1 |
commit: 38938220c8b6fde207fb7054dbdd8987bfa5085d |
2 |
Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
3 |
AuthorDate: Tue Apr 26 18:48:22 2016 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
5 |
CommitDate: Tue Apr 26 18:48:30 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=38938220 |
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|
8 |
sci-biology/emboss: Clean up of files dir |
9 |
|
10 |
Move to readme.gentoo-r1.eclass |
11 |
|
12 |
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=579728 |
13 |
|
14 |
Package-Manager: portage-2.2.28 |
15 |
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
16 |
|
17 |
sci-biology/emboss/emboss-6.6.0.ebuild | 9 +- |
18 |
sci-biology/emboss/files/22emboss | 4 - |
19 |
.../emboss/files/6.3.1_p4-unbundle-libs.patch | 600 --------------------- |
20 |
sci-biology/emboss/files/README.Gentoo | 28 - |
21 |
.../emboss/files/emboss-5.0.0-as-needed.patch | 24 - |
22 |
.../emboss/files/emboss-6.3.1_p4-r1_plcol.patch | 112 ---- |
23 |
sci-biology/emboss/files/emboss-README.Gentoo-1 | 34 -- |
24 |
sci-biology/emboss/files/emboss-README.Gentoo-2 | 34 -- |
25 |
8 files changed, 7 insertions(+), 838 deletions(-) |
26 |
|
27 |
diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild |
28 |
index a853743..5c4c77d 100644 |
29 |
--- a/sci-biology/emboss/emboss-6.6.0.ebuild |
30 |
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild |
31 |
@@ -1,11 +1,12 @@ |
32 |
-# Copyright 1999-2015 Gentoo Foundation |
33 |
+# Copyright 1999-2016 Gentoo Foundation |
34 |
# Distributed under the terms of the GNU General Public License v2 |
35 |
# $Id$ |
36 |
|
37 |
EAPI=5 |
38 |
|
39 |
AUTOTOOLS_AUTORECONF=1 |
40 |
-inherit autotools-utils emboss-r1 eutils readme.gentoo |
41 |
+ |
42 |
+inherit autotools-utils emboss-r1 eutils readme.gentoo-r1 |
43 |
|
44 |
DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" |
45 |
SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" |
46 |
@@ -59,3 +60,7 @@ src_install() { |
47 |
mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ |
48 |
die "Failed to move CODON directory." |
49 |
} |
50 |
+ |
51 |
+pkg_postinst() { |
52 |
+ readme.gentoo_print_elog |
53 |
+} |
54 |
|
55 |
diff --git a/sci-biology/emboss/files/22emboss b/sci-biology/emboss/files/22emboss |
56 |
deleted file mode 100644 |
57 |
index 177643c..0000000 |
58 |
--- a/sci-biology/emboss/files/22emboss |
59 |
+++ /dev/null |
60 |
@@ -1,4 +0,0 @@ |
61 |
-# plplot libs dir |
62 |
-PLPLOT_LIB="/usr/share/EMBOSS/" |
63 |
-# ACD files location |
64 |
-EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" |
65 |
|
66 |
diff --git a/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch |
67 |
deleted file mode 100644 |
68 |
index 5e46374..0000000 |
69 |
--- a/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch |
70 |
+++ /dev/null |
71 |
@@ -1,600 +0,0 @@ |
72 |
-diff --git a/Makefile.am b/Makefile.am |
73 |
-index 4fe2ed1..7f3a95f 100644 |
74 |
---- a/Makefile.am |
75 |
-+++ b/Makefile.am |
76 |
-@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4 |
77 |
- |
78 |
- AUTOMAKE_OPTIONS = gnits |
79 |
- |
80 |
--SUBDIRS = plplot ajax nucleus emboss test doc jemboss |
81 |
-+if !ESYSTEMLIBS |
82 |
-+EXTRA_DIRS = plplot |
83 |
-+endif |
84 |
-+ |
85 |
-+if GJEMBOSS |
86 |
-+JEMBOSS_DIR = jemboss |
87 |
-+endif |
88 |
-+ |
89 |
-+SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) |
90 |
-+DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) |
91 |
- |
92 |
- # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\" |
93 |
- |
94 |
- # files with nonstandard names in this directory |
95 |
--EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh |
96 |
-+EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh |
97 |
- |
98 |
- # tar to pick up the other directories |
99 |
- # then remove any CVS subdirectories |
100 |
-diff --git a/README.fixes b/README.fixes |
101 |
-new file mode 100644 |
102 |
-index 0000000..3c56d79 |
103 |
---- /dev/null |
104 |
-+++ b/README.fixes |
105 |
-@@ -0,0 +1,9 @@ |
106 |
-+The files in this directory are bugfix replacements for files in |
107 |
-+the EMBOSS-6.3.1 distribution. Just drop the replacement files in |
108 |
-+the location shown and redo the 'make install.' |
109 |
-+ |
110 |
-+Fix 1. EMBOSS-6.3.1/configure |
111 |
-+ EMBOSS-6.3.1/m4/mysql.m4 |
112 |
-+ |
113 |
-+21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of |
114 |
-+ hpdf support prevented inclusion of MySQL support. |
115 |
-diff --git a/ajax/Makefile.am b/ajax/Makefile.am |
116 |
-index 4a44f6f..cf27ff8 100644 |
117 |
---- a/ajax/Makefile.am |
118 |
-+++ b/ajax/Makefile.am |
119 |
-@@ -1,6 +1,6 @@ |
120 |
- ## Process this file with automake to produce Makefile.in |
121 |
- if !ESYSTEMLIBS |
122 |
--EXTRA_DIRS = expat zlib |
123 |
-+EXTRA_DIRS = pcre expat zlib |
124 |
- endif |
125 |
- |
126 |
--SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd |
127 |
-+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd |
128 |
-diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am |
129 |
-index 02bcaa7..368ddfe 100644 |
130 |
---- a/ajax/acd/Makefile.am |
131 |
-+++ b/ajax/acd/Makefile.am |
132 |
-@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ |
133 |
- endif |
134 |
- |
135 |
- if !ESYSTEMLIBS |
136 |
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib |
137 |
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ |
138 |
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre |
139 |
-+else |
140 |
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) |
141 |
- endif |
142 |
- |
143 |
--INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ |
144 |
-+INCLUDES = \ |
145 |
- $(EXTRA_INCLUDES) \ |
146 |
- -I$(top_srcdir)/ajax/core \ |
147 |
- -I$(top_srcdir)/ajax/graphics \ |
148 |
-@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF) |
149 |
- endif |
150 |
- |
151 |
- libacd_la_LDFLAGS = $(LINKFLAGS) |
152 |
-+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la |
153 |
-diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am |
154 |
-index da57727..857ca5f 100644 |
155 |
---- a/ajax/ajaxdb/Makefile.am |
156 |
-+++ b/ajax/ajaxdb/Makefile.am |
157 |
-@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ |
158 |
- endif |
159 |
- |
160 |
- if !ESYSTEMLIBS |
161 |
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib |
162 |
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ |
163 |
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre |
164 |
- endif |
165 |
- |
166 |
- |
167 |
--INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ |
168 |
-+INCLUDES = \ |
169 |
- $(EXTRA_INCLUDES) \ |
170 |
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl |
171 |
- |
172 |
-@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF) |
173 |
- endif |
174 |
- |
175 |
- libajaxdb_la_LDFLAGS = $(LINKFLAGS) |
176 |
-+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la |
177 |
-diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am |
178 |
-index af27cb0..8fa4a3a 100644 |
179 |
---- a/ajax/core/Makefile.am |
180 |
-+++ b/ajax/core/Makefile.am |
181 |
-@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \ |
182 |
- endif |
183 |
- |
184 |
- if !ESYSTEMLIBS |
185 |
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib |
186 |
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ |
187 |
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre |
188 |
-+else |
189 |
-+EXTRA_LIBS = -lexpat -lpcre |
190 |
- endif |
191 |
- |
192 |
-+EXTRA_DIST = ajax-pcre-config.h.in |
193 |
-+DISTCLEAN = ajax-pcre-config.h |
194 |
- |
195 |
- INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \ |
196 |
- -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \ |
197 |
---I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES) |
198 |
-+$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS) |
199 |
- |
200 |
- AJAXSRC = ajalign.c ajarr.c ajassert.c \ |
201 |
- ajbase.c ajcall.c ajcod.c \ |
202 |
-@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \ |
203 |
- ajmath.h ajmatrices.h ajmem.h ajmess.h \ |
204 |
- ajnam.h ajnexus.h ajobo.h \ |
205 |
- ajpat.h ajpdb.h ajpdbio.h ajphylo.h \ |
206 |
--ajrange.h ajreg.h ajreport.h ajresource.h \ |
207 |
-+ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \ |
208 |
- ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \ |
209 |
- ajsort.h ajsql.h ajstr.h ajsys.h \ |
210 |
- ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h |
211 |
-@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF) |
212 |
- endif |
213 |
- |
214 |
- libajax_la_LDFLAGS = $(LINKFLAGS) |
215 |
-+libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS) |
216 |
-diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in |
217 |
-new file mode 100644 |
218 |
-index 0000000..b09e4e6 |
219 |
---- /dev/null |
220 |
-+++ b/ajax/core/ajax-pcre-config.h.in |
221 |
-@@ -0,0 +1 @@ |
222 |
-+@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE |
223 |
-diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h |
224 |
-index 06793be..659f462 100644 |
225 |
---- a/ajax/core/ajreg.h |
226 |
-+++ b/ajax/core/ajreg.h |
227 |
-@@ -16,9 +16,14 @@ extern "C" |
228 |
- #define ajreg_h |
229 |
- |
230 |
- #include "ajax.h" |
231 |
-+#include "ajax-pcre-config.h" |
232 |
-+#ifndef AJAX_USE_SYSTEM_PCRE |
233 |
- #include "pcre_config.h" |
234 |
- #include "pcre_internal.h" |
235 |
- #include "pcreposix.h" |
236 |
-+#else |
237 |
-+#include <pcre.h> |
238 |
-+#endif |
239 |
- |
240 |
- #define AJREG_OVECSIZE 30 |
241 |
- |
242 |
-@@ -41,7 +46,11 @@ extern "C" |
243 |
- ******************************************************************************/ |
244 |
- |
245 |
- typedef struct AjSRegexp { |
246 |
-+#ifndef AJAX_USE_SYSTEM_PCRE |
247 |
- real_pcre *pcre; |
248 |
-+#else |
249 |
-+ pcre *pcre; |
250 |
-+#endif |
251 |
- pcre_extra *extra; |
252 |
- int *ovector; |
253 |
- const char* orig; |
254 |
-diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am |
255 |
-index ca33a84..87e51bd 100644 |
256 |
---- a/ajax/ensembl/Makefile.am |
257 |
-+++ b/ajax/ensembl/Makefile.am |
258 |
-@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo |
259 |
- endif |
260 |
- |
261 |
- if !ESYSTEMLIBS |
262 |
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat |
263 |
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ |
264 |
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre |
265 |
- endif |
266 |
- |
267 |
- |
268 |
--INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \ |
269 |
---I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core |
270 |
-+INCLUDES = $(EXTRA_INCLUDES) \ |
271 |
-+-I$(top_srcdir)/ajax/core |
272 |
- |
273 |
- ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \ |
274 |
- ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \ |
275 |
-@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF) |
276 |
- endif |
277 |
- |
278 |
- libensembl_la_LDFLAGS = $(LINKFLAGS) |
279 |
-+libensembl_la_LIBADD = ../core/libajax.la |
280 |
-diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am |
281 |
-index ab45afc..f61c605 100644 |
282 |
---- a/ajax/graphics/Makefile.am |
283 |
-+++ b/ajax/graphics/Makefile.am |
284 |
-@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot |
285 |
- endif |
286 |
- |
287 |
- if !ESYSTEMLIBS |
288 |
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat |
289 |
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ |
290 |
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre |
291 |
-+else |
292 |
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM |
293 |
-+EXTRA_LIBS = $(PLPLOT_LIBS) |
294 |
- endif |
295 |
- |
296 |
- |
297 |
--INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ |
298 |
-+INCLUDES = \ |
299 |
- $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core |
300 |
- |
301 |
- AJAXGSRC = ajgraph.c ajhist.c |
302 |
-@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF) |
303 |
- endif |
304 |
- |
305 |
- libajaxg_la_LDFLAGS = $(LINKFLAGS) |
306 |
-+libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS) |
307 |
-diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c |
308 |
-index 25e75e4..60f2743 100644 |
309 |
---- a/ajax/graphics/ajgraph.c |
310 |
-+++ b/ajax/graphics/ajgraph.c |
311 |
-@@ -34,10 +34,8 @@ |
312 |
- #include <float.h> |
313 |
- #define AZ 28 |
314 |
- |
315 |
-- |
316 |
- #include "plplotP.h" |
317 |
- |
318 |
-- |
319 |
- static void GraphArray(ajuint numofpoints, |
320 |
- float *x, float *y); |
321 |
- static void GraphArrayGaps(ajuint numofpoints, |
322 |
-@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size) |
323 |
- ** @@ |
324 |
- ******************************************************************************/ |
325 |
- |
326 |
-+#define _GNU_SOURCE |
327 |
-+#include <stdio.h> |
328 |
-+ |
329 |
- static void GraphSetName(const AjPGraph thys, |
330 |
- const AjPStr txt, const char *ext) |
331 |
- { |
332 |
- if(!thys->ready) |
333 |
- { |
334 |
-+#ifdef USE_PLXSFNAM_SHIM |
335 |
-+ char *fullname; |
336 |
-+#endif |
337 |
- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); |
338 |
-+#ifdef USE_PLXSFNAM_SHIM |
339 |
-+ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext); |
340 |
-+ ajDebug("=g= plsfnam ('%S') instead\n", fullname); |
341 |
-+ plsfnam(fullname); |
342 |
-+ free(fullname); |
343 |
-+#else |
344 |
- plxsfnam(ajStrGetPtr(txt), ext); |
345 |
-+#endif |
346 |
- ajStrAssignS(&graphBasename, txt); |
347 |
- ajStrAssignC(&graphExtension, ext); |
348 |
- if(ajStrGetCharFirst(graphExtension) == '.') |
349 |
-diff --git a/configure.in b/configure.in |
350 |
-index ddb4f81..3f4fe5e 100644 |
351 |
---- a/configure.in |
352 |
-+++ b/configure.in |
353 |
-@@ -235,15 +235,6 @@ AC_PROG_INSTALL |
354 |
- AC_PROG_LN_S |
355 |
- AC_PROG_MAKE_SET |
356 |
- |
357 |
--dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
358 |
--if test "${with_x}" != "no" ; then |
359 |
--if test "`uname -a | grep Darwin`"; then |
360 |
--OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` |
361 |
--if test ${OSXX} '>' '10.4'; then |
362 |
--CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" |
363 |
--fi |
364 |
--fi |
365 |
--fi |
366 |
- |
367 |
- # Checks for header files. |
368 |
- #as# AC_PATH_X |
369 |
-@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove) |
370 |
- #as# select socket sqrt strchr strcspn strdup strerror strpbrk \ |
371 |
- #as# strrchr strspn strstr strtol]) |
372 |
- |
373 |
--if test "${with_x}" != "no" ; then |
374 |
--LF_EMBOSS_PATH_XLIB |
375 |
--fi |
376 |
- |
377 |
- dnl Library checks |
378 |
- AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket") |
379 |
-@@ -316,14 +304,16 @@ CHECK_PNGDRIVER |
380 |
- CHECK_AUTH |
381 |
- CHECK_AMD64 |
382 |
- |
383 |
-+AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes") |
384 |
-+ |
385 |
- AX_LIB_MYSQL |
386 |
- AX_LIB_POSTGRESQL |
387 |
- |
388 |
- CFLAGS="$CFLAGS $MYSQL_CFLAGS" |
389 |
- LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS" |
390 |
- |
391 |
--CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS" |
392 |
--LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS" |
393 |
-+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS" |
394 |
-+LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS" |
395 |
- |
396 |
- |
397 |
- dnl Check for 'ant' for packaging Jemboss and export result |
398 |
-@@ -443,13 +433,36 @@ fi |
399 |
- |
400 |
- dnl Test if --enable-systemlibs given |
401 |
- have_systemlibs=no |
402 |
-+DEFINE_USE_SYSTEM_PCRE="#undef" |
403 |
- AC_ARG_ENABLE(systemlibs, |
404 |
- AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])) |
405 |
-+AC_MSG_CHECKING(for systemlib usage) |
406 |
- if test "${enable_systemlibs}" = "yes" ; then |
407 |
- have_systemlibs=yes |
408 |
-+ DEFINE_USE_SYSTEM_PCRE="#define" |
409 |
-+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
410 |
-+ PKG_CHECK_MODULES([ZLIB], [zlib]) |
411 |
-+else |
412 |
-+ dnl X11 is only used by plplot |
413 |
-+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
414 |
-+ if test "${with_x}" != "no" ; then |
415 |
-+ if test "`uname -a | grep Darwin`"; then |
416 |
-+ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` |
417 |
-+ if test ${OSXX} '>' '10.4'; then |
418 |
-+ CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" |
419 |
-+ fi |
420 |
-+ fi |
421 |
-+ fi |
422 |
-+ if test "${with_x}" != "no" ; then |
423 |
-+ LF_EMBOSS_PATH_XLIB |
424 |
-+ fi |
425 |
-+ AC_MSG_NOTICE(USING bundled LIBS) |
426 |
- fi |
427 |
- AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") |
428 |
- AC_SUBST(ESYSTEMLIBS) |
429 |
-+AC_SUBST(DEFINE_USE_SYSTEM_PCRE) |
430 |
-+AC_SUBST(PLPLOT_CFLAGS) |
431 |
-+AC_SUBST(PLPLOT_LIBS) |
432 |
- |
433 |
- |
434 |
- |
435 |
-@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS) |
436 |
- |
437 |
- dnl Test if purify exists and if --enable-purify given if so |
438 |
- dnl set "-g" |
439 |
-- |
440 |
- AC_MSG_CHECKING(for purify) |
441 |
- dnl if(purify -version) < /dev/null > /dev/null 2>&1; then |
442 |
- AC_ARG_ENABLE(purify, |
443 |
-@@ -683,6 +695,7 @@ CHECK_THREADS |
444 |
- |
445 |
- |
446 |
- AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile |
447 |
-+ajax/core/ajax-pcre-config.h |
448 |
- ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile |
449 |
- ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile |
450 |
- ajax/acd/Makefile |
451 |
-diff --git a/emboss/Makefile.am b/emboss/Makefile.am |
452 |
-index 0820517..a0257b2 100644 |
453 |
---- a/emboss/Makefile.am |
454 |
-+++ b/emboss/Makefile.am |
455 |
-@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \ |
456 |
- yank |
457 |
- |
458 |
- if !ESYSTEMLIBS |
459 |
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib |
460 |
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ |
461 |
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre |
462 |
-+else |
463 |
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) |
464 |
- endif |
465 |
- |
466 |
--INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \ |
467 |
-+INCLUDES = -I$(top_srcdir)/nucleus \ |
468 |
- $(EXTRA_INCLUDES) \ |
469 |
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ |
470 |
- -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ |
471 |
-- -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot |
472 |
-+ -I$(top_srcdir)/ajax/acd |
473 |
- |
474 |
- |
475 |
- aaindexextract_SOURCES = aaindexextract.c |
476 |
-@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c |
477 |
- treetypedisplay_SOURCES = treetypedisplay.c |
478 |
- |
479 |
- if !ESYSTEMLIBS |
480 |
--EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la |
481 |
-+EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la |
482 |
- endif |
483 |
- |
484 |
- |
485 |
-@@ -327,7 +330,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ |
486 |
- ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \ |
487 |
- ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \ |
488 |
- $(EXTRA_LDS) \ |
489 |
-- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \ |
490 |
- $(XLIB) |
491 |
- |
492 |
- pkgdata_DATA = emboss.default.template |
493 |
-diff --git a/m4/mysql.m4 b/m4/mysql.m4 |
494 |
-index fe413af..ebea25c 100644 |
495 |
---- a/m4/mysql.m4 |
496 |
-+++ b/m4/mysql.m4 |
497 |
-@@ -1,4 +1,6 @@ |
498 |
--##### http://autoconf-archive.cryp.to/ax_lib_mysql.html |
499 |
-+# =========================================================================== |
500 |
-+# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html |
501 |
-+# =========================================================================== |
502 |
- # |
503 |
- # SYNOPSIS |
504 |
- # |
505 |
-@@ -6,19 +8,18 @@ |
506 |
- # |
507 |
- # DESCRIPTION |
508 |
- # |
509 |
--# This macro provides tests of availability of MySQL client library |
510 |
--# of particular version or newer. |
511 |
-+# This macro provides tests of availability of MySQL client library of |
512 |
-+# particular version or newer. |
513 |
- # |
514 |
--# AX_LIB_MYSQL macro takes only one argument which is optional. If |
515 |
--# there is no required version passed, then macro does not run |
516 |
--# version test. |
517 |
-+# AX_LIB_MYSQL macro takes only one argument which is optional. If there |
518 |
-+# is no required version passed, then macro does not run version test. |
519 |
- # |
520 |
- # The --with-mysql option takes one of three possible values: |
521 |
- # |
522 |
- # no - do not check for MySQL client library |
523 |
- # |
524 |
--# yes - do check for MySQL library in standard locations |
525 |
--# (mysql_config should be in the PATH) |
526 |
-+# yes - do check for MySQL library in standard locations (mysql_config |
527 |
-+# should be in the PATH) |
528 |
- # |
529 |
- # path - complete path to mysql_config utility, use this option if |
530 |
- # mysql_config can't be found in the PATH |
531 |
-@@ -33,27 +34,23 @@ |
532 |
- # |
533 |
- # HAVE_MYSQL |
534 |
- # |
535 |
--# LAST MODIFICATION |
536 |
-+# LICENSE |
537 |
- # |
538 |
--# 2006-07-16 |
539 |
--# 2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers, |
540 |
--# which prevents gdb from displaying stack traces. |
541 |
--# Changed mysql_config --cflags to mysql_config --include |
542 |
-+# Copyright (c) 2008 Mateusz Loskot <mateusz@××××××.net> |
543 |
- # |
544 |
--# COPYLEFT |
545 |
--# |
546 |
--# Copyright (c) 2006 Mateusz Loskot <mateusz@××××××.net> |
547 |
--# |
548 |
--# Copying and distribution of this file, with or without |
549 |
--# modification, are permitted in any medium without royalty provided |
550 |
--# the copyright notice and this notice are preserved. |
551 |
-+# Copying and distribution of this file, with or without modification, are |
552 |
-+# permitted in any medium without royalty provided the copyright notice |
553 |
-+# and this notice are preserved. This file is offered as-is, without any |
554 |
-+# warranty. |
555 |
-+ |
556 |
-+#serial 12 |
557 |
- |
558 |
- AC_DEFUN([AX_LIB_MYSQL], |
559 |
- [ |
560 |
- AC_ARG_WITH([mysql], |
561 |
-- [AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], |
562 |
-+ AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], |
563 |
- [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config] |
564 |
-- )], |
565 |
-+ ), |
566 |
- [ |
567 |
- if test "$withval" = "no"; then |
568 |
- want_mysql="no" |
569 |
-@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL], |
570 |
- ], |
571 |
- [want_mysql="yes"] |
572 |
- ) |
573 |
-+ AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program]) |
574 |
- |
575 |
- MYSQL_CFLAGS="" |
576 |
- MYSQL_LDFLAGS="" |
577 |
- MYSQL_VERSION="" |
578 |
- |
579 |
- dnl |
580 |
-- dnl Check MySQL libraries (libpq) |
581 |
-+ dnl Check MySQL libraries |
582 |
- dnl |
583 |
- |
584 |
- if test "$want_mysql" = "yes"; then |
585 |
- |
586 |
-- if test -z "$MYSQL_CONFIG" -o test; then |
587 |
-- AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no]) |
588 |
-+ if test -z "$MYSQL_CONFIG" ; then |
589 |
-+ AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no]) |
590 |
- fi |
591 |
- |
592 |
- if test "$MYSQL_CONFIG" != "no"; then |
593 |
-@@ -90,35 +88,8 @@ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" |
594 |
- |
595 |
- MYSQL_VERSION=`$MYSQL_CONFIG --version` |
596 |
- |
597 |
--dnl It isn't enough to just test for mysql_config as Fedora |
598 |
--dnl provides it in the mysql RPM even though mysql-devel may |
599 |
--dnl not be installed |
600 |
-- |
601 |
-- EMBCFLAGS=$CFLAGS |
602 |
-- EMBLDFLAGS=$LDFLAGS |
603 |
-- CFLAGS=$MYSQL_CFLAGS |
604 |
-- LDFLAGS=$MYSQL_LDFLAGS |
605 |
-- |
606 |
-- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h> |
607 |
-- #include "mysql.h"]], |
608 |
-- [[mysql_info(NULL)]])], |
609 |
-- [havemysql=yes], |
610 |
-- [havemysql=no]) |
611 |
-- |
612 |
-- CFLAGS=$EMBCFLAGS |
613 |
-- LDFLAGS=$EMBLDFLAGS |
614 |
-- |
615 |
-- if test "$havemysql" = yes; then |
616 |
-- AC_DEFINE([HAVE_MYSQL], [1], |
617 |
-- [Define to 1 if MySQL libraries are available]) |
618 |
-- found_mysql="yes" |
619 |
-- AC_MSG_RESULT([yes]) |
620 |
-- else |
621 |
-- MYSQL_CFLAGS="" |
622 |
-- MYSQL_LDFLAGS="" |
623 |
-- found_mysql="no" |
624 |
-- AC_MSG_RESULT([no]) |
625 |
-- fi |
626 |
-+ found_mysql="yes" |
627 |
-+ AC_MSG_RESULT([yes]) |
628 |
- else |
629 |
- found_mysql="no" |
630 |
- AC_MSG_RESULT([no]) |
631 |
-@@ -170,6 +141,11 @@ dnl not be installed |
632 |
- fi |
633 |
- fi |
634 |
- |
635 |
-+ if test "$found_mysql" = "yes" ; then |
636 |
-+ AC_DEFINE([HAVE_MYSQL], [1], |
637 |
-+ [Define to 1 if MySQL libraries are available]) |
638 |
-+ fi |
639 |
-+ |
640 |
- AC_SUBST([MYSQL_VERSION]) |
641 |
- AC_SUBST([MYSQL_CFLAGS]) |
642 |
- AC_SUBST([MYSQL_LDFLAGS]) |
643 |
-diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am |
644 |
-index c244786..ff301b9 100644 |
645 |
---- a/nucleus/Makefile.am |
646 |
-+++ b/nucleus/Makefile.am |
647 |
-@@ -19,13 +19,16 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre -L../ajax/expat -L../ajax/zlib \ |
648 |
- -lezlib -leplplot |
649 |
- else |
650 |
- if !ESYSTEMLIBS |
651 |
--EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib |
652 |
-+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ |
653 |
-+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre |
654 |
-+else |
655 |
-+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) |
656 |
- endif |
657 |
- endif |
658 |
- |
659 |
- |
660 |
--INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \ |
661 |
-- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \ |
662 |
-+INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \ |
663 |
-+ -I$(top_srcdir)/ajax \ |
664 |
- $(EXTRA_INCLUDES) \ |
665 |
- -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ |
666 |
- -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ |
667 |
-@@ -55,3 +58,4 @@ LINKFLAGS = $(VERS_INF) |
668 |
- endif |
669 |
- |
670 |
- libnucleus_la_LDFLAGS = $(LINKFLAGS) |
671 |
-+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la |
672 |
|
673 |
diff --git a/sci-biology/emboss/files/README.Gentoo b/sci-biology/emboss/files/README.Gentoo |
674 |
deleted file mode 100644 |
675 |
index ce37576..0000000 |
676 |
--- a/sci-biology/emboss/files/README.Gentoo |
677 |
+++ /dev/null |
678 |
@@ -1,28 +0,0 @@ |
679 |
-Using EMBOSS on Gentoo systems |
680 |
- |
681 |
-Codon data files location |
682 |
- |
683 |
-The codon data files that are distributed with EMBOSS are installed in the |
684 |
-"/usr/share/EMBOSS/data/CODONS.orig" directory instead of the usual |
685 |
-"/usr/share/EMBOSS/data/CODONS". This is done to avoid confusion between these |
686 |
-codon files and those installed with the CUTG database. The names of these files |
687 |
-sometimes vary only by their case. Having both sets of files in the same directory |
688 |
-is also impossible on systems such as MacOSX, where the root filesystem is case |
689 |
-insensitive. If you do not have the CUTG database installed and want to use the |
690 |
-codon files distributed with EMBOSS, you can symlink the "CODONS.orig" directory |
691 |
-to "CODONS": |
692 |
- |
693 |
- cd /usr/share/EMBOSS/data |
694 |
- ln -s CODONS.orig CODONS |
695 |
- |
696 |
-Restriction enzymes equivalence file location |
697 |
- |
698 |
-The restriction enzymes equivalence file distributed with EMBOSS is installed as |
699 |
-"/usr/share/EMBOSS/data/embossre.equ.orig" rather than the usual |
700 |
-"/usr/share/EMBOSS/data/embossre.equ". This is done to avoid a file collision |
701 |
-with the equivalence file provided by the Rebase database. If you do not have the |
702 |
-Rebase database installed and want to use the equivalence file distributed with |
703 |
-EMBOSS, you can symlink the "embossre.equ.orig" file to "embossre.equ": |
704 |
- |
705 |
- cd /usr/share/EMBOSS/data |
706 |
- ln -s embossre.equ.orig embossre.equ |
707 |
|
708 |
diff --git a/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch b/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch |
709 |
deleted file mode 100644 |
710 |
index 9915f95..0000000 |
711 |
--- a/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch |
712 |
+++ /dev/null |
713 |
@@ -1,24 +0,0 @@ |
714 |
-diff -Naur EMBOSS-5.0.0.old/ajax/Makefile.in EMBOSS-5.0.0/ajax/Makefile.in |
715 |
---- EMBOSS-5.0.0.old/ajax/Makefile.in 2007-07-12 05:53:32.000000000 -0500 |
716 |
-+++ EMBOSS-5.0.0/ajax/Makefile.in 2008-01-25 16:43:51.000000000 -0500 |
717 |
-@@ -244,7 +244,7 @@ |
718 |
- top_srcdir = @top_srcdir@ |
719 |
- @ISCYGWIN_FALSE@lib_LTLIBRARIES = libajax.la libajaxg.la |
720 |
- @ISCYGWIN_TRUE@lib_LTLIBRARIES = libajax.la |
721 |
--@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = |
722 |
-+@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = -lm -L../plplot/.libs -leplplot |
723 |
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm |
724 |
- @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm |
725 |
- @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot |
726 |
-diff -Naur EMBOSS-5.0.0.old/plplot/Makefile.in EMBOSS-5.0.0/plplot/Makefile.in |
727 |
---- EMBOSS-5.0.0.old/plplot/Makefile.in 2007-07-12 05:53:36.000000000 -0500 |
728 |
-+++ EMBOSS-5.0.0/plplot/Makefile.in 2008-01-25 16:42:51.000000000 -0500 |
729 |
-@@ -229,7 +229,7 @@ |
730 |
- lib_LTLIBRARIES = libeplplot.la |
731 |
- @AMPNG_FALSE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lX11 |
732 |
- @AMPNG_TRUE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lgd -lpng -lz -lX11 -lm |
733 |
--@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = |
734 |
-+@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = PATCH_PLPLOT |
735 |
- @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -lX11 -lgd -lpng -lz |
736 |
- INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\" |
737 |
- PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \ |
738 |
|
739 |
diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch |
740 |
deleted file mode 100644 |
741 |
index 0f5e592..0000000 |
742 |
--- a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch |
743 |
+++ /dev/null |
744 |
@@ -1,112 +0,0 @@ |
745 |
---- EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2012-07-19 23:29:05.000000000 +0200 |
746 |
-+++ /tmp/ajgraph.c 2012-07-19 23:25:00.000000000 +0200 |
747 |
-@@ -1645,14 +1645,14 @@ |
748 |
- ** @return [void] |
749 |
- ** @@ |
750 |
- ******************************************************************************/ |
751 |
- |
752 |
- static void GraphSetPen(ajint colour) |
753 |
- { |
754 |
-- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); |
755 |
-- plcol((PLINT)colour); |
756 |
-+ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); |
757 |
-+ plcol0((PLINT)colour); |
758 |
- |
759 |
- return; |
760 |
- } |
761 |
- |
762 |
- |
763 |
- |
764 |
---- EMBOSS-6.3.1/plplot/plcore.c 2007-10-24 15:14:43.000000000 +0200 |
765 |
-+++ /tmp/plcore.c 2012-07-19 23:25:00.000000000 +0200 |
766 |
-@@ -1709,13 +1709,13 @@ |
767 |
- if (plsc->zdigmax == 0) |
768 |
- plsc->zdigmax = 3; |
769 |
- |
770 |
- /* Switch to graphics mode and set color and arrow style*/ |
771 |
- |
772 |
- plgra(); |
773 |
-- plcol(1); |
774 |
-+ plcol0(1); |
775 |
- |
776 |
- plstyl(0, &mk, &sp); |
777 |
- plpat(1, &inc, &del); |
778 |
- |
779 |
- plsvect(def_arrow_x, def_arrow_y, 6, 0); |
780 |
- |
781 |
---- EMBOSS-6.3.1/plplot/plstripc.c 2007-05-08 11:09:37.000000000 +0200 |
782 |
-+++ /tmp/plstripc.c 2012-07-19 23:25:00.000000000 +0200 |
783 |
-@@ -153,17 +153,17 @@ |
784 |
- |
785 |
- plgchr(&sc, &dy); |
786 |
- sc = dy = dy/100; |
787 |
- plwind(-0.01, 1.01, -0.01, 1.01); |
788 |
- for (i=0; i<PEN; i++) { |
789 |
- if (mystripc->npts[i] || first) { |
790 |
-- plcol(mystripc->colline[i]); |
791 |
-+ plcol0(mystripc->colline[i]); |
792 |
- pllsty(mystripc->styline[i]); |
793 |
- pljoin(mystripc->xlpos, mystripc->ylpos - sc, |
794 |
- mystripc->xlpos + 0.1, mystripc->ylpos - sc); |
795 |
-- plcol(mystripc->collab); |
796 |
-+ plcol0(mystripc->collab); |
797 |
- plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc, |
798 |
- 0., 0., 0, mystripc->legline[i]); |
799 |
- sc += dy; |
800 |
- } |
801 |
- } |
802 |
- plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax); |
803 |
-@@ -184,34 +184,34 @@ |
804 |
- PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.}; |
805 |
- |
806 |
- /* Set up window */ |
807 |
- |
808 |
- plvpor(0,1,0,1); |
809 |
- plwind(0,1,0,1); |
810 |
-- plcol(0);plpsty(0); |
811 |
-+ plcol0(0);plpsty(0); |
812 |
- plfill(4, &x[0], &y[0]); |
813 |
- plvsta(); |
814 |
- |
815 |
- /* Draw box and same window dimensions */ |
816 |
- mystrip->wxmin=mystrip->xmin; |
817 |
- mystrip->wxmax=mystrip->xmax; |
818 |
- mystrip->wymin=mystrip->ymin; |
819 |
- mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */ |
820 |
- |
821 |
- plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax); |
822 |
- |
823 |
- pllsty(1); |
824 |
-- plcol(mystrip->colbox); |
825 |
-+ plcol0(mystrip->colbox); |
826 |
- plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0); |
827 |
- |
828 |
-- plcol(mystrip->collab); |
829 |
-+ plcol0(mystrip->collab); |
830 |
- pllab(mystrip->labx, mystrip->laby, mystrip->labtop); |
831 |
- |
832 |
- for (i=0; i<PEN; i++) { |
833 |
- if (mystrip->npts[i] > 0) { |
834 |
-- plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]); |
835 |
-+ plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]); |
836 |
- plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]); |
837 |
- } |
838 |
- } |
839 |
- |
840 |
- plstrip_legend(mystrip,0); |
841 |
- } |
842 |
-@@ -269,13 +269,13 @@ |
843 |
- if (stripc->xmax - stripc->xmin < stripc->xlen) { |
844 |
- if( yasc == 0) { |
845 |
- |
846 |
- /* If user has changed subwindow, make shure we have the correct one */ |
847 |
- plvsta(); |
848 |
- plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */ |
849 |
-- plcol(stripc->colline[p]); pllsty(stripc->styline[p]); |
850 |
-+ plcol0(stripc->colline[p]); pllsty(stripc->styline[p]); |
851 |
- if ((stripc->npts[p]-2) < 0) |
852 |
- plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]); |
853 |
- else |
854 |
- plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]); |
855 |
- plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]); |
856 |
- plflush(); |
857 |
|
858 |
diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-1 b/sci-biology/emboss/files/emboss-README.Gentoo-1 |
859 |
deleted file mode 100644 |
860 |
index 81e7198..0000000 |
861 |
--- a/sci-biology/emboss/files/emboss-README.Gentoo-1 |
862 |
+++ /dev/null |
863 |
@@ -1,34 +0,0 @@ |
864 |
-Administrating EMBOSS on Gentoo systems |
865 |
-======================================= |
866 |
- |
867 |
- |
868 |
-Codon data files location |
869 |
-------------------------- |
870 |
- |
871 |
-The codon data files that are distributed with EMBOSS are installed in the |
872 |
-``/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual |
873 |
-``/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between |
874 |
-these codon files and those installed with the CUTG database. The names of |
875 |
-these files sometimes vary only by their case. Having both sets of files in |
876 |
-the same directory is also impossible on systems such as MacOSX, where the |
877 |
-root filesystem is case insensitive. If you do not have the CUTG database |
878 |
-installed and want to use the codon files distributed with EMBOSS, you can |
879 |
-symlink the ``CODONS.orig`` directory to ``CODONS``:: |
880 |
- |
881 |
- # cd /usr/share/EMBOSS/data |
882 |
- # ln -s CODONS.orig CODONS |
883 |
- |
884 |
- |
885 |
-Restriction enzymes equivalence file location |
886 |
---------------------------------------------- |
887 |
- |
888 |
-The restriction enzymes equivalence file distributed with EMBOSS is installed |
889 |
-as ``/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual |
890 |
-``/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file |
891 |
-collision with the equivalence file provided by the Rebase database. If you do |
892 |
-not have the Rebase database installed and want to use the equivalence file |
893 |
-distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to |
894 |
-``embossre.equ``:: |
895 |
- |
896 |
- # cd /usr/share/EMBOSS/data |
897 |
- # ln -s embossre.equ.orig embossre.equ |
898 |
|
899 |
diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2 |
900 |
deleted file mode 100644 |
901 |
index 72fa366..0000000 |
902 |
--- a/sci-biology/emboss/files/emboss-README.Gentoo-2 |
903 |
+++ /dev/null |
904 |
@@ -1,34 +0,0 @@ |
905 |
-Administrating EMBOSS on Gentoo systems |
906 |
-======================================= |
907 |
- |
908 |
- |
909 |
-Codon data files location |
910 |
-------------------------- |
911 |
- |
912 |
-The codon data files that are distributed with EMBOSS are installed in the |
913 |
-``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual |
914 |
-``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between |
915 |
-these codon files and those installed with the CUTG database. The names of |
916 |
-these files sometimes vary only by their case. Having both sets of files in |
917 |
-the same directory is also impossible on systems such as MacOSX, where the |
918 |
-root filesystem is case insensitive. If you do not have the CUTG database |
919 |
-installed and want to use the codon files distributed with EMBOSS, you can |
920 |
-symlink the ``CODONS.orig`` directory to ``CODONS``:: |
921 |
- |
922 |
- # cd EPREFIX/usr/share/EMBOSS/data |
923 |
- # ln -s CODONS.orig CODONS |
924 |
- |
925 |
- |
926 |
-Restriction enzymes equivalence file location |
927 |
---------------------------------------------- |
928 |
- |
929 |
-The restriction enzymes equivalence file distributed with EMBOSS is installed |
930 |
-as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual |
931 |
-``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file |
932 |
-collision with the equivalence file provided by the Rebase database. If you do |
933 |
-not have the Rebase database installed and want to use the equivalence file |
934 |
-distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to |
935 |
-``embossre.equ``:: |
936 |
- |
937 |
- # cd EPREFIX/usr/share/EMBOSS/data |
938 |
- # ln -s embossre.equ.orig embossre.equ |