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commit: 1d628ae01ed5cc7b4bf4502efab58fc104589428 |
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Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> |
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AuthorDate: Mon Aug 30 17:16:11 2021 +0000 |
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Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> |
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CommitDate: Mon Aug 30 17:38:49 2021 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1d628ae0 |
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|
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sci-biology/njplot: Remove last-rited package |
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|
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Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> |
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|
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profiles/package.mask | 1 - |
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sci-biology/njplot/Manifest | 1 - |
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.../njplot/files/njplot-2.3-buildsystem.patch | 59 ---------------------- |
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.../njplot/files/njplot-2.3-format-security.patch | 16 ------ |
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sci-biology/njplot/metadata.xml | 15 ------ |
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sci-biology/njplot/njplot-2.3-r2.ebuild | 38 -------------- |
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6 files changed, 130 deletions(-) |
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|
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diff --git a/profiles/package.mask b/profiles/package.mask |
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index 484e5b1182a..a91a2a5b53e 100644 |
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--- a/profiles/package.mask |
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+++ b/profiles/package.mask |
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@@ -285,7 +285,6 @@ sci-libs/sktime |
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# anymore, tons of bugs. Revdeps are unmaintained too and out of date. |
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# Bug #798015, removal in 30 days. |
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sci-biology/ncbi-tools |
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-sci-biology/njplot |
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|
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# Andreas K. Hüttel <dilfridge@g.o> (2021-07-31) |
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# Obsolete; all versions in current Perl core distributions |
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|
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diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest |
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deleted file mode 100644 |
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index 6cec177af40..00000000000 |
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--- a/sci-biology/njplot/Manifest |
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+++ /dev/null |
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@@ -1 +0,0 @@ |
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-DIST njplot-2.3.tar.gz 83641 BLAKE2B 3dd2798c190a103e88babb592cda184ae7ab4839cc779f739205480e2cce641bc9f8a57d20bd96ce8fc4a1e662a81de0bb13f2a4ffa9d03f8e0f286c762b993a SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 |
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|
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diff --git a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch |
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deleted file mode 100644 |
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index 61f8b95ea16..00000000000 |
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--- a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch |
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+++ /dev/null |
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@@ -1,59 +0,0 @@ |
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- makefile | 16 ++++++++-------- |
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- 1 file changed, 8 insertions(+), 8 deletions(-) |
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- |
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-diff --git a/makefile b/makefile |
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-index ccb7dc2..9488c2a 100644 |
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---- a/makefile |
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-+++ b/makefile |
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-@@ -7,10 +7,10 @@ NO_PDF = -DNO_PDF |
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- #PDFLIB = -L$(PDF) -lpdf |
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- |
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- # c compiler and linker |
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--CC = gcc |
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-+CC ?= gcc |
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- |
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- # Vibrant top directory |
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--VIBRANT = /banques0/ncbiJun04 |
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-+VIBRANT = /usr/include/ncbi |
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- |
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- |
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- # X11 include directory |
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-@@ -24,15 +24,15 @@ OBJECTS = njplot-vib.o |
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- OBJUNROOTED = unrooted-vib.o preptree.o |
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- |
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- |
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--CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ |
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-+CFLAGS += -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ |
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- -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \ |
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-- -Wimplicit-function-declaration -g |
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-+ -Wimplicit-function-declaration |
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- |
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- all: njplot unrooted newicktops newicktotxt |
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- |
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- |
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- njplot : $(OBJECTS) |
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-- $(CC) -g -o njplot $(OBJECTS) \ |
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-+ $(CC) $(LDFLAGS) -o njplot $(OBJECTS) \ |
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- -L$(VIBRANT)/lib \ |
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- -lvibrant -lncbi \ |
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- $(PDFLIB) \ |
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-@@ -40,16 +40,16 @@ njplot : $(OBJECTS) |
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- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm |
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- |
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- unrooted : $(OBJUNROOTED) |
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-- $(CC) -g -o unrooted $(OBJUNROOTED) \ |
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-+ $(CC) $(LDFLAGS) -o unrooted $(OBJUNROOTED) \ |
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- -L$(VIBRANT)/lib -lvibrant -lncbi \ |
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- -L$(MOTIFLIB) -lXm \ |
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- -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm |
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- |
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- newicktops: njplot-vib.c |
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-- $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm |
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-+ $(CC) $(LDFLAGS) $(CFLAGS) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm |
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- |
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- newicktotxt: njplot-vib.c |
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-- $(CC) -DTTY -o $@ njplot-vib.c -lm |
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-+ $(CC) -DTTY $(LDFLAGS) $(CFLAGS) -o $@ njplot-vib.c -lm |
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- |
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- |
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- .c.o : |
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|
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diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch |
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deleted file mode 100644 |
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index 686b8475e9e..00000000000 |
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--- a/sci-biology/njplot/files/njplot-2.3-format-security.patch |
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+++ /dev/null |
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@@ -1,16 +0,0 @@ |
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- njplot-vib.c | 2 +- |
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- 1 file changed, 1 insertion(+), 1 deletion(-) |
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- |
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-diff --git a/njplot-vib.c b/njplot-vib.c |
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-index fe55609..63fd3b6 100644 |
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---- a/njplot-vib.c |
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-+++ b/njplot-vib.c |
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-@@ -1976,7 +1976,7 @@ PDFONLY" no window interface, just write the PDF/PostScript tree plot\n" |
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- #else |
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- fprintf(stderr, |
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- #endif |
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-- message); |
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-+ "%s", message); |
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- exit(0); |
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- } |
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- } |
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|
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diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml |
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deleted file mode 100644 |
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index 2a3eb314096..00000000000 |
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--- a/sci-biology/njplot/metadata.xml |
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+++ /dev/null |
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@@ -1,15 +0,0 @@ |
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-<?xml version="1.0" encoding="UTF-8"?> |
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-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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-<pkgmetadata> |
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- <maintainer type="project"> |
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- <email>sci-biology@g.o</email> |
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- <name>Gentoo Biology Project</name> |
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- </maintainer> |
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- <longdescription> |
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- NJplot is a tree drawing program able to draw any phylogenetic tree |
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- expressed in the Newick phylogenetic tree format (e.g., the format used |
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- by the PHYLIP package). NJplot is especially convenient for rooting the |
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- unrooted trees obtained from parsimony, distance or maximum likelihood |
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- tree-building methods. |
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- </longdescription> |
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-</pkgmetadata> |
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|
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diff --git a/sci-biology/njplot/njplot-2.3-r2.ebuild b/sci-biology/njplot/njplot-2.3-r2.ebuild |
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deleted file mode 100644 |
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index 420861dac42..00000000000 |
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--- a/sci-biology/njplot/njplot-2.3-r2.ebuild |
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+++ /dev/null |
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@@ -1,38 +0,0 @@ |
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-# Copyright 1999-2017 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=6 |
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- |
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-inherit toolchain-funcs |
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- |
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-DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting" |
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-HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html" |
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-SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz" |
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- |
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-LICENSE="public-domain" |
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-SLOT="0" |
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-KEYWORDS="~amd64 ~x86" |
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-IUSE="" |
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- |
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-RDEPEND=" |
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- sci-biology/ncbi-tools[X,static-libs] |
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- x11-libs/libXmu" |
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-DEPEND="${RDEPEND}" |
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- |
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-PATCHES=( |
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- "${FILESDIR}"/${P}-format-security.patch |
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- "${FILESDIR}"/${P}-buildsystem.patch |
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-) |
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- |
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-src_prepare() { |
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- default |
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- sed -i -e "s:njplot.help:${EPREFIX}/usr/share/doc/${PF}/njplot.help:" njplot-vib.c || die |
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- |
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- tc-export CC |
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-} |
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- |
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-src_install() { |
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- dobin newicktops newicktotxt njplot unrooted |
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- doman *.1 |
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- dodoc README njplot.help |
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-} |
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