Fixed a few compilation bugs.

Package-Manager: portage-2.0.51-r13

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index 66aa899fe0d95c9046095fb1b161606deb954e5b..3850740444be6e702be5198d4dd022f889a0b6e5 100644 (file)
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/staden
 # Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/ChangeLog,v 1.7 2005/01/15 02:37:04 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/ChangeLog,v 1.8 2005/01/18 00:18:29 ribosome Exp $
+
+  17 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
+  +files/staden-1.5.3-mutscan.patch, +files/staden-1.5.3-prefinish.patch,
+  files/staden-1.5.3-tk_utils.patch, +files/staden-1.5.3-tracediff.patch,
+  staden-1.5.3.ebuild:
+  Fixed a few compilation bugs.
 
 *staden-1.5.3 (14 Jan 2005)
 

diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
index 4b9039890d6d3f4fc3d69954393d970ec9f806d4..92a85cc24430fb1755e1f52c8e89954549e7688f 100644 (file)
--- a/sci-biology/staden/Manifest
+++ b/sci-biology/staden/Manifest
@@ -1,6 +1,6 @@
-MD5 900e6d2666d723e0354fc7c334cdc9e4 staden-1.5.3.ebuild 9903
+MD5 269f8f498bc1c0fb2ec9d33bd2ee7623 staden-1.5.3.ebuild 10023
 MD5 fe19fbd7368ca77e37fab8ee461dddda staden-1.4.1-r7.ebuild 9894
-MD5 47b7572195599c28701e1ad577f035a8 ChangeLog 3529
+MD5 104405704662a5eaaef1121e34bfd1c1 ChangeLog 3786
 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
 MD5 6ce4d77a48d0377a1ada09f1990fb2af files/staden-1.5.3-text_utils.patch 478
 MD5 e908bf4692dd3494ec22f07db2e7a9f5 files/staden-1.4.1-env 225
@@ -8,13 +8,16 @@ MD5 3699a9d368068d835cbd8568d50d23e5 files/staden-1.4.1-gap4.patch 463
 MD5 ccf3b22c1399cd7f80f3f6f1caec2cda files/staden-1.4.1-tracediff.patch 334
 MD5 1026629ee4b47aea8043dd7f35eb2ffe files/staden-1.4.1-staden_help.new 159
 MD5 bd82265e893628c1b46329d77e1f11d8 files/staden-1.4.1-iwidgetsrc.new 445
+MD5 2d495d394e31807f84859f854024b3fc files/staden-1.5.3-mutscan.patch 330
 MD5 8650f58c55b83838846447c89543255d files/staden-1.4.1-getopt.patch 375
+MD5 690ec96f38a668c6cda216d7a3960ecf files/staden-1.5.3-tracediff.patch 334
 MD5 0857e0bf79953bfa46b1224f6218701a files/staden-1.5.3-top.patch 230
 MD5 7717f77ecd800d0b3049974db3fcd0a9 files/staden-1.4.1-prefinish.patch 362
 MD5 daf40c222b80ffc48d9a2ac2544ab631 files/staden-1.5.3-getopt.patch 367
+MD5 9f05ecafdd38d17d8dd40ff581dda1a2 files/staden-1.5.3-prefinish.patch 362
 MD5 a8ceefd2b3b2c1c0053a504561635379 files/staden-1.4.1-mutscan.patch 328
 MD5 cd40ea0a473054769a0963e708257f98 files/digest-staden-1.4.1-r7 213
 MD5 708ea4c4b4cbc7e2b6b88b5a09e1b564 files/staden-1.4.1-top.patch 230
-MD5 1ead6fa1e26351872c3404ab9da21416 files/staden-1.5.3-tk_utils.patch 547
+MD5 7e0b4d0414191e2d1e00c65c16f3c377 files/staden-1.5.3-tk_utils.patch 787
 MD5 e3ce8053514641a26df3ca33f2962e55 files/digest-staden-1.5.3 338
 MD5 ea4a62a1cd5070014d2c9352eeecf06a files/staden-1.4.1-tk_utils.patch 368

diff --git a/sci-biology/staden/files/staden-1.5.3-mutscan.patch b/sci-biology/staden/files/staden-1.5.3-mutscan.patch
new file mode 100644 (file)
index 0000000..82374a9
--- /dev/null
+++ b/sci-biology/staden/files/staden-1.5.3-mutscan.patch
@@ -0,0 +1,15 @@
+--- src/mutscan/Makefile.old   2004-11-09 04:53:46.000000000 -0500
++++ src/mutscan/Makefile       2005-01-17 19:06:25.913557696 -0500
+@@ -20,7 +20,11 @@
+       $(TEXTUTILS_LIB) \
+       $(MUT_LIB) \
+       $(IOLIB_LIB) \
+-      $(TK_LIB)
++      $(TK_LIB) \
++      -lmisc \
++      -lseq_utils \
++      -ltk_utils \
++      -L../lib/linux-binaries
+ 
+ OBJSD = \
+       $(MUTSCANBIN)/main.o \

diff --git a/sci-biology/staden/files/staden-1.5.3-prefinish.patch b/sci-biology/staden/files/staden-1.5.3-prefinish.patch
new file mode 100644 (file)
index 0000000..1614850
--- /dev/null
+++ b/sci-biology/staden/files/staden-1.5.3-prefinish.patch
@@ -0,0 +1,17 @@
+--- src/prefinish/Makefile.old 2004-11-09 04:53:37.000000000 -0500
++++ src/prefinish/Makefile     2005-01-17 18:53:38.119280168 -0500
+@@ -54,7 +54,13 @@
+       $(GAP_LIB) \
+       $(TEXTUTILS_LIB) \
+       $(MISC_LIB) \
+-      $(TCL_LIB)
++      $(TCL_LIB) \
++      -lmutlib \
++      -lprimer3 \
++      -ltk_utils \
++      -lread \
++      -lseq_utils \
++      -L../lib/linux-binaries
+ 
+ ISOBJS=\
+       $(O)/insert_size_dist.o

diff --git a/sci-biology/staden/files/staden-1.5.3-tk_utils.patch b/sci-biology/staden/files/staden-1.5.3-tk_utils.patch
index 58aa79afa9b34a4b138880161873ef9f6ddae7d6..fa2db6e466a26815c3c959c1e16ceeb1c540c158 100644 (file)
--- a/sci-biology/staden/files/staden-1.5.3-tk_utils.patch
+++ b/sci-biology/staden/files/staden-1.5.3-tk_utils.patch
@@ -1,6 +1,17 @@
 --- src/tk_utils/Makefile.old  2004-11-09 04:53:26.000000000 -0500
-+++ src/tk_utils/Makefile      2005-01-08 22:47:41.659544072 -0500
-@@ -105,16 +105,6 @@
++++ src/tk_utils/Makefile      2005-01-17 18:47:19.889779792 -0500
+@@ -97,7 +97,9 @@
+ 
+ STASH_LIBS = \
+       $(TKUTILS_LIB) \
+-      $(TK_LIB)
++      $(TK_LIB) \
++      $(IOLIB_LIB) \
++      $(MISC_LIB)
+ 
+ $(TKUTILSBIN)/stash: $(STASH_OBJS)
+       $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMWIN) $(STASH_OBJS) $(STASH_LIBS) $(LIBSC)
+@@ -105,16 +107,6 @@
  
  .PRECIOUS:    .links
  .links:

diff --git a/sci-biology/staden/files/staden-1.5.3-tracediff.patch b/sci-biology/staden/files/staden-1.5.3-tracediff.patch
new file mode 100644 (file)
index 0000000..65203dd
--- /dev/null
+++ b/sci-biology/staden/files/staden-1.5.3-tracediff.patch
@@ -0,0 +1,15 @@
+--- src/tracediff/Makefile.old 2004-11-09 04:53:40.000000000 -0500
++++ src/tracediff/Makefile     2005-01-17 19:00:15.023941488 -0500
+@@ -19,7 +19,11 @@
+ HLIBS=\
+       $(TEXTUTILS_LIB) \
+       $(MUT_LIB) \
+-      $(IOLIB_LIB)
++      $(IOLIB_LIB) \
++      -lmisc \
++      -lseq_utils \
++      -ltk_utils \
++      -L../lib/linux-binaries
+ 
+ OBJSD = \
+       $(TRACEDIFFBIN)/main.o \

diff --git a/sci-biology/staden/staden-1.5.3.ebuild b/sci-biology/staden/staden-1.5.3.ebuild
index 50b9c9a937ffd8fe9c7e826c57c1de9f95f9daad..f92e65b1c732ad9314cad6b97f4e3a4d39114245 100644 (file)
--- a/sci-biology/staden/staden-1.5.3.ebuild
+++ b/sci-biology/staden/staden-1.5.3.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2005 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/staden-1.5.3.ebuild,v 1.1 2005/01/15 02:37:04 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/staden-1.5.3.ebuild,v 1.2 2005/01/18 00:18:29 ribosome Exp $
 
 inherit eutils toolchain-funcs
 
@@ -70,6 +70,9 @@ src_unpack() {
        epatch ${FILESDIR}/${P}-top.patch
        epatch ${FILESDIR}/${P}-text_utils.patch
        epatch ${FILESDIR}/${P}-tk_utils.patch
+       epatch ${FILESDIR}/${P}-prefinish.patch
+       epatch ${FILESDIR}/${P}-tracediff.patch
+       epatch ${FILESDIR}/${P}-mutscan.patch
        cd ${S}/src/mk
        # Remove the "-fpic" flag. This will be replaced by "-fPIC".
        sed -i -e 's/SHLIB_CFLAGS               = -fpic/SHLIB_CFLAGS            = /' linux.mk
@@ -161,7 +164,7 @@ src_compile() {
        rm ${S}/lib/linux-binaries
        mkdir ${S}/lib/linux-binaries
 
-       # Moves executables in "${S}/linux-bin" and libraries to 
+       # Moves executables in "${S}/linux-bin" and libraries to
        # ${S}/lib/linux-binaries.
        cd ${S}
        make \