gentoo resync : 14.07.2018

4 files changed, 0 insertions, 231 deletions

diff --git a/dev-perl/librg-utils-perl/Manifest b/dev-perl/librg-utils-perl/Manifest
deleted file mode 100644
index f27ff3abcbc7..000000000000
--- a/dev-perl/librg-utils-perl/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX librg-utils-perl-1.0.43-defined-array.patch 6546 BLAKE2B eea57e7a175b0f1ef2963232e1db469ce6674dfe7d569bbedc362e4e4f05eba3ce5722ee418cc099c52433dd5b5426b2ef2287fbc88fac0e979b3c7a059a6353 SHA512 232c9f2a45c3c98a0d1019afe5380a33b079a615d1e3f0c7f563575fe3d5b0efc7ce6b30473dfd6a49ab9c4695797bf71ea4507ba20beb4bafe9e0d320ca09c1
-DIST librg-utils-perl-1.0.43.tar.gz 222433 BLAKE2B 8dad61ead9f33dc0ac3f3767a1f5e277ee65ebe8c3f97c4e318588303ea16c227cc22c22a7f085ca4fd0ae6ff60d0ce06e84682523f074c2717d0c4814b12143 SHA512 90480f8292e09277263808036e729b2e7e692a186b682466f491d5be90e5fa2accc11b1a1b694b32113b91af4ad56e9ccdf25e6c596759b9c4d45322687c1fa1
-EBUILD librg-utils-perl-1.0.43-r1.ebuild 1259 BLAKE2B b5b23ac8e6e09c0c283dba94b451badab82427559c72b9cc5fb342a886a3306e6fe1547fc717cd5edfd2c06518b9dbd4277f5694d50c723b4fd896ee70f27f5c SHA512 e7744e45c1b11cd066ef66f7a3ecc6f4c7826b89a459cfb3ac19bbb4fa3295ce896739752d63de820b090806224cea87544471b852a5b445812e5bc0da688526
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/dev-perl/librg-utils-perl/files/librg-utils-perl-1.0.43-defined-array.patch b/dev-perl/librg-utils-perl/files/librg-utils-perl-1.0.43-defined-array.patch
deleted file mode 100644
index 3042d3af5774..000000000000
--- a/dev-perl/librg-utils-perl/files/librg-utils-perl-1.0.43-defined-array.patch
+++ /dev/null
@@ -1,160 +0,0 @@
-From 73e9e3126de1ac485462284fd1d97cb2ea3b09e8 Mon Sep 17 00:00:00 2001
-From: Kent Fredric <kentnl@gentoo.org>
-Date: Mon, 30 Oct 2017 03:36:42 +1300
-Subject: Fix deprecated use of defined(@array)
-
----
- lib/RG/Utils/Conv_hssp2saf.pm |  4 ++--
- lib/RG/Utils/Copf.pm          | 14 +++++++-------
- lib/RG/Utils/Hssp_filter.pm   | 14 +++++++-------
- 3 files changed, 16 insertions(+), 16 deletions(-)
-
-diff --git a/lib/RG/Utils/Conv_hssp2saf.pm b/lib/RG/Utils/Conv_hssp2saf.pm
-index 20bd803..f4a309e 100644
---- a/lib/RG/Utils/Conv_hssp2saf.pm
-+++ b/lib/RG/Utils/Conv_hssp2saf.pm
-@@ -604,7 +604,7 @@ sub hsspRdAli {
- 				#                  of all numbers wanted (i.e. = $want[M])
-     undef @ptr_numFin2numWant;	# $ptr[M]=   N   : see previous, the other way around!
- 
--    $#want=0                    if (! defined @want);
-+    $#want=0                    if (!@want);
-     $LreadAll=0; 
- 				# ------------------------------
- 				# digest input
-@@ -657,7 +657,7 @@ sub hsspRdAli {
- 				# sort the array
-     @wantNum= sort bynumber (@wantNum);
- 				# too many wanted
--    if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
-+    if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
- 	$#tmp=0; 
- 	foreach $want (@wantNum){
- 	    if ($want <= $locNum[$#locNum]){
-diff --git a/lib/RG/Utils/Copf.pm b/lib/RG/Utils/Copf.pm
-index eb43700..c132f90 100644
---- a/lib/RG/Utils/Copf.pm
-+++ b/lib/RG/Utils/Copf.pm
-@@ -2112,7 +2112,7 @@ sub brIniSet {
- 	    $par{$kwd}=$par{"dirOut"}.$par{$kwd} if (-d $par{"dirOut"});}}
- 				# ------------------------------
- 				# push array of output files
--    $#fileOut=0 if (! defined @fileOut);
-+    $#fileOut=0 if (!@fileOut);
-     foreach $kwd (@kwdFileOut){
- 	push(@fileOut,$par{$kwd});}
- 				# ------------------------------
-@@ -2240,7 +2240,7 @@ sub brIniWrt {
- 	    printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}}
- 				# ------------------------------
- 				# input files
--    if    (defined @fileIn && $#fileIn>1){
-+    if    (@fileIn && $#fileIn>1){
- 				# get dirs
- 	$#tmpdir=0; undef %tmpdir;
- 	foreach $file (@fileIn){
-@@ -2262,10 +2262,10 @@ sub brIniWrt {
- 		$tmp=$fileIn[$it2]; $tmp=~s/^.*\///g;
- 		printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;}
- 	    print $fhTraceLocSbr "\n";}}
--    elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
-+    elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
- 	$tmp=0;
- 	$tmp=$fileIn    if (defined $fileIn && $fileIn);
--	$tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1);
-+	$tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1);
- 	print  $fhTraceLocSbr "--- \n";
- 	printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;}
-     print  $fhTraceLocSbr "--- \n";
-@@ -4737,7 +4737,7 @@ sub getSysARCH {
- 				# ------------------------------
- 				# (1) find in arguments passed
- 				# ------------------------------
--#    if (defined @argLoc && $#argLoc > 0) {
-+#    if (@argLoc && $#argLoc > 0) {
- #	foreach $arg (@argLoc) {
- #	    if ($arg=~/^ARCH=(\S+)/i) {
- #		$archFound=$1;
-@@ -5022,7 +5022,7 @@ sub hsspRdAli {
- 				#                  of all numbers wanted (i.e. = $want[M])
-     undef @ptr_numFin2numWant;	# $ptr[M]=   N   : see previous, the other way around!
- 
--    $#want=0                    if (! defined @want);
-+    $#want=0                    if (!@want);
-     $LreadAll=0; 
- 				# ------------------------------
- 				# digest input
-@@ -5075,7 +5075,7 @@ sub hsspRdAli {
- 				# sort the array
-     @wantNum= sort bynumber (@wantNum);
- 				# too many wanted
--    if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
-+    if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
- 	$#tmp=0; 
- 	foreach $want (@wantNum){
- 	    if ($want <= $locNum[$#locNum]){
-diff --git a/lib/RG/Utils/Hssp_filter.pm b/lib/RG/Utils/Hssp_filter.pm
-index 0172713..1e31573 100644
---- a/lib/RG/Utils/Hssp_filter.pm
-+++ b/lib/RG/Utils/Hssp_filter.pm
-@@ -1436,7 +1436,7 @@ sub brIniSet {
- 	    $par{"$kwd"}=$par{"dirOut"}.$par{"$kwd"} if (-d $par{"dirOut"});}}
- 				# ------------------------------
- 				# push array of output files
--    $#fileOut=0 if (! defined @fileOut);
-+    $#fileOut=0 if (!@fileOut);
-     foreach $kwd (@kwdFileOut){
- 	push(@fileOut,$par{"$kwd"});}
- 				# ------------------------------
-@@ -1564,7 +1564,7 @@ sub brIniWrt {
- 	    printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{"$kwd"};}}
- 				# ------------------------------
- 				# input files
--    if    (defined @fileIn && $#fileIn>1){
-+    if    (@fileIn && $#fileIn>1){
- 				# get dirs
- 	$#tmpdir=0; undef %tmpdir;
- 	foreach $file (@fileIn){
-@@ -1586,10 +1586,10 @@ sub brIniWrt {
- 		$tmp=$fileIn[$it2]; $tmp=~s/^.*\///g;
- 		printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;}
- 	    print $fhTraceLocSbr "\n";}}
--    elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
-+    elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
- 	$tmp=0;
- 	$tmp=$fileIn    if (defined $fileIn && $fileIn);
--	$tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1);
-+	$tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1);
- 	print  $fhTraceLocSbr "--- \n";
- 	printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;}
-     print  $fhTraceLocSbr "--- \n";
-@@ -1816,7 +1816,7 @@ sub getSysARCH {
- 				# ------------------------------
- 				# (1) find in arguments passed
- 				# ------------------------------
--    if (defined @argLoc && $#argLoc > 0) {
-+    if (@argLoc && $#argLoc > 0) {
- 	foreach $arg (@argLoc) {
- 	    if ($arg=~/^ARCH=(\S+)/i) {
- 		$archFound=$1;
-@@ -2318,7 +2318,7 @@ sub hsspFilterMarkFile {
- 				# check arguments
-     return(0,"*** $sbrName: not def fileInLoc!")          if (! defined $fileInLoc);
-     return(0,"*** $sbrName: not def fileOutLoc!")         if (! defined $fileOutLoc);
--    return(0,"*** $sbrName: not def \@takeLoc!")          if (! defined @takeLoc || $#takeLoc<1);
-+    return(0,"*** $sbrName: not def \@takeLoc!")          if (! @takeLoc || $#takeLoc<1);
-     return(0,"*** $sbrName: miss in file '$fileInLoc'!")  if (! -e $fileInLoc);
- 				# open files
-     &open_file("$fhinLoc","$fileInLoc") ||
-@@ -2371,7 +2371,7 @@ sub hsspGetFile {
-     $#dir2=$Lok=0;
-     return(0,"no input file")   if (! defined $fileInLoc);
-     $chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g;
--    $#dir=0                     if (! defined @dir);
-+    $#dir=0                     if (!@dir);
-     $Lscreen=0                  if (! defined $Lscreen);
- 				# passed dir instead of Lscreen
-     if (-d $Lscreen) { @dir=($Lscreen,@dir);
--- 
-2.14.3
-
diff --git a/dev-perl/librg-utils-perl/librg-utils-perl-1.0.43-r1.ebuild b/dev-perl/librg-utils-perl/librg-utils-perl-1.0.43-r1.ebuild
deleted file mode 100644
index 88b8d7cf6e04..000000000000
--- a/dev-perl/librg-utils-perl/librg-utils-perl-1.0.43-r1.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit perl-module
-
-DESCRIPTION="Parsers and format conversion utilities used by (e.g.) profphd"
-HOMEPAGE="http://rostlab.org/"
-SRC_URI="ftp://rostlab.org/librg-utils-perl/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	dev-perl/List-MoreUtils"
-DEPEND="${RDEPEND}
-	sci-libs/profphd-utils
-	dev-perl/Module-Build
-"
-PATCHES=("${FILESDIR}/${P}-defined-array.patch")
-src_configure() {
-	econf
-	perl-module_src_configure
-}
-
-src_install() {
-	rm mat/Makefile* || die
-	perl-module_src_install
-	insinto /usr/share/${PN}
-	doins -r mat
-	exeinto /usr/share/${PN}
-	doexe *.pl dbSwiss
-	doman blib/libdoc/*
-}
-src_test() {
-	local MODULES=(
-		"RG::Utils::Conv_hssp2saf"
-		"RG::Utils::Hssp_filter"
-		"RG::Utils::Copf"
-	)
-	local failed=()
-	for dep in "${MODULES[@]}"; do
-		ebegin "Compile testing ${dep}"
-			perl -Mblib="${S}" -M"${dep} ()" -e1
-		eend $? || failed+=( "$dep" )
-	done
-	if [[ ${failed[@]} ]]; then
-		echo
-		eerror "One or more modules failed compile:";
-		for dep in "${failed[@]}"; do
-			eerror "  ${dep}"
-		done
-		die "Failing due to module compilation errors";
-	fi
-	perl-module_src_test
-}
diff --git a/dev-perl/librg-utils-perl/metadata.xml b/dev-perl/librg-utils-perl/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/dev-perl/librg-utils-perl/metadata.xml
+++ /dev/null
@@ -1,8 +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>
-</pkgmetadata>