1 |
jlec 15/03/28 17:14:17 |
2 |
|
3 |
Added: embassy-mse-3.0.0.650_fix-build-system.patch |
4 |
Log: |
5 |
Import latest changes from science overlay, thanks Ted Tanberry for the work; fixes #335603 |
6 |
|
7 |
(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
8 |
|
9 |
Revision Changes Path |
10 |
1.1 sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch |
11 |
|
12 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch?rev=1.1&view=markup |
13 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch?rev=1.1&content-type=text/plain |
14 |
|
15 |
Index: embassy-mse-3.0.0.650_fix-build-system.patch |
16 |
=================================================================== |
17 |
--- MSE-3.0.0.650/configure.ac |
18 |
+++ MSE-3.0.0.650/configure.ac |
19 |
@@ -635,33 +635,6 @@ |
20 |
|
21 |
|
22 |
|
23 |
-dnl PCRE library definitions - see the MAJOR and MINOR values |
24 |
-dnl to see which version's configure.in these lines come from |
25 |
- |
26 |
-dnl Provide the current PCRE version information. Do not use numbers |
27 |
-dnl with leading zeros for the minor version, as they end up in a C |
28 |
-dnl macro, and may be treated as octal constants. Stick to single |
29 |
-dnl digits for minor numbers less than 10. There are unlikely to be |
30 |
-dnl that many releases anyway. |
31 |
- |
32 |
-PCRE_MAJOR="7" |
33 |
-PCRE_MINOR="9" |
34 |
-PCRE_DATE="11-Apr-2009" |
35 |
-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" |
36 |
- |
37 |
-dnl Default values for miscellaneous macros |
38 |
- |
39 |
-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" |
40 |
- |
41 |
-dnl Provide versioning information for libtool shared libraries that |
42 |
-dnl are built by default on Unix systems. |
43 |
- |
44 |
-PCRE_LIB_VERSION="0:1:0" |
45 |
-PCRE_POSIXLIB_VERSION="0:0:0" |
46 |
- |
47 |
- |
48 |
- |
49 |
- |
50 |
dnl FIXME: This does no longer seem required with Autoconf 2.67? |
51 |
dnl Intel MacOSX 10.6 puts X11 in a non-standard place |
52 |
dnl AS_IF([test "x${with_x}" != "xno"], |
53 |
@@ -737,21 +710,6 @@ |
54 |
|
55 |
|
56 |
|
57 |
-dnl "Export" these variables for PCRE |
58 |
- |
59 |
-AC_SUBST([HAVE_MEMMOVE]) |
60 |
-AC_SUBST([HAVE_STRERROR]) |
61 |
-AC_SUBST([PCRE_MAJOR]) |
62 |
-AC_SUBST([PCRE_MINOR]) |
63 |
-AC_SUBST([PCRE_DATE]) |
64 |
-AC_SUBST([PCRE_VERSION]) |
65 |
-AC_SUBST([PCRE_LIB_VERSION]) |
66 |
-AC_SUBST([PCRE_POSIXLIB_VERSION]) |
67 |
-AC_SUBST([POSIX_MALLOC_THRESHOLD]) |
68 |
- |
69 |
- |
70 |
- |
71 |
- |
72 |
dnl Test if --enable-localforce given |
73 |
locallink="no" |
74 |
embprefix="/usr/local" |
75 |
@@ -874,6 +832,11 @@ |
76 |
AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) |
77 |
|
78 |
|
79 |
+AS_IF([test "x${enable_systemlibs}" = "xyes"], |
80 |
+[ |
81 |
+dnl using system libraries |
82 |
+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) |
83 |
+]) |
84 |
|
85 |
|
86 |
# Enable the purify tool: --enable-purify, sets CC and LIBTOOL |
87 |
@@ -1000,17 +963,13 @@ |
88 |
|
89 |
|
90 |
|
91 |
-dnl emnu and mse only: uses curses |
92 |
-dnl Test if --with-curses is given |
93 |
-AC_ARG_WITH([curses], |
94 |
- [AS_HELP_STRING([--with-curses], |
95 |
- [curses (or ncurses)])]) |
96 |
-if test "${with_curses}" ; then |
97 |
-AC_MSG_CHECKING([for curses]) |
98 |
-CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" |
99 |
-LDFLAGS="$LDFLAGS -L${with_curses}/lib" |
100 |
-fi |
101 |
-AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses") |
102 |
+dnl Test if --enable-curses is given |
103 |
+AC_ARG_ENABLE([curses], |
104 |
+[AS_HELP_STRING([--enable-curses], [curses])]) |
105 |
+ |
106 |
+AS_IF([test "x$enable_curses" = "xyes"], [ |
107 |
+ PKG_CHECK_MODULES([NCURSES], [ncurses]) |
108 |
+]) |
109 |
|
110 |
|
111 |
|
112 |
--- MSE-3.0.0.650/src/Makefile.am |
113 |
+++ MSE-3.0.0.650/src/Makefile.am |
114 |
@@ -18,9 +18,7 @@ |
115 |
-I../../../ajax/ensembl -I../../../ajax/ajaxdb \ |
116 |
-I../../../ajax/acd -I../../../plplot |
117 |
else |
118 |
-AM_CPPFLAGS = -I../h -I${embprefix}/include \ |
119 |
- -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ |
120 |
- $(NLINCLUDES) |
121 |
+AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) |
122 |
endif |
123 |
|
124 |
if ISSHARED |
125 |
@@ -60,5 +58,5 @@ |
126 |
$(XLIB) |
127 |
else |
128 |
LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ |
129 |
- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) |
130 |
+ -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) |
131 |
endif |
132 |
--- MSE-3.0.0.650/ckit/Makefile.am |
133 |
+++ MSE-3.0.0.650/ckit/Makefile.am |
134 |
@@ -2,7 +2,7 @@ |
135 |
|
136 |
lib_LTLIBRARIES = libckit.la |
137 |
|
138 |
-AM_CPPFLAGS = -I../h |
139 |
+AM_CPPFLAGS = -I$(top_srcdir)/h |
140 |
|
141 |
CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ |
142 |
seqspec.c ttyinterface.c nextseqentry.c \ |
143 |
--- MSE-3.0.0.650/emboss_acd/Makefile.am |
144 |
+++ MSE-3.0.0.650/emboss_acd/Makefile.am |
145 |
@@ -1,3 +1,3 @@ |
146 |
|
147 |
-pkgdata_DATA = *.acd |
148 |
+pkgdata_DATA = $(srcdir)/*.acd |
149 |
pkgdatadir=$(prefix)/share/EMBOSS/acd |