ double min,max; |
456 |
-+ double *series; |
457 |
-+ double average,var; |
458 |
-+ long *box; |
459 |
- FILE *fout; |
460 |
- |
461 |
- if (scan_help(argc,argv)) |
462 |
-@@ -123,24 +124,36 @@ int main(int argc,char **argv) |
463 |
- |
464 |
- series=(double*)get_series(infile,&length,exclude,column,verbosity); |
465 |
- variance(series,length,&average,&var); |
466 |
-- rescale_data(series,length,&min,&max); |
467 |
-- |
468 |
-- |
469 |
-+ |
470 |
-+ min=max=series[0]; |
471 |
-+ for (i=1;i<length;i++) { |
472 |
-+ if (series[i] < min) min=series[i]; |
473 |
-+ else if (series[i] > max) max=series[i]; |
474 |
-+ } |
475 |
-+ max -= min; |
476 |
-+ |
477 |
-+ for (i=0;i<length;i++) |
478 |
-+ series[i]=(series[i]-min); |
479 |
-+ |
480 |
- if (base > 0) { |
481 |
- check_alloc(box=(long*)malloc(sizeof(long)*base)); |
482 |
- for (i=0;i<base;i++) |
483 |
- box[i]=0; |
484 |
- size=1./base; |
485 |
-- size2=size/2.0; |
486 |
-+ size2=(1.0-size/2.0)*max; |
487 |
- for (i=0;i<length;i++) { |
488 |
-- if (series[i] > (1.0-size2)) |
489 |
-- series[i]=1.0-size2; |
490 |
-- j=(long)(series[i]*base); |
491 |
-+ if (series[i] > size2) |
492 |
-+ series[i]=size2; |
493 |
-+ j=(long)(series[i]*base/max); |
494 |
- box[j]++; |
495 |
- } |
496 |
- } |
497 |
- |
498 |
-- norm=1.0/(double)length; |
499 |
-+ if (!density) |
500 |
-+ norm=1.0/(double)length; |
501 |
-+ else |
502 |
-+ norm=1.0/(double)length*(double)base/max; |
503 |
-+ |
504 |
- if (!my_stdout) { |
505 |
- fout=fopen(outfile,"w"); |
506 |
- if (verbosity&VER_INPUT) |
507 |
-@@ -150,7 +163,7 @@ int main(int argc,char **argv) |
508 |
- fprintf(fout,"#standard deviation= %e\n",var); |
509 |
- for (i=0;i<base;i++) { |
510 |
- x=(double)(i*size); |
511 |
-- fprintf(fout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm); |
512 |
-+ fprintf(fout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm); |
513 |
- } |
514 |
- fclose(fout); |
515 |
- } |
516 |
-@@ -162,7 +175,7 @@ int main(int argc,char **argv) |
517 |
- fprintf(stdout,"#standard deviation= %e\n",var); |
518 |
- for (i=0;i<base;i++) { |
519 |
- x=(double)(i*size); |
520 |
-- fprintf(stdout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm); |
521 |
-+ fprintf(stdout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm); |
522 |
- fflush(stdout); |
523 |
- } |
524 |
- } |
525 |
-diff --git a/source_c/lzo-run.c b/source_c/lzo-run.c |
526 |
-index 5393e9f..bc54fb5 100644 |
527 |
---- a/source_c/lzo-run.c |
528 |
-+++ b/source_c/lzo-run.c |
529 |
-@@ -49,7 +49,7 @@ unsigned int MINN=50; |
530 |
- unsigned int **indexes; |
531 |
- unsigned long LENGTH=ULONG_MAX,FLENGTH=1000,exclude=0; |
532 |
- unsigned long seed=0x9074325L; |
533 |
--double EPS0=1.e-3,EPSF=1.2,Q=10.0; |
534 |
-+double EPS0=1.e-3,EPSF=1.2,Q=0.0; |
535 |
- |
536 |
- double **mat,*vec,*hsum,*newav; |
537 |
- |
538 |
-diff --git a/source_c/mem_spec.c b/source_c/mem_spec.c |
539 |
-index a38fcfd..9821488 100644 |
540 |
---- a/source_c/mem_spec.c |
541 |
-+++ b/source_c/mem_spec.c |
542 |
-@@ -22,6 +22,7 @@ |
543 |
- Feb 19, 2007: changed meaning of -f flag and added -P flag to be |
544 |
- consistent with spectrum |
545 |
- Dec 5, 2006: Seg fault when poles > length; |
546 |
-+ Mar 15, 2007: normalization now the same as in spectrum |
547 |
- */ |
548 |
- #include <stdio.h> |
549 |
- #include <string.h> |
550 |
-@@ -216,7 +217,7 @@ int main(int argc,char **argv) |
551 |
- fdt=i/(2.0*out); |
552 |
- pow_spec=powcoef(fdt,cof); |
553 |
- fprintf(fout,"%e %e\n",fdt*samplingrate, |
554 |
-- pm/pow_spec/sqrt((double)length)); |
555 |
-+ pm/pow_spec/(double)length); |
556 |
- fflush(fout); |
557 |
- } |
558 |
- fclose(fout); |
559 |
-@@ -233,7 +234,7 @@ int main(int argc,char **argv) |
560 |
- fdt=i/(2.0*out); |
561 |
- pow_spec=powcoef(fdt,cof); |
562 |
- fprintf(stdout,"%e %e\n",fdt*samplingrate, |
563 |
-- pm/pow_spec/*/sqrt((double)length)*/); |
564 |
-+ pm/pow_spec/(double)length); |
565 |
- } |
566 |
- } |
567 |
- |
568 |
-diff --git a/source_c/mutual.c b/source_c/mutual.c |
569 |
-index fbea470..0496e92 100644 |
570 |
---- a/source_c/mutual.c |
571 |
-+++ b/source_c/mutual.c |
572 |
-@@ -17,7 +17,7 @@ |
573 |
- * along with TISEAN; if not, write to the Free Software |
574 |
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA |
575 |
- */ |
576 |
--/*Author: Rainer Hegger. Last modified, Sep 20, 2000 */ |
577 |
-+/*Author: Rainer Hegger. Last modified, Jul 13, 2010 */ |
578 |
- #include <stdio.h> |
579 |
- #include <stdlib.h> |
580 |
- #include <math.h> |
581 |
-@@ -26,16 +26,17 @@ |
582 |
- #include "routines/tsa.h" |
583 |
- |
584 |
- #define WID_STR "Estimates the time delayed mutual information\n\t\ |
585 |
--of the data set" |
586 |
-+of one or two data columns" |
587 |
- |
588 |
- |
589 |
--char *file_out=NULL,stout=1; |
590 |
-+char *file_out=NULL,stout=1,dimset=0; |
591 |
- char *infile=NULL; |
592 |
- unsigned long length=ULONG_MAX,exclude=0; |
593 |
--unsigned int column=1; |
594 |
-+unsigned int dim=1; |
595 |
- unsigned int verbosity=0xff; |
596 |
- long partitions=16,corrlength=20; |
597 |
--long *array,*h1,*h11,**h2; |
598 |
-+long **array,*h1,*h11,**h2; |
599 |
-+char *column=NULL; |
600 |
- |
601 |
- void show_options(char *progname) |
602 |
- { |
603 |
-@@ -48,7 +49,7 @@ void show_options(char *progname) |
604 |
- " means stdin\n"); |
605 |
- fprintf(stderr,"\t-l # of points to be used [Default is all]\n"); |
606 |
- fprintf(stderr,"\t-x # of lines to be ignored [Default is 0]\n"); |
607 |
-- fprintf(stderr,"\t-c column to read [Default is 1]\n"); |
608 |
-+ fprintf(stderr,"\t-c columns to read [Default is 1]\n"); |
609 |
- fprintf(stderr,"\t-b # of boxes [Default is 16]\n"); |
610 |
- fprintf(stderr,"\t-D max. time delay [Default is 20]\n"); |
611 |
- fprintf(stderr,"\t-o output file [-o without name means 'datafile'.mut;" |
612 |
-@@ -69,8 +70,8 @@ void scan_options(int n,char** in) |
613 |
- sscanf(out,"%lu",&length); |
614 |
- if ((out=check_option(in,n,'x','u')) != NULL) |
615 |
- sscanf(out,"%lu",&exclude); |
616 |
-- if ((out=check_option(in,n,'c','u')) != NULL) |
617 |
-- sscanf(out,"%u",&column); |
618 |
-+ if ((out=check_option(in,n,'c','s')) != NULL) |
619 |
-+ column=out; |
620 |
- if ((out=check_option(in,n,'b','u')) != NULL) |
621 |
- sscanf(out,"%lu",&partitions); |
622 |
- if ((out=check_option(in,n,'D','u')) != NULL) |
623 |
-@@ -86,7 +87,7 @@ void scan_options(int n,char** in) |
624 |
- |
625 |
- double make_cond_entropy(long t) |
626 |
- { |
627 |
-- long i,j,hi,hii,count=0; |
628 |
-+ long i,j,hi,hii,count=0,start,stop; |
629 |
- double hpi,hpj,pij,cond_ent=0.0,norm; |
630 |
- |
631 |
- for (i=0;i<partitions;i++) { |
632 |
-@@ -94,15 +95,23 @@ double make_cond_entropy(long t) |
633 |
- for (j=0;j<partitions;j++) |
634 |
- h2[i][j]=0; |
635 |
- } |
636 |
-- for (i=0;i<length;i++) |
637 |
-- if (i >= t) { |
638 |
-- hii=array[i]; |
639 |
-- hi=array[i-t]; |
640 |
-- h1[hi]++; |
641 |
-- h11[hii]++; |
642 |
-- h2[hi][hii]++; |
643 |
-- count++; |
644 |
-- } |
645 |
-+ if (t < 0) { |
646 |
-+ start=0; |
647 |
-+ stop=length+t; |
648 |
-+ } |
649 |
-+ else { |
650 |
-+ start=t; |
651 |
-+ stop=length; |
652 |
-+ } |
653 |
-+ |
654 |
-+ for (i=start;i<stop;i++) { |
655 |
-+ hii=array[0][i]; |
656 |
-+ hi=array[1][i+t]; |
657 |
-+ h1[hi]++; |
658 |
-+ h11[hii]++; |
659 |
-+ h2[hi][hii]++; |
660 |
-+ count++; |
661 |
-+ } |
662 |
- |
663 |
- norm=1.0/(double)count; |
664 |
- cond_ent=0.0; |
665 |
-@@ -127,8 +136,8 @@ double make_cond_entropy(long t) |
666 |
- int main(int argc,char** argv) |
667 |
- { |
668 |
- char stdi=0; |
669 |
-- long tau,i; |
670 |
-- double *series,min,interval,shannon; |
671 |
-+ long tau,i,j; |
672 |
-+ double **series,min1,min2,interval1,interval2,shannon,condent; |
673 |
- FILE *file; |
674 |
- |
675 |
- if (scan_help(argc,argv)) |
676 |
-@@ -140,7 +149,7 @@ int main(int argc,char** argv) |
677 |
- what_i_do(argv[0],WID_STR); |
678 |
- #endif |
679 |
- |
680 |
-- infile=search_datafile(argc,argv,&column,verbosity); |
681 |
-+ infile=search_datafile(argc,argv,NULL,verbosity); |
682 |
- if (infile == NULL) |
683 |
- stdi=1; |
684 |
- |
685 |
-@@ -158,20 +167,44 @@ int main(int argc,char** argv) |
686 |
- if (!stout) |
687 |
- test_outfile(file_out); |
688 |
- |
689 |
-- series=(double*)get_series(infile,&length,exclude,column,verbosity); |
690 |
-- rescale_data(series,length,&min,&interval); |
691 |
-+ if (column == NULL) { |
692 |
-+ series=(double**)get_multi_series(infile,&length,exclude,&dim,"", |
693 |
-+ dimset,verbosity); |
694 |
-+ } |
695 |
-+ else { |
696 |
-+ series=(double**)get_multi_series(infile,&length,exclude,&dim,column, |
697 |
-+ dimset,verbosity); |
698 |
-+ } |
699 |
- |
700 |
- check_alloc(h1=(long *)malloc(sizeof(long)*partitions)); |
701 |
- check_alloc(h11=(long *)malloc(sizeof(long)*partitions)); |
702 |
- check_alloc(h2=(long **)malloc(sizeof(long *)*partitions)); |
703 |
- for (i=0;i<partitions;i++) |
704 |
- check_alloc(h2[i]=(long *)malloc(sizeof(long)*partitions)); |
705 |
-- check_alloc(array=(long *)malloc(sizeof(long)*length)); |
706 |
-- for (i=0;i<length;i++) |
707 |
-- if (series[i] < 1.0) |
708 |
-- array[i]=(long)(series[i]*(double)partitions); |
709 |
-- else |
710 |
-- array[i]=partitions-1; |
711 |
-+ check_alloc(array=(long **)malloc(sizeof(long*)*2)); |
712 |
-+ check_alloc(array[0]=(long *)malloc(sizeof(long)*length)); |
713 |
-+ check_alloc(array[1]=(long *)malloc(sizeof(long)*length)); |
714 |
-+ if (dim == 1) { |
715 |
-+ rescale_data(series[0],length,&min1,&interval1); |
716 |
-+ for (i=0;i<length;i++) |
717 |
-+ if (series[0][i] < 1.0) |
718 |
-+ array[0][i]=array[1][i]=(long)(series[0][i]*(double)partitions); |
719 |
-+ else |
720 |
-+ array[0][i]=array[1][i]=partitions-1; |
721 |
-+ free(series[0]); |
722 |
-+ } |
723 |
-+ else { |
724 |
-+ rescale_data(series[0],length,&min1,&interval1); |
725 |
-+ rescale_data(series[1],length,&min2,&interval2); |
726 |
-+ for (j=0;j<2;j++) { |
727 |
-+ for (i=0;i<length;i++) |
728 |
-+ if (series[j][i] < 1.0) |
729 |
-+ array[j][i]=(long)(series[j][i]*(double)partitions); |
730 |
-+ else |
731 |
-+ array[j][i]=partitions-1; |
732 |
-+ free(series[j]); |
733 |
-+ } |
734 |
-+ } |
735 |
- free(series); |
736 |
- |
737 |
- shannon=make_cond_entropy(0); |
738 |
-@@ -182,10 +215,9 @@ int main(int argc,char** argv) |
739 |
- file=fopen(file_out,"w"); |
740 |
- if (verbosity&VER_INPUT) |
741 |
- fprintf(stderr,"Opened %s for writing\n",file_out); |
742 |
-- fprintf(file,"#shannon= %e\n",shannon); |
743 |
-- fprintf(file,"%d %e\n",0,shannon); |
744 |
-- for (tau=1;tau<=corrlength;tau++) { |
745 |
-- fprintf(file,"%ld %e\n",tau,make_cond_entropy(tau)); |
746 |
-+ for (tau=-corrlength;tau<=corrlength;tau++) { |
747 |
-+ condent=make_cond_entropy(tau); |
748 |
-+ fprintf(file,"%ld %e %e\n",tau,condent,condent/log((double)partitions)); |
749 |
- fflush(file); |
750 |
- } |
751 |
- fclose(file); |
752 |
-@@ -193,10 +225,9 @@ int main(int argc,char** argv) |
753 |
- else { |
754 |
- if (verbosity&VER_INPUT) |
755 |
- fprintf(stderr,"Writing to stdout\n"); |
756 |
-- fprintf(stdout,"#shannon= %e\n",shannon); |
757 |
-- fprintf(stdout,"%d %e\n",0,shannon); |
758 |
-- for (tau=1;tau<=corrlength;tau++) { |
759 |
-- fprintf(stdout,"%ld %e\n",tau,make_cond_entropy(tau)); |
760 |
-+ for (tau=-corrlength;tau<=corrlength;tau++) { |
761 |
-+ condent=make_cond_entropy(tau); |
762 |
-+ fprintf(stdout,"%ld %e %e\n",tau,condent,condent/log((double)partitions)); |
763 |
- fflush(stdout); |
764 |
- } |
765 |
- } |
766 |
-diff --git a/source_c/polynom.c b/source_c/polynom.c |
767 |
-index bc57ba8..6448f49 100644 |
768 |
---- a/source_c/polynom.c |
769 |
-+++ b/source_c/polynom.c |
770 |
-@@ -20,6 +20,8 @@ |
771 |
- /*Author: Rainer Hegger*/ |
772 |
- /* Changes: |
773 |
- 6/30/2006: Norm of the errors was wrong |
774 |
-+ 6/5/2008: Norm was still wrong. Now its given as an absolute value in |
775 |
-+ units of the data |
776 |
- */ |
777 |
- #include <stdio.h> |
778 |
- #include <stdlib.h> |
779 |
-@@ -265,6 +267,7 @@ int main(int argc,char **argv) |
780 |
- |
781 |
- series=(double*)get_series(infile,&LENGTH,exclude,COLUMN,verbosity); |
782 |
- variance(series,LENGTH,&av,&std_dev); |
783 |
-+ |
784 |
- for (i=0;i<LENGTH;i++) |
785 |
- series[i] /= std_dev; |
786 |
- |
787 |
-@@ -307,11 +310,11 @@ int main(int argc,char **argv) |
788 |
- |
789 |
- in_error=make_error((unsigned long)0,INSAMPLE); |
790 |
- |
791 |
-- fprintf(file,"#average insample error= %e\n",sqrt(in_error)); |
792 |
-+ fprintf(file,"#average insample error= %e\n",sqrt(in_error)*std_dev); |
793 |
- |
794 |
- if (INSAMPLE < LENGTH) { |
795 |
- out_error=make_error(INSAMPLE,LENGTH); |
796 |
-- fprintf(file,"#average out of sample error= %e\n",sqrt(out_error)); |
797 |
-+ fprintf(file,"#average out of sample error= %e\n",sqrt(out_error)*std_dev); |
798 |
- } |
799 |
- |
800 |
- if (CAST) |
801 |
-diff --git a/source_c/polynomp.c b/source_c/polynomp.c |
802 |
-index 6021e19..5b32e58 100644 |
803 |
---- a/source_c/polynomp.c |
804 |
-+++ b/source_c/polynomp.c |
805 |
-@@ -239,7 +239,7 @@ int main(int argc,char **argv) |
806 |
- fclose(file); |
807 |
- |
808 |
- dummy=(double**)get_multi_series(parin,&plength,0LU, |
809 |
-- &dim,"",(char)"1",verbosity); |
810 |
-+ &dim,"",1,verbosity); |
811 |
- |
812 |
- check_alloc(order=(unsigned int**)malloc(sizeof(int*)*plength)); |
813 |
- for (i=0;i<plength;i++) { |
814 |
-diff --git a/source_c/xcor.c b/source_c/xcor.c |
815 |
-index ec1ed7f..8f50609 100644 |
816 |
---- a/source_c/xcor.c |
817 |
-+++ b/source_c/xcor.c |
818 |
-@@ -30,7 +30,7 @@ given as two columns of one file." |
819 |
- |
820 |
- char *columns=NULL,*outfile=NULL,stout=1; |
821 |
- unsigned long length=ULONG_MAX,exclude=0; |
822 |
--long tau=100; |
823 |
-+unsigned long tau=100; |
824 |
- unsigned int verbosity=0xff; |
825 |
- double *array1,*array2; |
826 |
- char *infile=NULL; |
827 |
-diff --git a/source_f/cluster.f b/source_f/cluster.f |
828 |
-index 61357ff..d564fc7 100644 |
829 |
---- a/source_f/cluster.f |
830 |
-+++ b/source_f/cluster.f |
831 |
-@@ -47,7 +47,8 @@ |
832 |
- d(i,j)=dij |
833 |
- np=max(i,j,np) |
834 |
- goto 1 |
835 |
-- 999 if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np |
836 |
-+c 999 if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np |
837 |
-+ 999 if(iv_io(iverb).eq.1) write(0,*) "matrix size ", np |
838 |
- dmean=0 |
839 |
- nd=0 |
840 |
- do 20 i=1,np |
841 |
|
842 |
diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch b/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch |
843 |
deleted file mode 100644 |
844 |
index 7f80f6276..000000000 |
845 |
--- a/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch |
846 |
+++ /dev/null |
847 |
@@ -1,57 +0,0 @@ |
848 |
-diff --git a/Makefile.in b/Makefile.in |
849 |
-index c1f3e0c..60f9720 100644 |
850 |
---- a/Makefile.in |
851 |
-+++ b/Makefile.in |
852 |
-@@ -9,8 +9,8 @@ HAVE_NR = @HAVE_NR@ |
853 |
- |
854 |
- all: |
855 |
- @head -20 README |
856 |
-- -if test -n "${FC}"; then (cd source_f && $(MAKE) $@); fi |
857 |
-- -if test -n "${CC}"; then (cd source_c && $(MAKE) $@); fi |
858 |
-+ $(MAKE) -C source_f $@ |
859 |
-+ $(MAKE) -C source_c $@ |
860 |
- |
861 |
- install: do_install missing |
862 |
- @echo "******************************************************************" |
863 |
-diff --git a/source_c/Makefile.in b/source_c/Makefile.in |
864 |
-index 1ab10e4..2efb803 100644 |
865 |
---- a/source_c/Makefile.in |
866 |
-+++ b/source_c/Makefile.in |
867 |
-@@ -23,10 +23,10 @@ LOADLIBS = routines/libddtsa.a -lm |
868 |
- all: $(ALL) |
869 |
- |
870 |
- routines/libddtsa.a: |
871 |
-- (cd routines && $(MAKE)) |
872 |
-+ $(MAKE) -C routines |
873 |
- |
874 |
- $(ALL): routines/libddtsa.a *.c |
875 |
-- -$(CC) $(CFLAGS) $(COPTS) -o $@ $@.c $(LOADLIBS) |
876 |
-+ -$(CC) $(LDFLAGS) $(CFLAGS) $(COPTS) -o $@ $@.c $(LOADLIBS) |
877 |
- |
878 |
- install: all |
879 |
- -for bin in $(ALL); do $(INSTALL) $$bin $(BINDIR); done |
880 |
-diff --git a/source_f/Makefile.in b/source_f/Makefile.in |
881 |
-index 6525b72..e45eea7 100644 |
882 |
---- a/source_f/Makefile.in |
883 |
-+++ b/source_f/Makefile.in |
884 |
-@@ -37,17 +37,17 @@ istdio.o: istdio_temp.f |
885 |
- $(FC) $(FFLAGS) -c istdio.f -o istdio.o |
886 |
- |
887 |
- $(BINS): libtsa.a libsla.a *.f |
888 |
-- -$(FC) $(FFLAGS) -o $@ $@.f $(LOADLIBES) $(LDFLAGS) |
889 |
-+ -$(FC) $(LDFLAGS) $(FFLAGS) -o $@ $@.f $(LOADLIBES) |
890 |
- |
891 |
- libtsa.a: $(INC) |
892 |
- $(AR) $(ARFLAGS) libtsa.a $? |
893 |
- $(RANLIB) libtsa.a |
894 |
- |
895 |
- libsla.a: slatec/*.f |
896 |
-- (cd slatec && $(MAKE)) |
897 |
-+ $(MAKE) -C slatec |
898 |
- |
899 |
- Randomize: libtsa.a libsla.a |
900 |
-- -(cd randomize && $(MAKE)) |
901 |
-+ $(MAKE) -C randomize |
902 |
- |
903 |
- clean: |
904 |
- @rm -f istdio.f |
905 |
|
906 |
diff --git a/sci-mathematics/tisean/metadata.xml b/sci-mathematics/tisean/metadata.xml |
907 |
deleted file mode 100644 |
908 |
index 02d26ebf3..000000000 |
909 |
--- a/sci-mathematics/tisean/metadata.xml |
910 |
+++ /dev/null |
911 |
@@ -1,11 +0,0 @@ |
912 |
-<?xml version="1.0" encoding="UTF-8"?> |
913 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
914 |
-<pkgmetadata> |
915 |
- <maintainer type="person"> |
916 |
- <email>jlec@g.o</email> |
917 |
- <name>Justin Lecher (jlec)</name> |
918 |
- </maintainer> |
919 |
- <upstream> |
920 |
- <remote-id type="github">heggus/Tisean</remote-id> |
921 |
- </upstream> |
922 |
-</pkgmetadata> |
923 |
|
924 |
diff --git a/sci-mathematics/tisean/tisean-3.0.1.ebuild b/sci-mathematics/tisean/tisean-3.0.1.ebuild |
925 |
deleted file mode 100644 |
926 |
index f43138ee6..000000000 |
927 |
--- a/sci-mathematics/tisean/tisean-3.0.1.ebuild |
928 |
+++ /dev/null |
929 |
@@ -1,45 +0,0 @@ |
930 |
-# Copyright 1999-2017 Gentoo Foundation |
931 |
-# Distributed under the terms of the GNU General Public License v2 |
932 |
- |
933 |
-EAPI=5 |
934 |
- |
935 |
-inherit eutils toolchain-funcs |
936 |
- |
937 |
-MY_P="Tisean_${PV}" |
938 |
- |
939 |
-DESCRIPTION="Time series analytics with theory of non-liner deterministic dynamical systems" |
940 |
-HOMEPAGE=" |
941 |
- https://github.com/heggus/Tisean |
942 |
- http://www.mpipks-dresden.mpg.de/%7Etisean/Tisean_3.0.1/index.html" |
943 |
-SRC_URI="http://www.mpipks-dresden.mpg.de/~tisean/TISEAN_3.0.1.tar.gz" |
944 |
- |
945 |
-LICENSE="GPL-2" |
946 |
-SLOT="0" |
947 |
-KEYWORDS="~amd64 ~x86" |
948 |
-IUSE="" |
949 |
- |
950 |
-S="${WORKDIR}/${MY_P}" |
951 |
- |
952 |
-src_prepare() { |
953 |
- tc-export FC CC |
954 |
- epatch \ |
955 |
- "${FILESDIR}"/${P}-gentoo.patch \ |
956 |
- "${FILESDIR}"/${P}-backport.patch |
957 |
-} |
958 |
- |
959 |
-src_configure() { |
960 |
- econf \ |
961 |
- --prefix="${ED}/usr" |
962 |
-} |
963 |
- |
964 |
-src_install() { |
965 |
- # TODO: fix file collisions with: |
966 |
- # media-gfx/graphviz: /usr/bin/cluster |
967 |
- # media-gfx/imagemagick: /usr/bin/compare |
968 |
- dodir /usr/bin |
969 |
- default |
970 |
-} |
971 |
- |
972 |
-pkg_postinst() { |
973 |
- optfeature "plotting support" sci-visualization/gnuplot |
974 |
-} |