commit: 1863d5b30160a7b46c7bb5dc4ea68df4e29cdf8d Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Fri Jan 27 11:02:24 2023 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Fri Jan 27 11:07:28 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1863d5b3
sci-biology/phred: treeclean Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 1 - sci-biology/phred/Manifest | 1 - .../files/phred-071220-fix-build-system.patch | 82 ---------------------- sci-biology/phred/files/phred-071220-fix-qa.patch | 36 ---------- sci-biology/phred/metadata.xml | 8 --- sci-biology/phred/phred-071220-r2.ebuild | 46 ------------ 6 files changed, 174 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index a6565c66251e..6496beff8e24 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -709,7 +709,6 @@ app-eselect/eselect-sh # last release 8 years ago. Removal on 2023-01-25. sci-biology/consed sci-biology/phrap -sci-biology/phred # Ionen Wolkens <[email protected]> (2022-12-24) # Upstream dropped wxGTK support in >=games-emulation/pcsx2-1.7.3773, diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest deleted file mode 100644 index 1c0aa1a3ee91..000000000000 --- a/sci-biology/phred/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST phred-dist-071220.b-acd.tar.gz 357767 BLAKE2B ae1180f54eaa3631a4e32c2ffe388b35745302e3d014c8fa893119e7e488d4bb4316f7ee0588cd12db5cbbc23033f689f4a0a487cdc7fe42e8c7a67ceb3c43ae SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276 diff --git a/sci-biology/phred/files/phred-071220-fix-build-system.patch b/sci-biology/phred/files/phred-071220-fix-build-system.patch deleted file mode 100644 index 997f39941a07..000000000000 --- a/sci-biology/phred/files/phred-071220-fix-build-system.patch +++ /dev/null @@ -1,82 +0,0 @@ -* Fix build system to honour CC, CFLAGS, CPPFLAGS and LDFLAGS -* Specify a default target, in order to keep the ebuild slim - ---- a/Makefile -+++ b/Makefile -@@ -12,9 +12,9 @@ - - # UNIX specific definitions (default) - # --CC= cc --CFLAGS= -O -DANSI_C $(LXFLAGS) --CLIB= -lm -+CC ?= cc -+CPPFLAGS += -DANSI_C $(LXFLAGS) -+LIBS += -lm - - # Windows 'nmake' specific definitions - # -@@ -133,9 +133,6 @@ - $(objdir)writeSDF.o \ - $(objdir)writeSeq.o - --SRCS = $(OBJS:.o=.c) --WOBJ = $(OBJS:.o=.obj) -- - INCS = \ - $(incdir)chromatData.h \ - $(incdir)freeChromatData.h \ -@@ -179,48 +176,18 @@ - # UNIX make specific phred target - # note: a horizontal tab character must precede `$(CC)' - # --phred: $(OBJS) -- $(CC) $(CFLAGS) -o phred $(OBJS) $(CLIB) - - --# Windows nmake specific phred target --# --forwindows: $(WOBJ) -- $(CC) $(CFLAGS) /Fephred $(WOBJ) --# $(CC) $(CFLAGS) /Fedaev daev.c -+.PHONY: all -+all: phred daev - - --# test CC: refuse to compile if --# --# o SunOS --# --# AND --# --# o using /usr/ucb/cc compiler --# --# NOTE: this compiler causes problems: see PHRED.DOC --# --test_cc: -- @if [ `uname` = SunOS ] ; \ -- then \ -- if [ `which $(CC)` = "/usr/ucb/cc" ] ; \ -- then \ -- echo ""; \ -- echo "============================================================"; \ -- echo "| |"; \ -- echo "| This SUN C compiler produces a bad phred executable. |"; \ -- echo "| |"; \ -- echo "| Please see the PHRED.DOC file for more information. |"; \ -- echo "| |"; \ -- echo "============================================================"; \ -- echo ""; \ -- exit 1; \ -- fi \ -- fi -+phred: $(OBJS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o phred $^ $(LIBS) - - - daev: daev.o -- $(CC) $(CFLAGS) -o daev daev.o -lm -+ $(CC) $(LDFLAGS) $(CFLAGS) -o daev $^ $(LIBS) - - - clean: diff --git a/sci-biology/phred/files/phred-071220-fix-qa.patch b/sci-biology/phred/files/phred-071220-fix-qa.patch deleted file mode 100644 index ab4d2ea023f6..000000000000 --- a/sci-biology/phred/files/phred-071220-fix-qa.patch +++ /dev/null @@ -1,36 +0,0 @@ -Fix implicit declarations: -* daev.c: In function ‘processParameters’: -* daev.c:849:14: warning: implicit declaration of function ‘isdigit’ [-Wimplicit-function-declaration] -* if( !isdigit( argv[iarg][0] ) ) - ---- a/autoPhred.c -+++ b/autoPhred.c -@@ -57,6 +57,7 @@ - static int xstrcmp(); - #endif - -+int freeMBRData( MBRData *mbrData ); - #ifdef ANSI_C - int autoPhred( Option *option ) - #else ---- a/daev.c -+++ b/daev.c -@@ -58,6 +58,7 @@ - #include <sys/stat.h> - #include <time.h> - #include <math.h> -+#include <ctype.h> - - #ifndef _WIN32 - #include <dirent.h> ---- a/mergedBaseRead.c -+++ b/mergedBaseRead.c -@@ -63,7 +63,7 @@ - Peak *peak; - Observed_peak *obs_peak; - -- static initFlag = 0; -+ static int initFlag = 0; - static char mchar[256][256]; - - if( initFlag == 0 ) diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml deleted file mode 100644 index ccdff086e20b..000000000000 --- a/sci-biology/phred/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/phred/phred-071220-r2.ebuild b/sci-biology/phred/phred-071220-r2.ebuild deleted file mode 100644 index 2d33df654a1b..000000000000 --- a/sci-biology/phred/phred-071220-r2.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="A base caller for Sanger DNA sequencing" -HOMEPAGE="http://phrap.org/phredphrapconsed.html"; -SRC_URI="${PN}-dist-${PV}.b-acd.tar.gz" -S="${WORKDIR}" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -RESTRICT="fetch" - -PATCHES=( - "${FILESDIR}"/${PN}-071220-fix-build-system.patch - "${FILESDIR}"/${PN}-071220-fix-qa.patch -) - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "${SRC_URI}, then place it into your DISTDIR directory." -} - -src_compile() { - emake CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - dobin phred daev - - insinto /usr/share/phred - doins phredpar.dat - - newenvd - 99phred <<- EOF - PHRED_PARAMETER_FILE="${EPREFIX}/usr/share/phred/phredpar.dat" - EOF - - newdoc DAEV.DOC DAEV.DOC.txt - newdoc PHRED.DOC PHRED.DOC.txt -}
