diff options
Diffstat (limited to 'dev-perl/librg-utils-perl')
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 +} |