commit: 1df82e97d59d38e7705fffc949fa8a5d242ea471 Author: Michał Górny <mgorny <AT> gentoo <DOT> org> AuthorDate: Fri Oct 9 07:34:28 2020 +0000 Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> CommitDate: Fri Oct 9 07:35:01 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1df82e97
sci-biology/amos: Remove last-rited pkg Closes: https://bugs.gentoo.org/735448 Signed-off-by: Michał Górny <mgorny <AT> gentoo.org> profiles/package.mask | 1 - sci-biology/amos/Manifest | 2 - sci-biology/amos/amos-3.1.0-r4.ebuild | 52 -------- .../amos/files/amos-3.1.0-fix-build-system.patch | 116 ------------------ sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 --- ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 ---- sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch | 136 --------------------- sci-biology/amos/metadata.xml | 11 -- 8 files changed, 358 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index f8f963cefb2..5c533d582fd 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -514,7 +514,6 @@ net-misc/pssh net-misc/ris-linux net-wireless/mousejack net-wireless/python-wifi -sci-biology/amos # Arfrever Frehtes Taifersar Arahesis <[email protected]> (2020-09-01) # Mismatched version (bug #695022). Masked to force upgrade to 2.0.4_pre20200306162733. diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest deleted file mode 100644 index 1dcaaed1bb9..00000000000 --- a/sci-biology/amos/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST amos-3.1.0-fix-c++14.patch.bz2 8033 BLAKE2B 942248f64906253205392df71010bf41105d2985fc8112e7443975d776cc484a4e2b6cf34284d4c384145bf32601892c06f156a0b0ccf0f2ce721de242e02e9b SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634 -DIST amos-3.1.0.tar.gz 2094268 BLAKE2B b9fb80d4e7b7e9e7769081c2680a3cba26591f00a4d9fdb17ad602e581dea5e8e2add4b0d9d3821a7f8a4ec1a45dfd867037baf35ecd401584f030c86b2b0f83 SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 diff --git a/sci-biology/amos/amos-3.1.0-r4.ebuild b/sci-biology/amos/amos-3.1.0-r4.ebuild deleted file mode 100644 index 0dbcaffd81d..00000000000 --- a/sci-biology/amos/amos-3.1.0-r4.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools flag-o-matic python-single-r1 - -DESCRIPTION="A Modular, Open-Source whole genome assembler" -HOMEPAGE="http://amos.sourceforge.net/"; -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz - https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2"; - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="" -RDEPEND="${DEPEND} - ${PYTHON_DEPS} - dev-perl/DBI - dev-perl/Statistics-Descriptive - sci-biology/mummer" - -PATCHES=( - "${FILESDIR}"/${P}-gcc-4.7.patch - "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch - "${WORKDIR}"/${P}-fix-c++14.patch - "${FILESDIR}"/${P}-qa-Wformat.patch - "${FILESDIR}"/${P}-fix-build-system.patch -) - -src_prepare() { - default - eautoreconf - - # prevent GCC 6 log pollution due - # to hash_map deprecation in C++11 - append-cxxflags -Wno-cpp -} - -src_configure() { - econf --with-qmake-qt4=no -} - -src_install() { - default - python_fix_shebang "${ED%/}"/usr/bin/goBambus2 -} diff --git a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch deleted file mode 100644 index 9c824dd2f12..00000000000 --- a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch +++ /dev/null @@ -1,116 +0,0 @@ -* Use proper AR and not just 'ar' -* Fix build system to build in parallel - ---- a/configure.ac -+++ b/configure.ac -@@ -34,6 +34,7 @@ - AC_PROG_INSTALL - AC_PROG_LN_S - AC_PROG_RANLIB -+AM_PROG_AR - AC_PROG_CPP - AC_PATH_PROG(PERL, [perl], [:]) - AC_PATH_PROG(PYTHON, [python], [:]) ---- a/src/Align/Makefile.am -+++ b/src/Align/Makefile.am -@@ -133,7 +133,7 @@ - - ##-- hash-overlap - hash_overlap_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -172,7 +172,7 @@ - - ##-- make-consensus - make_consensus_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -182,7 +182,7 @@ - - ##-- make-consensus_poly - make_consensus_poly_LDADD = \ -- $(top_builddir)/src/Align/libAlign_poly.a \ -+ libAlign_poly.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -192,7 +192,7 @@ - - ##-- maligntest - maligntest_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -202,7 +202,7 @@ - - ##-- merge-contigs - merge_contigs_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -235,7 +235,7 @@ - - ##-- show-ma-asm - show_ma_asm_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a - show_ma_asm_SOURCES = \ -@@ -261,7 +261,7 @@ - - ##-- simple-overlap - simple_overlap_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ -@@ -272,7 +272,7 @@ - - ##-- test-align - test_align_LDADD = \ -- $(top_builddir)/src/Align/libAlign.a \ -+ libAlign.a \ - $(top_builddir)/src/CelMsg/libCelMsg.a \ - $(top_builddir)/src/Slice/libSlice.a \ - $(top_builddir)/src/Common/libCommon.a \ ---- a/src/Bambus/Bundler/Makefile.am -+++ b/src/Bambus/Bundler/Makefile.am -@@ -47,7 +47,7 @@ - clk.cc - - MarkRepeats_LDADD = \ -- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ -+ libBundler.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a \ - $(top_builddir)/src/GNU/libGNU.a -@@ -55,7 +55,7 @@ - MarkRepeats.cc - - OrientContigs_LDADD = \ -- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ -+ libBundler.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a \ - $(top_builddir)/src/GNU/libGNU.a -@@ -63,7 +63,7 @@ - OrientContigs.cc - - FilterEdgesByCluster_LDADD = \ -- $(top_builddir)/src/Bambus/Bundler/libBundler.a \ -+ libBundler.a \ - $(top_builddir)/src/Common/libCommon.a \ - $(top_builddir)/src/AMOS/libAMOS.a \ - $(top_builddir)/src/GNU/libGNU.a diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch deleted file mode 100644 index de2a41184c5..00000000000 --- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - src/Align/find-tandem.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc -index ddf1cab..a29e21e 100644 ---- a/src/Align/find-tandem.cc -+++ b/src/Align/find-tandem.cc -@@ -7,6 +7,7 @@ - #include <vector> - #include <ctime> - #include <sys/time.h> -+#include <unistd.h> - using namespace std; - - const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch deleted file mode 100644 index 97a8f59d020..00000000000 --- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch +++ /dev/null @@ -1,25 +0,0 @@ ---- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 -+++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 -@@ -1,7 +1,7 @@ - #pipeline script for assembly + Bambus 2 - #contributed by Todd J Treangen - --import string, sys, os, subprocess#, spincursor -+import sys, os, subprocess#, spincursor - - RED = "\033[0;31m" - GREEN = "\033[0;32m" -@@ -360,7 +360,7 @@ - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) - -- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) -+ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) - - if xopt_dict["verbose"] == 1: - print "10) running OutputResults" -@@ -388,4 +388,3 @@ - else: - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) --) diff --git a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch b/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch deleted file mode 100644 index 13f4eeb247a..00000000000 --- a/sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch +++ /dev/null @@ -1,136 +0,0 @@ -Fix QA warnings, due to using incorrect format specifiers in printf: -* contig-cmp.cc:237:50: warning: format ‘%u’ expects argument of type ‘unsigned int’, -* but argument 3 has type ‘std::vector<Contig_t>::size_type {aka long unsigned int}’ [-Wformat=] -* fprintf (stderr, "%u b contigs\n", b . size ()); - ---- a/src/Align/align.cc -+++ b/src/Align/align.cc -@@ -1936,7 +1936,7 @@ - n = align . size (); - con = consensus . c_str (); - -- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); -+ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); - - for (i = 0; i < n; i ++) - { -@@ -3936,7 +3936,7 @@ - } - - // Array of sum of quality scores in the slice for A,C,G,T,- resp. -- for (j = 0; j < 6; j ++) -+ for (j = 0; j < 5; j ++) - qvsum [j] = 0; - - int nof_ambiguities = 0; ---- a/src/Align/align_poly.cc -+++ b/src/Align/align_poly.cc -@@ -1761,7 +1761,7 @@ - n = align . size (); - con = consensus . c_str (); - -- fprintf (fp, "\nConsensus len = %d\n", consensus . length ()); -+ fprintf (fp, "\nConsensus len = %zu\n", consensus . length ()); - for (i = 0; i < n; i ++) - { - fprintf (fp, "\nString #%d:\n", i); ---- a/src/Align/count-qmers.cc -+++ b/src/Align/count-qmers.cc -@@ -191,8 +191,8 @@ - - PrintMers(mer_table, min_count); - -- fprintf(stderr, "reporter:counter:asm,reads_total,%ld\n", COUNT); -- fprintf(stderr, "reporter:counter:asm,reads_bp,%ld\n", LEN); -+ fprintf(stderr, "reporter:counter:asm,reads_total,%lld\n", COUNT); -+ fprintf(stderr, "reporter:counter:asm,reads_bp,%lld\n", LEN); - } - catch (Exception_t & e) - { ---- a/src/Align/kmer-cov.cc -+++ b/src/Align/kmer-cov.cc -@@ -485,7 +485,7 @@ - Kmer_Len = s . length (); - else if (Kmer_Len != int (s . length ())) - { -- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", -+ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", - s . c_str (), s . length (), Kmer_Len); - Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); - } ---- a/src/Align/kmer-cov-plot.cc -+++ b/src/Align/kmer-cov-plot.cc -@@ -316,7 +316,7 @@ - } - else if (Kmer_Len != int (s . length ())) - { -- sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %d instead of %d", -+ sprintf (Clean_Exit_Msg_Line, "New kmer \"%s\" length is %zu instead of %d", - s . c_str (), s . length (), Kmer_Len); - Clean_Exit (Clean_Exit_Msg_Line, __FILE__, __LINE__); - } ---- a/src/Align/make-consensus.cc -+++ b/src/Align/make-consensus.cc -@@ -303,7 +303,7 @@ - break; - } - -- sprintf (sid, "%ld", ++layout_id); -+ sprintf (sid, "%u", ++layout_id); - cid = string (sid); - ID_t lid = layout.getIID (); - if (lid == 0) ---- a/src/Align/make-consensus_poly.cc -+++ b/src/Align/make-consensus_poly.cc -@@ -279,7 +279,7 @@ - break; - } - -- sprintf(sid, "%ld", ++layout_id); -+ sprintf(sid, "%u", ++layout_id); - cid = string(sid); - ID_t lid = layout.getIID(); - if (lid == 0) { ---- a/src/Align/simple-overlap.cc -+++ b/src/Align/simple-overlap.cc -@@ -422,7 +422,7 @@ - "Options:\n" - " -a Also show alignments of overlaps \n" - " -E <x> Maximum error rate for overlaps is <x>\n" -- " e.g., -E 0.06 for 6% error rate\n" -+ " e.g., -E 0.06 for 6%% error rate\n" - " -F Input is a fasta file\n" - " -h Print this usage message\n" - " -o <n> Set minimum overlap length to <n>\n" ---- a/src/Compare/contig-cmp.cc -+++ b/src/Compare/contig-cmp.cc -@@ -145,7 +145,7 @@ - - fclose (fp); - -- fprintf (stderr, "%u a contigs\n", a . size ()); -+ fprintf (stderr, "%zu a contigs\n", a . size ()); - vector <Unitig_t> a_contig (max_id + 1); - n = a . size (); - for (i = 0; i < n; i ++) -@@ -234,7 +234,7 @@ - - fclose (fp); - -- fprintf (stderr, "%u b contigs\n", b . size ()); -+ fprintf (stderr, "%zu b contigs\n", b . size ()); - vector <Unitig_t> b_contig (max_id + 1); - n = b . size (); - for (i = 0; i < n; i ++) ---- a/src/Staden/progs/trace_convert.c -+++ b/src/Staden/progs/trace_convert.c -@@ -6,6 +6,9 @@ - #include "traceType.h" - #include "seqIOABI.h" - -+#include <fcntl.h> -+#include <unistd.h> -+ - static char fileIdentifier[] = "$Id$"; - - struct opts { diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml deleted file mode 100644 index 2668bce2ac8..00000000000 --- a/sci-biology/amos/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">amos</remote-id> - </upstream> -</pkgmetadata>
