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sci-biology/phred: treeclean
Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
This commit is contained in:
Jakov Smolić
@@ -709,7 +709,6 @@ app-eselect/eselect-sh
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# last release 8 years ago. Removal on 2023-01-25.
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sci-biology/consed
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sci-biology/phrap
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sci-biology/phred
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# Ionen Wolkens <ionen@gentoo.org> (2022-12-24)
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# Upstream dropped wxGTK support in >=games-emulation/pcsx2-1.7.3773,
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@@ -1 +0,0 @@
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DIST phred-dist-071220.b-acd.tar.gz 357767 BLAKE2B ae1180f54eaa3631a4e32c2ffe388b35745302e3d014c8fa893119e7e488d4bb4316f7ee0588cd12db5cbbc23033f689f4a0a487cdc7fe42e8c7a67ceb3c43ae SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276
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@@ -1,82 +0,0 @@
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* Fix build system to honour CC, CFLAGS, CPPFLAGS and LDFLAGS
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* Specify a default target, in order to keep the ebuild slim
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--- a/Makefile
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+++ b/Makefile
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@@ -12,9 +12,9 @@
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# UNIX specific definitions (default)
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#
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-CC= cc
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-CFLAGS= -O -DANSI_C $(LXFLAGS)
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-CLIB= -lm
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+CC ?= cc
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+CPPFLAGS += -DANSI_C $(LXFLAGS)
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+LIBS += -lm
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# Windows 'nmake' specific definitions
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#
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@@ -133,9 +133,6 @@
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$(objdir)writeSDF.o \
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$(objdir)writeSeq.o
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-SRCS = $(OBJS:.o=.c)
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-WOBJ = $(OBJS:.o=.obj)
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-
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INCS = \
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$(incdir)chromatData.h \
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$(incdir)freeChromatData.h \
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@@ -179,48 +176,18 @@
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# UNIX make specific phred target
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# note: a horizontal tab character must precede `$(CC)'
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#
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-phred: $(OBJS)
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- $(CC) $(CFLAGS) -o phred $(OBJS) $(CLIB)
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-# Windows nmake specific phred target
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-#
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-forwindows: $(WOBJ)
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- $(CC) $(CFLAGS) /Fephred $(WOBJ)
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-# $(CC) $(CFLAGS) /Fedaev daev.c
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+.PHONY: all
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+all: phred daev
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-# test CC: refuse to compile if
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-#
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-# o SunOS
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-#
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-# AND
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-#
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-# o using /usr/ucb/cc compiler
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-#
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-# NOTE: this compiler causes problems: see PHRED.DOC
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-#
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-test_cc:
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- @if [ `uname` = SunOS ] ; \
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- then \
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- if [ `which $(CC)` = "/usr/ucb/cc" ] ; \
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- then \
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- echo ""; \
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- echo "============================================================"; \
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- echo "| |"; \
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- echo "| This SUN C compiler produces a bad phred executable. |"; \
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- echo "| |"; \
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- echo "| Please see the PHRED.DOC file for more information. |"; \
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- echo "| |"; \
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- echo "============================================================"; \
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- echo ""; \
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- exit 1; \
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- fi \
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- fi
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+phred: $(OBJS)
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+ $(CC) $(LDFLAGS) $(CFLAGS) -o phred $^ $(LIBS)
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daev: daev.o
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- $(CC) $(CFLAGS) -o daev daev.o -lm
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+ $(CC) $(LDFLAGS) $(CFLAGS) -o daev $^ $(LIBS)
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clean:
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@@ -1,36 +0,0 @@
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Fix implicit declarations:
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* daev.c: In function ‘processParameters’:
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* daev.c:849:14: warning: implicit declaration of function ‘isdigit’ [-Wimplicit-function-declaration]
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* if( !isdigit( argv[iarg][0] ) )
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--- a/autoPhred.c
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+++ b/autoPhred.c
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@@ -57,6 +57,7 @@
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static int xstrcmp();
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#endif
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+int freeMBRData( MBRData *mbrData );
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#ifdef ANSI_C
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int autoPhred( Option *option )
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#else
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--- a/daev.c
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+++ b/daev.c
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@@ -58,6 +58,7 @@
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#include <sys/stat.h>
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#include <time.h>
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#include <math.h>
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+#include <ctype.h>
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#ifndef _WIN32
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#include <dirent.h>
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--- a/mergedBaseRead.c
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+++ b/mergedBaseRead.c
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@@ -63,7 +63,7 @@
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Peak *peak;
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Observed_peak *obs_peak;
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- static initFlag = 0;
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+ static int initFlag = 0;
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static char mchar[256][256];
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if( initFlag == 0 )
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@@ -1,8 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "https://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@gentoo.org</email>
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<name>Gentoo Biology Project</name>
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</maintainer>
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</pkgmetadata>
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@@ -1,46 +0,0 @@
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# Copyright 1999-2022 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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inherit toolchain-funcs
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DESCRIPTION="A base caller for Sanger DNA sequencing"
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HOMEPAGE="http://phrap.org/phredphrapconsed.html"
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SRC_URI="${PN}-dist-${PV}.b-acd.tar.gz"
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S="${WORKDIR}"
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LICENSE="phrap"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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RESTRICT="fetch"
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PATCHES=(
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"${FILESDIR}"/${PN}-071220-fix-build-system.patch
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"${FILESDIR}"/${PN}-071220-fix-qa.patch
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)
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pkg_nofetch() {
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einfo "Please visit ${HOMEPAGE} and obtain the file"
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einfo "${SRC_URI}, then place it into your DISTDIR directory."
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}
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src_compile() {
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emake CC="$(tc-getCC)" \
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CFLAGS="${CFLAGS}" \
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LDFLAGS="${LDFLAGS}"
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}
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src_install() {
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dobin phred daev
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insinto /usr/share/phred
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doins phredpar.dat
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newenvd - 99phred <<- EOF
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PHRED_PARAMETER_FILE="${EPREFIX}/usr/share/phred/phredpar.dat"
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EOF
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newdoc DAEV.DOC DAEV.DOC.txt
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newdoc PHRED.DOC PHRED.DOC.txt
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}
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