gentoo resync : 25.11.2020

7 files changed, 0 insertions, 363 deletions

diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
deleted file mode 100644
index 0749a737c777..000000000000
--- a/sci-biology/amos/Manifest
+++ /dev/null
@@ -1,8 +0,0 @@
-AUX amos-3.1.0-fix-build-system.patch 3132 BLAKE2B a7758991b5916cec6e9a2a39ee55beef73d14c19b7154ab2ced8e41eca411d1b6cacda5b7388e3ee48f330e489e4012660b3c08383c423a8553d283cd1cc4764 SHA512 b23c168c166f8a1dad89d1b25536a59be3e68a6478cef3db5664dc901cef0547213a8622a72ee1a2e1d5b8930c65d95e309573f903423e8fb80fb7312d89f863
-AUX amos-3.1.0-gcc-4.7.patch 400 BLAKE2B af160452d1bf52df204156dc9039645483c0ee349b96c2562eba4608695ac76b308c9cc2bc82a55401b3d56c33c4d2bae9e07a0a62ed4a3b15becb8f95ecda7f SHA512 3777885d5cd5edcb881abfbe1580092e073311797bd4776cd3ec9d27b634339718238be7f452f1ea1a0aea5fb9f6059d6b6f6a47bc2a0fb6d1811a2ec51a0835
-AUX amos-3.1.0-goBambus2.py-indent-and-cleanup.patch 1057 BLAKE2B fde1011da762750140f8880968c952b275d625f92b43ee8c35aaa23b687cc8d6cda441aa7b7cc883a67efe2a0d4a9cc13ee9f6b3663fef9f8274693350fe8e87 SHA512 5d2a0d4b222a23f30db560937b1c0e447f61dc786e097b259696fa41dca1e57a17a1e684bbd9fa9ddcee1334f7e6e3a91ccb7567d4fe079c3bdb3bb54034d11f
-AUX amos-3.1.0-qa-Wformat.patch 4511 BLAKE2B 64064175db625a098a528f0c8036196968c58dae445edd3c98fc5627e3a84d593abc438958573ef7a28193d0d2fc76db30fe16a180a383dec9bae5084305505d SHA512 de0382f9128b46fef8e87d14de75bbc9f0af3e8bcbb915edab26a883186109ab29ddbb31c5cf70fc8d37700abe36fb73a7bdca46c29672052d01ebebffd52abe
-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
-EBUILD amos-3.1.0-r4.ebuild 1110 BLAKE2B 4730d6a04ba727fd72ea825c6c57d65079ae9ddb29411f0a26aa94653309364ddec742104783044549adc2a60f06a7452f76e392145aa02db472042dde05e1d5 SHA512 7cb40d45dabc4e6cc188d3edf8347f34578d1f955b2d522273f3b551be6974023145e35a443f0e4495d70746aa40b6c451cedf999c102f1f8f7ffbab09748d61
-MISC metadata.xml 345 BLAKE2B 750928cf3e96c24e2af8e84d5889100c1954eb140596368dc00d479f63898c82e3bb0e07a9e970c6c12eb36ed3ae84c6bcc7913cf3ed56e2d71120185d24a4f0 SHA512 a31ba5660e524b70517f2644bb929d4bc0428d1ea682752ca2ddefd3b5a8a5c8aabf7a9877fa61e8fe12599da65e9f0a6c1e7db90d61729e26c33b76303ff497
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 0dbcaffd81da..000000000000
--- 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 9c824dd2f122..000000000000
--- 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 de2a41184c52..000000000000
--- 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 97a8f59d0208..000000000000
--- 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 13f4eeb247a1..000000000000
--- 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 2668bce2ac8a..000000000000
--- 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>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">amos</remote-id>
-  </upstream>
-</pkgmetadata>