gentoo resync : 31.10.2017

3 files changed, 221 insertions, 0 deletions

diff --git a/dev-perl/librg-utils-perl/Manifest b/dev-perl/librg-utils-perl/Manifest
index 8ce5ebcfb4ce..ea6afd8532d5 100644
--- a/dev-perl/librg-utils-perl/Manifest
+++ b/dev-perl/librg-utils-perl/Manifest
@@ -1,4 +1,6 @@
+AUX librg-utils-perl-1.0.43-defined-array.patch 6546 SHA256 8343a9c9595259cea10162c76ba031039599595f86ad92793565e3f1a63bac81 SHA512 232c9f2a45c3c98a0d1019afe5380a33b079a615d1e3f0c7f563575fe3d5b0efc7ce6b30473dfd6a49ab9c4695797bf71ea4507ba20beb4bafe9e0d320ca09c1 WHIRLPOOL 0955f37e75c8a67ba4e99771d55c34273c97849b4e722deb62c38af19ca9f89a2ba114376397ec1571b5944e37b5699f7b304574e86c798f250d9bf733a96786
 DIST librg-utils-perl-1.0.43.tar.gz 222433 SHA256 961dda0196688e156a0702ff4609067a3454199ee1e537a5b9229ebe9310a260 SHA512 90480f8292e09277263808036e729b2e7e692a186b682466f491d5be90e5fa2accc11b1a1b694b32113b91af4ad56e9ccdf25e6c596759b9c4d45322687c1fa1 WHIRLPOOL d14dd27e9796022d9c0d76f87d0fa735ce5ae067476b01dc998ca592f564fdcce721430fb6dc4125a2f7d25bc8a1b345dcc99798ea8fdf0d2140c2eddcc95756
+EBUILD librg-utils-perl-1.0.43-r1.ebuild 1259 SHA256 7d2cd98ed1beeb788bcf5add4b88cb00dc4ca17badd496a6419472cc7b91bdb8 SHA512 e7744e45c1b11cd066ef66f7a3ecc6f4c7826b89a459cfb3ac19bbb4fa3295ce896739752d63de820b090806224cea87544471b852a5b445812e5bc0da688526 WHIRLPOOL 9bb24d70f2bb363e2fa5420ee99d3ed45fc2584c52353b40a4bbcc994f7b0ab20bb5fce01611e9716300fa3ebde06aeee9aff3767c0129cc8d6ddf6d278ef49b
 EBUILD librg-utils-perl-1.0.43.ebuild 719 SHA256 f37ff52101da37160865527074c0564540a11cb7fa91af5e12183fe9c13a5d19 SHA512 ac64bdecd85551f72fda5537908c52c41645c3e5371354d9dc0d91879553e5493cb7bf952b14e21782e73d4bb01f6d2b702cfb0d27c47ac32b01580841c6c57e WHIRLPOOL d5bc2496de9bd711172159c2e331283835b0a81acff524a1b3cf50dfceca185ec7ea02b250cc2c5cfdcf51c8aa4f06244501869f86500b50a7bd69a120901d44
 MISC ChangeLog 2456 SHA256 4517a04c0cef2eecd8cc90e567278769c999ce411879fb906b88f79e5d95693a SHA512 2aca12fcea6b94a1a28429d86719da6f23aef9f3e3218112a45e415c702c66ea770d8e4342d865d6b09d3807365901cd3689d63c02b86841362c2c7904db9393 WHIRLPOOL b223f8435f2374e9fe61f2eb13faa025e6018a37bbbed994eab7100e7a791d3a54d91797cea8002c5e1ae24b5115cd0b76d13de555c48b2f28486ab77522792a
 MISC ChangeLog-2015 658 SHA256 b02f04925ddb581e46ad5159a3c21cf901ca3f588239a13334562d9e3d095684 SHA512 748052dd8a4a6c1776a96b964aa8ec1d917dec66f66d905678d5110445993dcaa6c14498926bc8a17930343f02db9bef996be795c91b8c72b6e48dbf254ceda9 WHIRLPOOL 489697e800362f46ddf6a5b627d3e9a21ee89fe738be27daad41e547706c8e9a4f20986be58ca329864cfb8e64fe547b1fbf35a64c6eaebeff4dfc0fedac123f
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
new file mode 100644
index 000000000000..3042d3af5774
--- /dev/null
+++ b/dev-perl/librg-utils-perl/files/librg-utils-perl-1.0.43-defined-array.patch
@@ -0,0 +1,160 @@
+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
new file mode 100644
index 000000000000..88b8d7cf6e04
--- /dev/null
+++ b/dev-perl/librg-utils-perl/librg-utils-perl-1.0.43-r1.ebuild
@@ -0,0 +1,59 @@
+# 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
+}