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sci-biology/amos: Remove last-rited pkg

Browse Source 
Closes: https://bugs.gentoo.org/735448
Signed-off-by: Michał Górny <mgorny@gentoo.org>
This commit is contained in:
Michał Górny
2020-10-09 09:34:28 +02:00
parent 96c3a9acc9
commit 1df82e97d5
8 changed files with 0 additions and 358 deletions
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1
profiles/package.mask
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@@ -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 <arfrever.fta@gmail.com> (2020-09-01)
# Mismatched version (bug #695022). Masked to force upgrade to 2.0.4_pre20200306162733.

2
sci-biology/amos/Manifest
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@@ -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

52
sci-biology/amos/amos-3.1.0-r4.ebuild
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@@ -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
}

116
sci-biology/amos/files/amos-3.1.0-fix-build-system.patch
View File

@@ -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

15
sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
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@@ -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;

25
sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
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@@ -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)
-)

136
sci-biology/amos/files/amos-3.1.0-qa-Wformat.patch
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@@ -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 {

11
sci-biology/amos/metadata.xml
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@@ -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>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
<upstream>
<remote-id type="sourceforge">amos</remote-id>
</upstream>
</pkgmetadata>