sci-biology/rnaview: Respect CFLAGS, #429536; Bump to EAPI=4

Package-Manager: portage-2.2.0_alpha120/cvs/Linux x86_64

4 files changed, 112 insertions, 43 deletions

diff --git a/sci-biology/rnaview/ChangeLog b/sci-biology/rnaview/ChangeLog
index cf3cc33e592a..5241f8d0cd39 100644
--- a/sci-biology/rnaview/ChangeLog
+++ b/sci-biology/rnaview/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/rnaview
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/rnaview/ChangeLog,v 1.12 2010/09/06 12:24:45 xarthisius Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/rnaview/ChangeLog,v 1.13 2012/08/03 15:04:03 jlec Exp $
+
+*rnaview-20040713-r3 (03 Aug 2012)
+
+  03 Aug 2012; Justin Lecher <jlec@gentoo.org> +rnaview-20040713-r3.ebuild,
+  files/rnaview-20040713-makefile.patch:
+  Respect CFLAGS, #429536; Bump to EAPI=4
 
 *rnaview-20040713-r2 (06 Sep 2010)
 
diff --git a/sci-biology/rnaview/Manifest b/sci-biology/rnaview/Manifest
index 91b495be60d6..a4b898ca52a8 100644
--- a/sci-biology/rnaview/Manifest
+++ b/sci-biology/rnaview/Manifest
@@ -1,7 +1,19 @@
-AUX rnaview-20040713-implicit.patch 343 RMD160 78f8aa760b811b5b54ec4ac48ad2ed2c9e3258e9 SHA1 71940d96d6f8e8f355a8d77948f9c2493d9e9a58 SHA256 a1275154ad6ee0a3213a8ab9f3d58a231bfbe780db380a72e06891bec7f89708
-AUX rnaview-20040713-makefile.patch 1593 RMD160 0f71321b9bde5f6a6ab137b4e5f86c7ba838ba30 SHA1 48a96f263f5162fed7bc5a79519427f0112e9d33 SHA256 2bbfb8f427bc8c062292ee1115597326a87301ef2c32b95196fc32826f667f01
-DIST rnaview-20040713.tar.bz2 433916 RMD160 1aa0a3dd7af24a543c00027b958bbaaedd0f163a SHA1 b87d6b6936f2942fadbd4e339632effd0835239e SHA256 0961779c83e247a4b04c02d90d3850e8c4c889b630194ea1516cbeb6c6dbad17
-EBUILD rnaview-20040713-r2.ebuild 851 RMD160 2c33eb159aca4360c506af787db2573d54f75ae4 SHA1 107c60c4a0503871e6532e9814fe10db117b7414 SHA256 2016c4ab6f99d13565795d5e23ffa9696d35e5fe77f52936bd2b7f344b943643
-EBUILD rnaview-20040713.ebuild 953 RMD160 84b48d31ecf519973ee2b2fb840985a387987530 SHA1 51e3894d8e91a41b9d27c9c95e000b681a1db656 SHA256 bb72d245280de8c2d2f79bc8bb451d3db6283de58786e93d991cca8745f42f8d
-MISC ChangeLog 1908 RMD160 5edb141c84e26ad3f450fe01c0d4e9060e70d6cd SHA1 265fb67651032eb02315043fb2baf49ac2f8de63 SHA256 b42b093558225f1d632b7ec1980d0d6d7f3cecd2e520407794522139b1beedff
-MISC metadata.xml 570 RMD160 e4eaa219425a7d2522fd1d148d6ea6bd4940a3cf SHA1 00a65e9b64e6e8a6071fec4abad0d41038872c81 SHA256 361679aa0f120fbb2370915ad12b84a7c1f707fd6c5de1da049d4c131986aea3
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
+AUX rnaview-20040713-implicit.patch 343 SHA256 a1275154ad6ee0a3213a8ab9f3d58a231bfbe780db380a72e06891bec7f89708 SHA512 3cfe234423d076dd931d13ab757c661f4471fdc9cbbe10725aebf93cc0f4dd25fdb5a03b72c6d82ee8ceaaa825c31d7ec9e1825a794c07439a6ae218a93a667c WHIRLPOOL 8439c974857cf217f5ca94fecaa5efd5b3a3652cdf7d70f67e5e329c2fd1199bbfee30b6fa86d9f0e6e316596be7afd31d073c260aaefead8991da9b42a7825d
+AUX rnaview-20040713-makefile.patch 2131 SHA256 dc2324a361132df317683a3a9d835364a7e3cff73f953920a97ca53bfc951c1a SHA512 9cde6186c0865405546bbee68ec64bd11cdfe91747b90739b237368b2724763ac4dd9206defec7f00a918449fc2a8451c3a5e447cfddfb7ca5c5fed00bb29de6 WHIRLPOOL 5f0d15d5df23d759448b763ec9c204a86658a852040c6b9e60f3dc07b37d45073c82e8ab83d0da7e2abc6bdf483b6d1258401ff0d730d24809941072aa5eba17
+DIST rnaview-20040713.tar.bz2 433916 SHA256 0961779c83e247a4b04c02d90d3850e8c4c889b630194ea1516cbeb6c6dbad17 SHA512 c63bb728bad0f358ab36f4ca18f4f9ef046811f21d3b8f3c6fdd3e6e6fcb367a9a52710476c5daea001f8f3262f72b64f0c0546f0c1423f463f2e0d288809e8e WHIRLPOOL 7ae8953a8028da0eb525a6b33964267b15721dbe148f5077cf2c7e47c7cc2e3a47616bcc944e7f8180c0696c27ac16c53bd3847d02db5a575df3cebba29dd169
+EBUILD rnaview-20040713-r2.ebuild 851 SHA256 2016c4ab6f99d13565795d5e23ffa9696d35e5fe77f52936bd2b7f344b943643 SHA512 40f3af2fb4606efac5eb2f763ca51e1b9323fb91ec9c5e146e9432bb9a73aca643ae66c68e853c113146d7aa2c5fa342ce508f117533d2ecf01e3b2152f88d23 WHIRLPOOL 7ebd55f494d4c2e852adab263b008455fe652fc2a31a5791e00da8eda8dc556b27b09ee77f564decc17f7d18ea00d7c8284a43161233bf71ac53a6e2f00ca278
+EBUILD rnaview-20040713-r3.ebuild 767 SHA256 7f72c41e0d62d174939fbb86533b11ce231aaf710aba7bbc637e6b6350171236 SHA512 26f5fe4f02c02b5b7010c6a6475af89c78e40bee7fc8843feceab668856c7dfcbe1594f7f2a5269180db85fda61873ede428a095481bc87e32a857148145398f WHIRLPOOL 7c28ebf2987de6db28385285a58f8cec28b9fc4b6476b162b6e08851aa7864a3dfa0a311691414918307523866df68eb626872c54b978636be69c16eb5ee0417
+EBUILD rnaview-20040713.ebuild 953 SHA256 bb72d245280de8c2d2f79bc8bb451d3db6283de58786e93d991cca8745f42f8d SHA512 ff3fe95d76118cf916ed4b24b5186c2835ffbc668b2ca126d28b07a57b354517c45222c3c80b9594600064b3611f750b7c12b82829ec4f4c4d6904fc08b7cc5a WHIRLPOOL f0885afc365415504a7764ead56224d540e6fa03ff2d46412a2bc5ddf884dfe7094c9208b68f7327dcef51627048684cd9b104143a0d6689ebfb0efdb5f53661
+MISC ChangeLog 2098 SHA256 2357f106dbfddb6705444747a5f16ae3dc5209853222057da45aa8312b70a99e SHA512 5ad5c09bf14cfefa9281b88db3ea8b23365c36bc4574ef309f3745b7ca560302e8b3f98ab201ed940c123fbd1968507208b8d6655d85c4fa937518aab1404d06 WHIRLPOOL 8f795a1decab226ce65affc5234c79852bc979580dddbdc116e41182f59a8aba0231c7bea737b3d089f4db5b6eb2aa6e87128bda6daabe97df711540b9044f06
+MISC metadata.xml 570 SHA256 361679aa0f120fbb2370915ad12b84a7c1f707fd6c5de1da049d4c131986aea3 SHA512 d658b5d2f1fbd7b3969c054e6aef57203ad858b19dfd1b89270e5ac6216bb260ec16ac489c7242b81af6568466c3c6bbbf0b6c97bc5bf12211bcdb9ebae82414 WHIRLPOOL 5bcf88b490a17ec0aaacdbe9f964f5f242c6719121e728a79014a460c9e6bb78daa561a9e7ab9dcdccdbf20f92a6514bd71b482b271b015e8f45ece8a6e0e99c
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
+
+iEYEAREIAAYFAlAb6GkACgkQgAnW8HDreRZQlQCgyw63TvKLfgDZXo0xjKdB6B1B
+xLgAoIpdxUttdBl9WyPVpWKBzrDP88KB
+=3dsH
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/rnaview/files/rnaview-20040713-makefile.patch b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch
index 5d9ecd99cf25..1af72f581fbf 100644
--- a/sci-biology/rnaview/files/rnaview-20040713-makefile.patch
+++ b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch
@@ -1,39 +1,18 @@
-Fix install paths, respect LDFLAGS, CFLAGS
+ Makefile          |   20 +++++++++++++++++---
+ rnaml2ps/Makefile |   19 ++++++++++++-------
+ 2 files changed, 29 insertions(+), 10 deletions(-)
 
-http://bugs.gentoo.org/show_bug.cgi?id=336196
-
---- rnaml2ps/Makefile
-+++ rnaml2ps/Makefile
-@@ -5,16 +5,21 @@
- RNADRAW = rnaml2ps
- OBJS_RNADRAW = rnaml2ps.o nrutil.o 
+diff --git a/Makefile b/Makefile
+index 452e6c4..00d35f0 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,4 +1,4 @@
+-CC        = cc
++CC        ?= cc
  
-+all: $(RNADRAW)
-+
- $(RNADRAW):   $(OBJS_RNADRAW)
--	$(CC) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
-+	$(CC) $(LDFLAGS) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
  
- nrutil.o : nrutil.c 
--	cc -c  nrutil.c
-+	$(CC) $(CFLAGS) -c  nrutil.c
  
- rnaml2ps.o :  rnaml2ps.c
--	cc -c  rnaml2ps.c
-+	$(CC) $(CFLAGS) -c  rnaml2ps.c
- 
- 
--.PHONY : clean
-+.PHONY : clean all install
- clean:
--	rm *.o
-+	rm -f *.o
-+
-+install:
-+	install -D -m 0755 $(RNADRAW) $(DESTDIR)/usr/bin/$(RNADRAW)
---- Makefile
-+++ Makefile
-@@ -56,9 +56,14 @@
+@@ -56,12 +56,17 @@ OBJ_FILE = $(OBJ)/rnaview.o \
             $(OBJ)/multiple.o \
             $(OBJ)/statistics.o
  
@@ -48,8 +27,12 @@ http://bugs.gentoo.org/show_bug.cgi?id=336196
 +CFLAGS  +=  $(LINCLUDES)
  
  $(RNAVIEW) : $(HFILES) $(OBJ_FILE) 
- 	$(CC) $(CFLAGS) -o $@ $(OBJ_FILE) $(LDFLAGS) -lm $(MALLOCLIB)
-@@ -111,6 +116,15 @@
+-	$(CC) $(CFLAGS) -o $@ $(OBJ_FILE) $(LDFLAGS) -lm $(MALLOCLIB)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJ_FILE) -lm $(MALLOCLIB)
+ 
+ 
+ 
+@@ -111,6 +116,15 @@ $(OBJ)/statistics.o :  $(SRC)/statistics.c
  clean:
  	@rm -f $(OBJ)/*.o
  	@rm -f $(ALLTARGETS)
@@ -65,3 +48,40 @@ http://bugs.gentoo.org/show_bug.cgi?id=336196
  
  export:
  	mkdir -p $(EXPORT_DIR)
+diff --git a/rnaml2ps/Makefile b/rnaml2ps/Makefile
+index d207655..2278ccc 100644
+--- a/rnaml2ps/Makefile
++++ b/rnaml2ps/Makefile
+@@ -1,20 +1,25 @@
+-CFLAGS        = -O
+-CC            = cc
++CFLAGS        ?= -O
++CC            ?= cc
+ 
+ # ++++++++++++++++++++++++++++ Program RNADRAW
+ RNADRAW = rnaml2ps
+ OBJS_RNADRAW = rnaml2ps.o nrutil.o 
+ 
++all: $(RNADRAW)
++
+ $(RNADRAW):   $(OBJS_RNADRAW)
+-	$(CC) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
++	$(CC) $(LDFLAGS) -o $(RNADRAW) $(OBJS_RNADRAW) -lm
+ 
+ nrutil.o : nrutil.c 
+-	cc -c  nrutil.c
++	$(CC) $(CFLAGS) -c  nrutil.c
+ 
+ rnaml2ps.o :  rnaml2ps.c
+-	cc -c  rnaml2ps.c
++	$(CC) $(CFLAGS) -c  rnaml2ps.c
+ 
+ 
+-.PHONY : clean
++.PHONY : clean all install
+ clean:
+-	rm *.o
++	rm -f *.o
++
++install:
++	install -D -m 0755 $(RNADRAW) $(DESTDIR)/usr/bin/$(RNADRAW)
diff --git a/sci-biology/rnaview/rnaview-20040713-r3.ebuild b/sci-biology/rnaview/rnaview-20040713-r3.ebuild
new file mode 100644
index 000000000000..7aa14415141d
--- /dev/null
+++ b/sci-biology/rnaview/rnaview-20040713-r3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/rnaview/rnaview-20040713-r3.ebuild,v 1.1 2012/08/03 15:04:03 jlec Exp $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions"
+HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-makefile.patch \
+		"${FILESDIR}"/${P}-implicit.patch
+	cat <<- EOF > 22rnaview
+		RNAVIEW="${EPREFIX}/usr/share/${PN}"
+	EOF
+	tc-export CC
+}
+
+src_install() {
+	default
+	doenvd 22rnaview
+}