diff options
Diffstat (limited to 'dev-perl/librg-utils-perl')
4 files changed, 231 insertions, 0 deletions
diff --git a/dev-perl/librg-utils-perl/Manifest b/dev-perl/librg-utils-perl/Manifest new file mode 100644 index 000000000000..f27ff3abcbc7 --- /dev/null +++ b/dev-perl/librg-utils-perl/Manifest @@ -0,0 +1,4 @@ +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 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 +} diff --git a/dev-perl/librg-utils-perl/metadata.xml b/dev-perl/librg-utils-perl/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/dev-perl/librg-utils-perl/metadata.xml @@ -0,0 +1,8 @@ +<?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> |