gentoo auto-resync : 27:01:2023 - 13:58:28

5 files changed, 0 insertions, 177 deletions

diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest
deleted file mode 100644
index 4807ae1d7349..000000000000
--- a/sci-biology/phred/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX phred-071220-fix-build-system.patch 1981 BLAKE2B 0c9ae75ecf54eadd1d6cd3cfeed5d2f949f234b77d4f329133e2c176207410e93a35341c43636c5b2f742a2ee2d20825cf79bb65d5dac43ba28fc07f7c6bb69b SHA512 7647f6f6e9a1ae51cbf1aa3e39b337288e22fc26a95fdd88f92ce43fc6c0ef6ff59ec26919d14dfefff70be48e4a5604ddefef98bddf5d1d14d1e656665c878d
-AUX phred-071220-fix-qa.patch 787 BLAKE2B 79f687dc1e51dd51e9f97886e0ada9b515d7e4255dff0ec3e81dccb2103ba8b4bee691c8a5b9a321cbdde5576fe8d80dbadafdb740c2cdee81fe9748255084ab SHA512 27811a834358d0e1bf8281882e0420e0eb6bd9586871c8c72a4de79badc9539ea8e9258b9c3a3bf8ca1d3f6924d61abce2dcc0c0ed3b64e5fa53d4548109f5bc
-DIST phred-dist-071220.b-acd.tar.gz 357767 BLAKE2B ae1180f54eaa3631a4e32c2ffe388b35745302e3d014c8fa893119e7e488d4bb4316f7ee0588cd12db5cbbc23033f689f4a0a487cdc7fe42e8c7a67ceb3c43ae SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276
-EBUILD phred-071220-r2.ebuild 941 BLAKE2B a2351e95dd63ab0655c6dc009dabffbc2bea88e2c4c45536094ca5b7e18c22e6040a44b2362b56a58cdb2ba002d2f5c3d9527b5775ba073c29ed70b6e0d25198 SHA512 5b0fc5afeb3847d9a8729b14addca1508add1a0cf6f857273c9a5671b65c82385b82c62e9545caa9b3a8f470b1852d9655ac8ca3ca33f745937a3101f7ebe084
-MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
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>sci-biology@gentoo.org</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
-}