QA fixes, including bug 298223

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

4 files changed, 51 insertions, 13 deletions

diff --git a/sci-biology/glimmer/ChangeLog b/sci-biology/glimmer/ChangeLog
index 1dccf70808bd..5780aef0e1c4 100644
--- a/sci-biology/glimmer/ChangeLog
+++ b/sci-biology/glimmer/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/glimmer
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.3 2009/01/04 01:24:22 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/ChangeLog,v 1.4 2009/12/28 19:14:26 weaver Exp $
+
+  28 Dec 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/glimmer-3.02-glibc210.patch, glimmer-3.02-r1.ebuild:
+  QA fixes, including bug 298223
 
 *glimmer-3.02-r1 (04 Jan 2009)
 
diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest
index ab599ee58718..1d624ae15c5a 100644
--- a/sci-biology/glimmer/Manifest
+++ b/sci-biology/glimmer/Manifest
@@ -1,4 +1,5 @@
+AUX glimmer-3.02-glibc210.patch 799 RMD160 92e91e8ce9a39dd004152df712171052b726b0c5 SHA1 1a3f502692923f8b64e252c1b44f9ff68d343505 SHA256 6b0655e796a938990c29070950b36e861bdb6dd3ee1a0ae962590585976e7c5b
 DIST glimmer302.tar.gz 5637075 RMD160 bc29bb045f7a4179504cb3843741393f42e11ab8 SHA1 e2f27fdab82cd8978f1452bfcd4c0287c52b77b7 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221
-EBUILD glimmer-3.02-r1.ebuild 1069 RMD160 a13e38d86cccb667c29551d56dcaec13e228c54e SHA1 79eef25e14c8f55507e1dbe332a3b3f47d5c82ff SHA256 4976d80b9bde54c5947801a52f7e2f669cb7d9677ca1c103966776e02409d1b6
-MISC ChangeLog 631 RMD160 d3cd14428f1ae35748a80a3352044a18c7cc64f7 SHA1 e314eb9e1245c79e732f3defb2816c90b1d4b98f SHA256 ceebaa6e5d381f8719d99813606293659530338e3dcdeaca7fb1eb5342e2326e
+EBUILD glimmer-3.02-r1.ebuild 1273 RMD160 f0b6622a628940640c68dd58c754337c7786dfa9 SHA1 3a823ab62692ca8ffb5f2a93aff26c2a16481a7c SHA256 5762df4618f5d7b3b7fda91a8bd08a4befbeb82b9ecfdd927c0fc11072c1d0e2
+MISC ChangeLog 777 RMD160 308b1feed975657cc8d36c032551ebe353e7c950 SHA1 807ccd6b4e7c7215cb96f3475a815e4b6d58a27e SHA256 5eb0b481eed6d314921f0ad57c1ddc987839c1753ca1dc9c7f7ce734fb6aefd5
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
new file mode 100644
index 000000000000..f6051ec82054
--- /dev/null
+++ b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch
@@ -0,0 +1,24 @@
+diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc
+--- glimmer3.02-orig/src/Common/gene.cc	2009-12-28 13:34:21.577437056 +0000
++++ glimmer3.02/src/Common/gene.cc	2009-12-28 13:36:06.914974685 +0000
+@@ -443,7 +443,7 @@
+ //  Return a subscript corresponding to character  ch .
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (CONVERSION_STRING, tolower (ch));
+    if  (p == NULL)
+diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc
+--- glimmer3.02-orig/src/ICM/icm.cc	2009-12-28 13:34:21.577437056 +0000
++++ glimmer3.02/src/ICM/icm.cc	2009-12-28 13:36:44.649451803 +0000
+@@ -1981,7 +1981,7 @@
+ //  model) for character  ch .
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (ALPHA_STRING, tolower (Filter (ch)));
+    if  (p == NULL)
diff --git a/sci-biology/glimmer/glimmer-3.02-r1.ebuild b/sci-biology/glimmer/glimmer-3.02-r1.ebuild
index d83c29e0e9a4..8a65fc316036 100644
--- a/sci-biology/glimmer/glimmer-3.02-r1.ebuild
+++ b/sci-biology/glimmer/glimmer-3.02-r1.ebuild
@@ -1,10 +1,12 @@
 # Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r1.ebuild,v 1.1 2009/01/04 01:24:22 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmer/glimmer-3.02-r1.ebuild,v 1.2 2009/12/28 19:14:26 weaver Exp $
 
-inherit versionator
+EAPI="2"
 
-MY_PV=$(delete_all_version_separators)
+inherit eutils
+
+MY_PV=${PV//./}
 
 DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
 HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/"
@@ -16,26 +18,33 @@ IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
-RDEPEND="!app-crypt/pkcrack
+RDEPEND="app-shells/tcsh
+	!app-crypt/pkcrack
 	!media-libs/libextractor"
 
 S="${WORKDIR}/${PN}${PV}"
 
-src_compile() {
+src_prepare() {
 	sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
 		-e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
-	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh
-	cd src
-	emake || die "emake failed"
+	# Fix Makefile to die on failure
+	sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
+	# GCC 4.3 include fix
+	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
+	epatch "${FILESDIR}/${PN}-${PV}-glibc210.patch"
+}
+
+src_compile() {
+	emake -C src || die
 }
 
 src_install() {
 	rm bin/test
-	dobin bin/*
+	dobin bin/* || die
 
 	dodir /usr/share/${PN}/scripts
 	insinto /usr/share/${PN}/scripts
-	doins scripts/*
+	doins scripts/* || die
 
 	dodoc glim302notes.pdf
 }