forked from gentoo/gentoo
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
dev-perl/librg-utils-perl: Add tests, fixed defined(@array)
- EAPI6 - Add basic compile test - fix defined(@array) bug exposed by basic compile test - Clearly nobody is actually using this. Package-Manager: Portage-2.3.8, Repoman-2.3.3
- Loading branch information
1 parent
5efa970
commit aadc48d
Showing
2 changed files
with
219 additions
and
0 deletions.
There are no files selected for viewing
160 changes: 160 additions & 0 deletions
160
dev-perl/librg-utils-perl/files/librg-utils-perl-1.0.43-defined-array.patch
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,160 @@ | ||
| From 73e9e3126de1ac485462284fd1d97cb2ea3b09e8 Mon Sep 17 00:00:00 2001 | ||
| From: Kent Fredric <[email protected]> | ||
| 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 | ||
|
|
59 changes: 59 additions & 0 deletions
59
dev-perl/librg-utils-perl/librg-utils-perl-1.0.43-r1.ebuild
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
| } |