commit: fb89f8f6053ab2d65cd1c7b1604aa0a1df8bf216 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Tue Oct 27 20:56:15 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Tue Oct 27 20:56:15 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fb89f8f6
sci-biology/phylip: Version bump to 3.698 Bug: https://bugs.gentoo.org/707150 Bug: https://bugs.gentoo.org/727982 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/phylip/Manifest | 1 + .../phylip/files/phylip-3.698-fno-common.patch | 70 ++++++ .../phylip/files/phylip-3.698-makefile.patch | 266 +++++++++++++++++++++ sci-biology/phylip/phylip-3.698.ebuild | 60 +++++ 4 files changed, 397 insertions(+) diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest index 5a714766bc1..2f29996a668 100644 --- a/sci-biology/phylip/Manifest +++ b/sci-biology/phylip/Manifest @@ -1,2 +1,3 @@ DIST phylip-3.69.tar.gz 1511935 BLAKE2B 76aa5a79d2553c6f269c011f633d1101ee4d85ac398a36dd463e5605d90833ecb1e5f6c21edba3e142e2d4ab5ef034fa739e52e0ab3f941a7987915ae352be0b SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d DIST phylip-3.696.tar.gz 3955721 BLAKE2B dc75fc442eb63e44bc2e68e5dc97b3ff8f741bfa53740ed57ca114b53dcb71db9baeb9a96c3e693f7fae92afbaa71c7b5acfb39e7770bacb6aafa8c33b355be6 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be +DIST phylip-3.698.zip 9675991 BLAKE2B 8d020cf17b3245b9827af4bdd1d17167c3e1a41ae805766c4b72f09de107775314a2a296c00f84f928487403cc02741fd46ae73585d0dba143f4b926777e9add SHA512 7f822dabd1ffdb6a689e0c308f5a3ae129bd86e305086a18c0c755ac3c6ca28a4337d52ced76b280706926370e23f19f304851ef82e32833d1945ed277f7d70d 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 00000000000..986b1d9650a --- /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 00000000000..f55ab98dd9c --- /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 $(LIBS) -o treedist + + + # ---------------------------------------------------------------------------- diff --git a/sci-biology/phylip/phylip-3.698.ebuild b/sci-biology/phylip/phylip-3.698.ebuild new file mode 100644 index 00000000000..0a8ef8f815e --- /dev/null +++ b/sci-biology/phylip/phylip-3.698.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION=" The PHYLogeny Inference Package" +HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html"; +SRC_URI="http://evolution.gs.washington.edu/${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 +}
