7 files changed, 400 insertions, 165 deletions
diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
index 4a74a1a8a1f8..c88142631f51 100644
--- a/sci-biology/phylip/Manifest
+++ b/sci-biology/phylip/Manifest
@@ -1,7 +1,6 @@
 AUX README.Gentoo 643 BLAKE2B 95193d4c9c8fc8fb5796bb0a8ca470f440ac66eb1da9b9ed4784494a6a4c9bb12a451223c0ff81ae3ba80da81f4d8d3a00a21cad557f575a81325a180a819c0e SHA512 63ec15ce2788171e5351977bae21e11a7c8609eeed4893849fabc909f0c6713033e253768ea3f485245456a9083ad4aa613e2503ebb4eb71f7b670f1af593f2a
-DIST phylip-3.69.tar.gz 1511935 BLAKE2B 76aa5a79d2553c6f269c011f633d1101ee4d85ac398a36dd463e5605d90833ecb1e5f6c21edba3e142e2d4ab5ef034fa739e52e0ab3f941a7987915ae352be0b SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d
-DIST phylip-3.696.tar.gz 3955721 BLAKE2B dc75fc442eb63e44bc2e68e5dc97b3ff8f741bfa53740ed57ca114b53dcb71db9baeb9a96c3e693f7fae92afbaa71c7b5acfb39e7770bacb6aafa8c33b355be6 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be
-EBUILD phylip-3.69-r1.ebuild 1146 BLAKE2B 690bd802cb7ed4dce34de3c272357df93c528881efe5b40c8b4e3f6c281791eb6809559a5f1680da55d5c9466cac666d290722a513eb3364245bf5f6bcd9204e SHA512 7e7eada3c9c1b6ae479360749d40943ec977505986871ffe8f5972604e2834aaddfd015f49b9e60f3f3292f8e98f410fdeecd240f34a47b86046972f067111c5
-EBUILD phylip-3.696-r1.ebuild 1130 BLAKE2B 94c4b4213d24b46fe60f3d180a1d8a742f9c173f5482e18e1521b0f3e61ac2738038c5a558fdbdeaece2f9887e08796d6981bc3ff54bec2e60dfb0ebffa7d156 SHA512 02e33c7a34910a006fb0e63d9cac40b9e71446b5b64185b968d46fdcb78217c4f2bdfe02b96ae2eefe10839e892c2c533581e9d149cfc63f1d64b2b87b1416a9
-EBUILD phylip-3.696-r2.ebuild 1204 BLAKE2B d6fcbe08f0528d657bc30da9c61c67571ee403c7f15caec8a86d2ed9a75958e471f8b2582d39c86f1ddb675636bf9d211665d398593651c968b9d87b9fac4a2a SHA512 2827584e9293a5bc95087c0d3f19b4d0ac1a7ecac6b5b81738abb16ee007d65ab91e14baf0885578afc4c369841456583d88ee51bf0738b3d04d4924eb086e5c
+AUX phylip-3.698-fno-common.patch 1934 BLAKE2B 613149dd930aa3efc921d5844e97c76475bffaedfe701d46ae980a4fabd0896d6d81fde4722599217508689d41ec70e110cbf0638abad13b2c0dbbf1c6c2f159 SHA512 4e89f330338da601ac7311995a341cab235288d82b9a63ba632b830eb99052191a920f51f43236c1a71f07ce3e427dd58ff5bc0004d1ed4ebbea8bf223390aa1
+AUX phylip-3.698-makefile.patch 9481 BLAKE2B fc8b863c05953333588f174251e40a86138a5cf2b08206861bef594ebea1d7d63b53895517bb6916e1c06c700b379cd93e76a673af4ec225502ac886dbe702d5 SHA512 6713644543f676dd6b21408675ac65c38f6a2fed4bd04619c19de881e5269e4c0bb89e440cf59dd0f1f13ad72cbbf420baccdaeb6a0c7a2a807895f87376d76f
+DIST phylip-3.698.zip 9675991 BLAKE2B 8d020cf17b3245b9827af4bdd1d17167c3e1a41ae805766c4b72f09de107775314a2a296c00f84f928487403cc02741fd46ae73585d0dba143f4b926777e9add SHA512 7f822dabd1ffdb6a689e0c308f5a3ae129bd86e305086a18c0c755ac3c6ca28a4337d52ced76b280706926370e23f19f304851ef82e32833d1945ed277f7d70d
+EBUILD phylip-3.698.ebuild 1193 BLAKE2B c196d7cdfe79a17691c2fe5567a30c0b937015ef3f8f1ce11a317dd1c86913487e6ac9a80f6ec21b80be804e7fcc1193522d3c4879d32e7510e7a9b89f1ce3b3 SHA512 da567382dfd57d40fca30845346f6ae8a5ce1bf16475bb1bdd5a220eb47d629b9904d4e0e76797971fcb2cfa795cc69a1480292a262350eb891b407e44f00509
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/phylip/files/phylip-3.698-fno-common.patch b/sci-biology/phylip/files/phylip-3.698-fno-common.patch
new file mode 100644
index 000000000000..986b1d9650ab
--- /dev/null
+++ b/sci-biology/phylip/files/phylip-3.698-fno-common.patch
@@ -0,0 +1,70 @@
+--- a/src/draw.c
++++ b/src/draw.c
+@@ -34,6 +34,11 @@
+ 
+ char fontname[LARGE_BUF_LENGTH];
+ 
++long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
++     vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
++
++char afmfile[FNMLNGTH];
++
+ /* format of matrix: capheight,  length[32],length[33],..length[256]*/
+ 
+ byte *full_pic ;
+--- a/src/draw.h
++++ b/src/draw.h
+@@ -52,10 +52,10 @@
+   double intensity, x, y, z;
+ } vrmllighttype;
+ 
+-long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
++extern long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
+      vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
+      
+-char afmfile[FNMLNGTH];
++extern char afmfile[FNMLNGTH];
+ 
+ double lengthtext(char *, long, char *, fonttype);
+ double heighttext(fonttype, char *);
+--- a/src/drawtree.c
++++ b/src/drawtree.c
+@@ -69,7 +69,7 @@
+              uselengths, regular, rotate, empty, rescaled,
+              notfirst, improve, nbody, firstscreens, labelavoid;
+ boolean     pictbold,pictitalic,pictshadow,pictoutline;
+-boolean javarun;
++extern boolean javarun;
+ 
+ striptype stripe;
+ plottertype plotter, oldplotter;
+--- a/src/phylip.c
++++ b/src/phylip.c
+@@ -34,6 +34,8 @@
+ 
+ #include "phylip.h"
+ 
++boolean javarun;
++
+ #ifdef WIN32
+ #include <windows.h>
+ /* for console code (clear screen, text color settings) */
+--- a/src/phylip.h
++++ b/src/phylip.h
+@@ -331,7 +331,7 @@
+ /* Lower-triangular format. */
+ #define MAT_LOWERTRI    (MAT_LOWER | MAT_MACHINE)
+ 
+-boolean javarun;
++extern boolean javarun;
+ 
+ typedef long *steptr;
+ typedef long longer[6];
+@@ -351,7 +351,6 @@
+ extern long spp, words, bits;
+ extern boolean ibmpc, ansi, tranvsp;
+ extern naym *nayme;                     /* names of species */
+-boolean firstplotblock; // for debugging BMP output
+ 
+ #define ebcdic          EBCDIC
+ 
diff --git a/sci-biology/phylip/files/phylip-3.698-makefile.patch b/sci-biology/phylip/files/phylip-3.698-makefile.patch
new file mode 100644
index 000000000000..f55ab98dd9cb
--- /dev/null
+++ b/sci-biology/phylip/files/phylip-3.698-makefile.patch
@@ -0,0 +1,266 @@
+--- a/src/Makefile.unx
++++ b/src/Makefile.unx
+@@ -81,7 +81,6 @@
+ #CC        = cc
+ #
+ #  To use GCC instead:
+-CC        = gcc
+ #
+ # ----------------------------------------------------------------------------
+ #
+@@ -91,7 +90,6 @@
+ #
+ #
+ #A minimal one
+-CFLAGS = 
+ #
+ # A basic one for debugging
+ #CFLAGS  = -g 
+@@ -220,7 +218,7 @@
+ 	@echo "Done."
+ 	@echo ""
+ 
+-put:
++put: all
+ 	@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
+ 	@mkdir -p $(EXEDIR)
+ 	@cp $(PROGS) $(EXEDIR)
+@@ -270,195 +268,195 @@
+ clique.o:       clique.c disc.h phylip.h
+ 
+ clique:         clique.o disc.o phylip.o
+-	$(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
++	$(CC) $(LDFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
+ 
+ cons.o:         cons.c cons.h phylip.h 
+ 
+ consense.o:     consense.c cons.h phylip.h
+ 
+ consense:       consense.o phylip.o cons.o
+-	$(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
++	$(CC) $(LDFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
+ 
+ contml.o:       contml.c cont.h phylip.h
+ 
+ contml:       contml.o cont.o phylip.o
+-	$(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
++	$(CC) $(LDFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
+ 
+ contrast.o:       contrast.c cont.h phylip.h
+ 
+ contrast:       contrast.o cont.o phylip.o
+-	$(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
++	$(CC) $(LDFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
+ 
+ dnacomp.o:      dnacomp.c seq.h phylip.h
+ 
+ dnacomp:      dnacomp.o seq.o phylip.o
+-	$(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
++	$(CC) $(LDFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
+ 
+ dnadist.o:      dnadist.c seq.h phylip.h
+ 
+ dnadist:      dnadist.o seq.o phylip.o
+-	$(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
++	$(CC) $(LDFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
+ 
+ dnainvar.o:      dnainvar.c seq.h phylip.h
+ 
+ dnainvar:      dnainvar.o seq.o phylip.o
+-	$(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
++	$(CC) $(LDFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
+ 
+ dnaml.o:      dnaml.c seq.h phylip.h
+ 
+ dnaml:      dnaml.o seq.o phylip.o
+-	$(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
++	$(CC) $(LDFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
+ 
+ dnamlk.o:      dnamlk.c seq.h phylip.h mlclock.h printree.h
+ 
+ dnamlk:      dnamlk.o seq.o phylip.o mlclock.o printree.o
+-	$(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
++	$(CC) $(LDFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
+ 
+ dnamove.o:      dnamove.c seq.h moves.h phylip.h
+ 
+ dnamove:      dnamove.o seq.o moves.o phylip.o
+-	$(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
++	$(CC) $(LDFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
+ 
+ dnapenny.o:      dnapenny.c seq.h phylip.h
+ 
+ dnapenny:      dnapenny.o seq.o phylip.o
+-	$(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
++	$(CC) $(LDFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
+ 
+ dnapars.o:      dnapars.c seq.h phylip.h
+ 
+ dnapars:      dnapars.o seq.o phylip.o
+-	$(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
++	$(CC) $(LDFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
+ 
+ dolmove.o:       dolmove.c disc.h moves.h dollo.h phylip.h
+ 
+ dolmove:       dolmove.o disc.o moves.o dollo.o phylip.o
+-	$(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
++	$(CC) $(LDFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
+ 
+ dollop.o:       dollop.c disc.h dollo.h phylip.h
+ 
+ dollop:       dollop.o disc.o dollo.o phylip.o
+-	$(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
++	$(CC) $(LDFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
+ 
+ dolpenny.o:       dolpenny.c disc.h dollo.h phylip.h
+ 
+ dolpenny:       dolpenny.o disc.o dollo.o phylip.o
+-	$(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
++	$(CC) $(LDFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
+ 
+ draw.o:   draw.c draw.h phylip.h 
+-	$(CC) $(DFLAGS) -c draw.c
++	$(CC) $(DFLAGS) $(CPPFLAGS) -c draw.c
+ 
+ draw2.o:   draw2.c draw.h phylip.h 
+-	$(CC) $(DFLAGS) -c draw2.c
++	$(CC) $(DFLAGS) $(CPPFLAGS) -c draw2.c
+ 
+ drawgram.o:     drawgram.c draw.h phylip.h
+-	$(CC) $(DFLAGS) -c drawgram.c
++	$(CC) $(DFLAGS) $(CPPFLAGS) -c drawgram.c
+ 
+ drawgram:     drawgram.o draw.o draw2.o phylip.o
+-	$(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
++	$(CC) $(LDFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
+ 	
+ # needed by java	
+-libdrawgram.so:   drawgram.o draw.o draw2.o phylip.o
+-	$(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
++libdrawgram.so:
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawgram.so -Wl,-soname,libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
+ 
+ drawtree.o:     drawtree.c draw.h phylip.h
+-	$(CC) $(DFLAGS)  -shared -fPIC -c drawtree.c
++	$(CC) $(DFLAGS) $(CPPFLAGS) -c drawtree.c
+ 
+ drawtree:     drawtree.o draw.o draw2.o phylip.o
+-	$(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
++	$(CC) $(LDFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
+ 
+ # needed by java	
+-libdrawtree.so:     drawtree.o draw.o draw2.o phylip.o
+-	$(CC) $(CFLAGS) -o libdrawtree.so  -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
++libdrawtree.so:
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawtree.so -Wl,-soname,libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
+ 
+ factor.o:       factor.c phylip.h
+ 
+ factor:       factor.o phylip.o
+-	$(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor
++	$(CC) $(LDFLAGS) factor.o phylip.o $(LIBS) -o factor
+ 
+ fitch.o:        fitch.c dist.h phylip.h
+ 
+ fitch:        fitch.o dist.o phylip.o
+-	$(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
++	$(CC) $(LDFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
+ 
+ gendist.o:      gendist.c phylip.h
+ 
+ gendist:      gendist.o phylip.o
+-	$(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist
++	$(CC) $(LDFLAGS) gendist.o phylip.o $(LIBS) -o gendist
+ 
+ kitsch.o:        kitsch.c dist.h phylip.h
+ 
+ kitsch:        kitsch.o dist.o phylip.o
+-	$(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
++	$(CC) $(LDFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
+ 
+ mix.o:        mix.c disc.h wagner.h phylip.h
+ 
+ mix:        mix.o disc.o wagner.o phylip.o
+-	$(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
++	$(CC) $(LDFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
+ 
+ move.o:        move.c disc.h moves.h wagner.h phylip.h
+ 
+ move:        move.o disc.o moves.o wagner.o phylip.o
+-	$(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
++	$(CC) $(LDFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
+ 
+ neighbor.o:        neighbor.c dist.h phylip.h
+ 
+ neighbor:        neighbor.o dist.o phylip.o
+-	$(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
++	$(CC) $(LDFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
+ 
+ pars.o:   pars.c discrete.h phylip.h
+ 
+ pars: pars.o discrete.o phylip.o
+-	$(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
++	$(CC) $(LDFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
+ 
+ penny.o:  penny.c disc.h wagner.h phylip.h
+ 
+ penny:  penny.o disc.o wagner.o phylip.o
+-	$(CC) $(CFLAGS) penny.o disc.o wagner.o  phylip.o $(LIBS) -o penny
++	$(CC) $(LDFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny
+ 
+ proml.o:      proml.c seq.h phylip.h
+ 
+ proml:      proml.o seq.o phylip.o
+-	$(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
++	$(CC) $(LDFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
+ 
+ promlk.o:      promlk.c seq.h phylip.h mlclock.h printree.h
+ 
+ promlk:      promlk.o seq.o phylip.o mlclock.o printree.o
+-	$(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
++	$(CC) $(LDFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
+ 
+ protdist.o:      protdist.c seq.h phylip.h
+ 
+ protdist:      protdist.o seq.o phylip.o
+-	$(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
++	$(CC) $(LDFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
+ 
+ protpars.o: protpars.c seq.h phylip.h
+ 
+ protpars: protpars.o seq.o phylip.o
+-	$(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
++	$(CC) $(LDFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
+ 
+ restdist.o: restdist.c seq.h phylip.h
+ 
+ restdist: restdist.o seq.o phylip.o
+-	$(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
++	$(CC) $(LDFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
+ 
+ restml.o: restml.c seq.h phylip.h
+ 
+ restml: restml.o seq.o phylip.o
+-	$(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
++	$(CC) $(LDFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
+ 
+ retree.o:       retree.c moves.h phylip.h
+ 
+ retree:       retree.o moves.o phylip.o
+-	$(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
++	$(CC) $(LDFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
+ 
+ seqboot.o:      seqboot.c phylip.h
+ 
+ seqboot:      seqboot.o seq.o phylip.o
+-	$(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
++	$(CC) $(LDFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
+ 
+ treedist.o:     treedist.c cons.h phylip.h
+ 
+ treedist:     treedist.o phylip.o cons.o
+-	$(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
++	$(CC) $(LDFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
+ 
+ 
+ # ----------------------------------------------------------------------------
diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild
deleted file mode 100644
index e54c75d9b356..000000000000
--- a/sci-biology/phylip/phylip-3.69-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="free-noncomm"
-IUSE=""
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
-
-RDEPEND="x11-libs/libXaw"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/src"
-
-src_prepare() {
-	sed \
-		-e "s/CFLAGS  = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \
-		-e "s/CC        = cc/CC        = $(tc-getCC)/" \
-		-e "s/DC        = cc/DC        = $(tc-getCC)/" \
-		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts || die
-}
-
-src_compile() {
-	emake -j1 all put
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}" || die
-
-	mv exe/font* fonts || die "Font move failed."
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
-
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-
-	dohtml -r phylip.html doc
-
-	insinto /usr/share/${PN}/
-	doins -r fonts
-}
diff --git a/sci-biology/phylip/phylip-3.696-r1.ebuild b/sci-biology/phylip/phylip-3.696-r1.ebuild
deleted file mode 100644
index 85150acaf9cb..000000000000
--- a/sci-biology/phylip/phylip-3.696-r1.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD-2"
-IUSE=""
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-
-RDEPEND="x11-libs/libXaw"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/src"
-
-src_prepare() {
-	mv Makefile.unx Makefile || die
-	sed \
-		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts || die
-}
-
-src_compile() {
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		DC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS} -Wno-unused-result" \
-		all put
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}" || die
-
-	mv exe/font* fonts || die "Font move failed."
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
-
-	dolib.so exe/*so && rm exe/*so
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-
-	dohtml -r phylip.html doc
-
-	insinto /usr/share/${PN}/
-	doins -r fonts
-}
diff --git a/sci-biology/phylip/phylip-3.696-r2.ebuild b/sci-biology/phylip/phylip-3.696-r2.ebuild
deleted file mode 100644
index 66391e0e662d..000000000000
--- a/sci-biology/phylip/phylip-3.696-r2.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD-2"
-IUSE=""
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-# 'mix' tool collides with dev-lang/elixir, bug #537514
-RDEPEND="x11-libs/libXaw
-	!!dev-lang/elixir"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/src"
-
-src_prepare() {
-	mv Makefile.unx Makefile || die
-	sed \
-		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts || die
-}
-
-src_compile() {
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		DC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS} -Wno-unused-result" \
-		all put
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}" || die
-
-	mv exe/font* fonts || die "Font move failed."
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
-
-	dolib.so exe/*so && rm exe/*so
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-
-	dohtml -r phylip.html doc
-
-	insinto /usr/share/${PN}/
-	doins -r fonts
-}
diff --git a/sci-biology/phylip/phylip-3.698.ebuild b/sci-biology/phylip/phylip-3.698.ebuild
new file mode 100644
index 000000000000..0a8ef8f815ec
--- /dev/null
+++ b/sci-biology/phylip/phylip-3.698.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION=" The PHYLogeny Inference Package"
+HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"
+SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.zip"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+# 'mix' tool collides with dev-lang/elixir, bug #537514
+RDEPEND="
+	x11-libs/libXaw
+	!dev-lang/elixir"
+DEPEND="${RDEPEND}
+	x11-base/xorg-proto"
+BDEPEND="app-arch/unzip"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-fno-common.patch
+)
+
+src_prepare() {
+	default
+
+	mkdir fonts || die
+	# clear out old binaries
+	rm -r exe || die
+}
+
+src_configure() {
+	tc-export CC
+	append-cflags -Wno-unused-result
+}
+
+src_compile() {
+	emake -C src -f Makefile.unx all put
+}
+
+src_install() {
+	mv exe/font* fonts || die "Font move failed"
+	mv exe/factor exe/factor-${PN} || die "Renaming factor failed"
+
+	dolib.so exe/*so
+	rm exe/*so || die
+	dobin exe/*
+
+	dodoc "${FILESDIR}"/README.Gentoo
+	docinto html
+	dodoc -r phylip.html doc
+
+	insinto /usr/share/phylip
+	doins -r fonts
+}