1 |
commit: 5bd35d2287f51fa70024ffc977d34d8e15d8a168 |
2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
3 |
AuthorDate: Sat Sep 24 14:20:44 2016 +0000 |
4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
5 |
CommitDate: Sat Sep 24 19:02:03 2016 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5bd35d22 |
7 |
|
8 |
sci-biology/eugene: Bump to 4.1d from science-overlay |
9 |
|
10 |
Gentoo-bug: 594700 |
11 |
* EAPI=6 |
12 |
* Fix -Wformat warnings |
13 |
|
14 |
Package-Manager: portage-2.3.1 |
15 |
|
16 |
sci-biology/eugene/Manifest | 1 + |
17 |
sci-biology/eugene/eugene-4.1d.ebuild | 42 +++++++++++ |
18 |
sci-biology/eugene/files/eugene-4.1d-Wformat.patch | 84 ++++++++++++++++++++++ |
19 |
.../eugene/files/eugene-4.1d-fix-c++14.patch | 17 +++++ |
20 |
4 files changed, 144 insertions(+) |
21 |
|
22 |
diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest |
23 |
index 015da1f..d017c65 100644 |
24 |
--- a/sci-biology/eugene/Manifest |
25 |
+++ b/sci-biology/eugene/Manifest |
26 |
@@ -1 +1,2 @@ |
27 |
DIST eugene-4.1.tar.gz 7393361 SHA256 faff769f68e1ab1fdec61be34ec7fef3c73805734199765ba11cf1ea9c02f800 SHA512 f4bcf63103754f8fb577d311d181375732411fa926fb0cef86fcd00c373ed5cc5637f1b55fa375a4bb14c5181f7de1dc244570f74cdd1887b6107d5c6cea37b3 WHIRLPOOL 32f4539456c243dd3c6a9d5a986fea210e53e5566aaa0849a26f34832957100623570a0814193059420d53e553247584360635706844ed0ec55c4cc65e235ad4 |
28 |
+DIST eugene-4.1d.tar.gz 7473965 SHA256 c160e6b4206e6700c866f38fee2c8fd0d69972d51ebc5b4cb7680774a419f4c0 SHA512 dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5 WHIRLPOOL 7ab116acd48648673d2cc633bae26908bf8250c5a17b9d5e8719dfd56edcdf716406b80af26a99700d9ec81e625737c57fe16493f670245f21999fef1c6911eb |
29 |
|
30 |
diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d.ebuild |
31 |
new file mode 100644 |
32 |
index 00000000..55a73bc |
33 |
--- /dev/null |
34 |
+++ b/sci-biology/eugene/eugene-4.1d.ebuild |
35 |
@@ -0,0 +1,42 @@ |
36 |
+# Copyright 1999-2016 Gentoo Foundation |
37 |
+# Distributed under the terms of the GNU General Public License v2 |
38 |
+# $Id$ |
39 |
+ |
40 |
+EAPI=6 |
41 |
+ |
42 |
+inherit autotools |
43 |
+ |
44 |
+DESCRIPTION="Prokaryotic and Eukaryotic gene predictor" |
45 |
+HOMEPAGE="http://eugene.toulouse.inra.fr/" |
46 |
+SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz" |
47 |
+ |
48 |
+LICENSE="Artistic" |
49 |
+SLOT="0" |
50 |
+KEYWORDS="~amd64 ~x86" |
51 |
+IUSE="" |
52 |
+ |
53 |
+DEPEND=" |
54 |
+ media-libs/gd[png] |
55 |
+ media-libs/libpng:0= |
56 |
+ " |
57 |
+RDEPEND="${DEPEND}" |
58 |
+ |
59 |
+RESTRICT="test" |
60 |
+ |
61 |
+PATCHES=( |
62 |
+ # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170 |
63 |
+ "${FILESDIR}"/${PN}-3.6-overflow.patch |
64 |
+ "${FILESDIR}"/${PN}-3.6-plugins.patch |
65 |
+ "${FILESDIR}"/${PN}-4.1-format-security.patch |
66 |
+ "${FILESDIR}"/${PN}-4.1d-fix-c++14.patch |
67 |
+ "${FILESDIR}"/${PN}-4.1d-Wformat.patch |
68 |
+) |
69 |
+ |
70 |
+src_prepare() { |
71 |
+ default |
72 |
+ sed \ |
73 |
+ -e '/SUBDIRS/ s/doc//' \ |
74 |
+ -e '/INSTALL.*doc/ s/\(.*\)//' \ |
75 |
+ -i Makefile.am || die |
76 |
+ eautoreconf |
77 |
+} |
78 |
|
79 |
diff --git a/sci-biology/eugene/files/eugene-4.1d-Wformat.patch b/sci-biology/eugene/files/eugene-4.1d-Wformat.patch |
80 |
new file mode 100644 |
81 |
index 00000000..ab6d2bd |
82 |
--- /dev/null |
83 |
+++ b/sci-biology/eugene/files/eugene-4.1d-Wformat.patch |
84 |
@@ -0,0 +1,84 @@ |
85 |
+Fix -Wformat warnings caused by wrong printf specifiers: |
86 |
+* Sensor.Riken.cc:95:61: warning: format ‘%d’ expects argument of type ‘int’, but |
87 |
+* argument 3 has type ‘std::vector<RAFLgene>::size_type {aka long unsigned int}’ [-Wformat=] |
88 |
+* fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size()); |
89 |
+ |
90 |
+--- a/src/Hits.cc |
91 |
++++ b/src/Hits.cc |
92 |
+@@ -163,7 +163,7 @@ |
93 |
+ if (ThisHit != NULL) |
94 |
+ for (int i=0; i<*NumHits-1; i++) ThisHit = ThisHit->Next; |
95 |
+ |
96 |
+- while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin, |
97 |
++ while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %ss\n", &deb, &fin, |
98 |
+ &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8) |
99 |
+ { |
100 |
+ if (HSP) fprintf(stderr, "%s", HSP); |
101 |
+--- a/src/SensorPlugins/Est/Sensor.Est.cc |
102 |
++++ b/src/SensorPlugins/Est/Sensor.Est.cc |
103 |
+@@ -1353,13 +1353,13 @@ |
104 |
+ exit(2); |
105 |
+ } |
106 |
+ |
107 |
+- fprintf(fp, "vPos %d\n", vPos.size()); |
108 |
++ fprintf(fp, "vPos %zu\n", vPos.size()); |
109 |
+ for (int i=0; i< vPos.size();i++ ) |
110 |
+ { |
111 |
+ fprintf(fp, "vPos %d\t%d\n",i, vPos[i]); |
112 |
+ } |
113 |
+ |
114 |
+- fprintf(fp, "vESTMatch %d\n", vESTMatch.size()); |
115 |
++ fprintf(fp, "vESTMatch %zu\n", vESTMatch.size()); |
116 |
+ for (int i=0; i< vESTMatch.size();i++ ) |
117 |
+ { |
118 |
+ fprintf(fp, "vESTMatch %d\t\n", vESTMatch[i]); |
119 |
+--- a/src/SensorPlugins/Riken/Sensor.Riken.cc |
120 |
++++ b/src/SensorPlugins/Riken/Sensor.Riken.cc |
121 |
+@@ -92,7 +92,7 @@ |
122 |
+ |
123 |
+ |
124 |
+ |
125 |
+- fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size()); |
126 |
++ fprintf(stderr, "%zu RAFL EST pairs read, ", RAFLtmp.size()); |
127 |
+ |
128 |
+ sort(RAFLtmp.begin(), RAFLtmp.end(), Before); |
129 |
+ |
130 |
+@@ -148,7 +148,7 @@ |
131 |
+ } |
132 |
+ } |
133 |
+ |
134 |
+- fprintf(stderr,"resulting %d\n",RAFL.size()); |
135 |
++ fprintf(stderr,"resulting %zu\n",RAFL.size()); |
136 |
+ fflush(stderr); |
137 |
+ |
138 |
+ // for (RAFLtmpindice=0; RAFLtmpindice< (int)RAFL.size(); RAFLtmpindice++) { |
139 |
+--- a/src/SensorPlugins/SMachine/Sensor.SMachine.cc |
140 |
++++ b/src/SensorPlugins/SMachine/Sensor.SMachine.cc |
141 |
+@@ -197,7 +197,7 @@ |
142 |
+ fclose(fp); |
143 |
+ |
144 |
+ if (end ==2) { |
145 |
+- fprintf(stderr, "Error in SpliceMachine splice site file %s, line %d\n", name, len); |
146 |
++ fprintf(stderr, "Error in SpliceMachine splice site file %s, line %zu\n", name, len); |
147 |
+ exit(2); |
148 |
+ } |
149 |
+ } |
150 |
+--- a/src/SoTerms.cc |
151 |
++++ b/src/SoTerms.cc |
152 |
+@@ -67,14 +67,14 @@ |
153 |
+ j++; |
154 |
+ if (line[0] == 'i' && line[1] == 'd') |
155 |
+ { |
156 |
+- i = sscanf(line, "id: %s", &value); |
157 |
++ i = sscanf(line, "id: %s", value); |
158 |
+ if (i > 0) |
159 |
+ { |
160 |
+ char soId[60]; |
161 |
+ char soName[60]; |
162 |
+ strcpy (soId, value ); |
163 |
+ fgets (line, MAX_LINE, fp); |
164 |
+- i = sscanf(line, "name: %s", &value); |
165 |
++ i = sscanf(line, "name: %s", value); |
166 |
+ strcpy (soName, value ); |
167 |
+ idToName_[to_string(soId)]=to_string(soName); |
168 |
+ nameToId_[to_string(soName)]=to_string(soId); |
169 |
|
170 |
diff --git a/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch b/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch |
171 |
new file mode 100644 |
172 |
index 00000000..a27261c |
173 |
--- /dev/null |
174 |
+++ b/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch |
175 |
@@ -0,0 +1,17 @@ |
176 |
+Fix building with C++14, which errors out due to collisions with isinf |
177 |
+from cmath. We don't need to fix ancient broken OSX toolchains. |
178 |
+See also: https://bugs.gentoo.org/show_bug.cgi?id=594700 |
179 |
+ |
180 |
+--- a/src/SensorPlugins/Tester/Sensor.Tester.cc |
181 |
++++ b/src/SensorPlugins/Tester/Sensor.Tester.cc |
182 |
+@@ -18,9 +18,7 @@ |
183 |
+ // ------------------------------------------------------------------ |
184 |
+ |
185 |
+ // MacOS-X kludge. cmath undefines these macros. Turn them into inlines |
186 |
+-#include <math.h> |
187 |
+-inline int (isinf)(double r) { return isinf(r); } |
188 |
+-inline int (isnan)(double r) { return isnan(r); } |
189 |
++#include <cmath> |
190 |
+ |
191 |
+ #include <iomanip> |
192 |
+ #include <fstream> |