commit: bbd189a0826dc274c1378aa8a791b63c9d101c5a Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Sun Jan 23 12:54:13 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Sun Jan 23 12:54:13 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bbd189a0
sci-biology/quorum: remove old java package Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> profiles/package.mask | 7 -- .../quorum/files/quorum-0.2.1-use-jellyfish1.patch | 74 ---------------------- sci-biology/quorum/metadata.xml | 12 ---- sci-biology/quorum/quorum-1.1.1.ebuild | 28 -------- 4 files changed, 121 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 020a30666..cfebeb744 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -64,10 +64,3 @@ sci-misc/opennlp-maxent # Broken, no consumers # Removal in 30 days dev-lang/terra - -# Andrew Ammerlaan <andrewammerl...@gentoo.org (14 Jan 2022) -# Does not compile, no upstream activity since 2016 -# https://github.com/gmarcais/Quorum/issues/2 -# https://github.com/gmarcais/Quorum/issues/1 -# Removal in 30 days -sci-biology/quorum diff --git a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch b/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch deleted file mode 100644 index b5b68a8fb..000000000 --- a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch +++ /dev/null @@ -1,74 +0,0 @@ ---- src/error_correct_reads.cc 2018-04-21 14:25:41.310473159 +0200 -+++ src/error_correct_reads.cc 2018-04-21 14:26:58.262493179 +0200 -@@ -25,9 +25,9 @@ - #endif - - //#define DEBUG 1 --#include <jellyfish/dbg.hpp> --#include <jellyfish/atomic_gcc.hpp> --#include <jellyfish/mer_counting.hpp> -+#include <jellyfish1/dbg.hpp> -+#include <jellyfish1/atomic_gcc.hpp> -+#include <jellyfish1/mer_counting.hpp> - - #include <jflib/multiplexed_io.hpp> - #include <gzip_stream.hpp> ---- src/combine_jf_dbs.cc 2018-04-21 14:25:50.220707057 +0200 -+++ src/combine_jf_dbs.cc 2018-04-21 14:27:04.652660923 +0200 -@@ -1,9 +1,9 @@ --#include <jellyfish/err.hpp> --#include <jellyfish/misc.hpp> --#include <jellyfish/mer_counting.hpp> --#include <jellyfish/compacted_hash.hpp> --#include <jellyfish/thread_exec.hpp> --#include <jellyfish/misc.hpp> -+#include <jellyfish1/err.hpp> -+#include <jellyfish1/misc.hpp> -+#include <jellyfish1/mer_counting.hpp> -+#include <jellyfish1/compacted_hash.hpp> -+#include <jellyfish1/thread_exec.hpp> -+#include <jellyfish1/misc.hpp> - #include <src/combine_jf_dbs.hpp> - - int main(int argc, char *argv[]) ---- src/error_correct_reads.hpp 2018-04-21 14:26:10.091228666 +0200 -+++ src/error_correct_reads.hpp 2018-04-21 14:27:09.792795853 +0200 -@@ -2,12 +2,12 @@ - #define __ERROR_CORRECT_READS_HPP__ - - #include <config.h> --#include <jellyfish/err.hpp> --#include <jellyfish/mapped_file.hpp> --#include <jellyfish/invertible_hash_array.hpp> --#include <jellyfish/allocators_mmap.hpp> --#include <jellyfish/parse_read.hpp> --#include <jellyfish/thread_exec.hpp> -+#include <jellyfish1/err.hpp> -+#include <jellyfish1/mapped_file.hpp> -+#include <jellyfish1/invertible_hash_array.hpp> -+#include <jellyfish1/allocators_mmap.hpp> -+#include <jellyfish1/parse_read.hpp> -+#include <jellyfish1/thread_exec.hpp> - #include <iostream> - #include <fstream> - #include <assert.h> ---- configure.ac.ori 2018-04-21 15:00:35.225439196 +0200 -+++ configure.ac 2018-04-21 15:01:37.977086449 +0200 -@@ -28,7 +28,7 @@ - JELLYFISH_VERSION=$(pkg-config --modversion jellyfish-1.1) - AC_SUBST([JELLYFISH_VERSION]) - AC_ARG_VAR([JELLYFISH], [Jellyfish executable absolute path (default to looking in PATH)]) --AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish], [false])]) -+AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish1], [false])]) - - AC_ARG_VAR([JF_LIB_PATH], [Append this path to LD_LIBRARY_PATH in quorum]) - -@@ -47,7 +47,7 @@ - # --with-relative-jf-path - AC_ARG_WITH([relative-jf-path], - [AC_HELP_STRING([--with-relative-jf-path], [relative path from quorum to jellyfish (use an absolute path if not given. default to "." if given with no argument)])], -- [case "$withval" in (yes) with_relative_jf_path="jellyfish" ;; (no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish ;; esac], -+ [case "$withval" in (yes) with_relative_jf_path="jellyfish1" ;; (no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish1 ;; esac], - [with_relative_jf_path= ]) - AC_SUBST([RELATIVE_JF_PATH], $with_relative_jf_path) - AM_CONDITIONAL([HAVE_RELATIVE_JF_PATH], [test x$with_relative_jf_path != x]) diff --git a/sci-biology/quorum/metadata.xml b/sci-biology/quorum/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/quorum/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/quorum/quorum-1.1.1.ebuild b/sci-biology/quorum/quorum-1.1.1.ebuild deleted file mode 100644 index 4af286fcb..000000000 --- a/sci-biology/quorum/quorum-1.1.1.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Correct substitution errors in Illumina reads" -HOMEPAGE="http://www.genome.umd.edu/quorum.html - https://github.com/gmarcais/Quorum"; -SRC_URI="https://github.com/gmarcais/Quorum/releases/download/v${PV}/${P}.tar.gz"; - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=">=sci-biology/jellyfish-2.1.4:2" -RDEPEND="${DEPEND}" - -src_prepare() { - default - # fix jellyfish include path - find -type f -name "*.cc" -exec sed -i -e 's/<jellyfish\//<jellyfish2\//g' {} + || die - find -type f -name "*.hpp" -exec sed -i -e 's/<jellyfish\//<jellyfish2\//g' {} + || die -} - -src_configure(){ - econf --enable-relative-paths --with-relative-jf-path - default -}
