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commit: aadc48d174804624649c8414d352091f72455f28 |
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Author: Kent Fredric <kentnl <AT> gentoo <DOT> org> |
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AuthorDate: Sun Oct 29 14:42:57 2017 +0000 |
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Commit: Kent Fredric <kentnl <AT> gentoo <DOT> org> |
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CommitDate: Sun Oct 29 15:07:06 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=aadc48d1 |
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|
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dev-perl/librg-utils-perl: Add tests, fixed defined(@array) |
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|
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- EAPI6 |
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- Add basic compile test |
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- fix defined(@array) bug exposed by basic compile test |
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- Clearly nobody is actually using this. |
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|
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Package-Manager: Portage-2.3.8, Repoman-2.3.3 |
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|
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.../librg-utils-perl-1.0.43-defined-array.patch | 160 +++++++++++++++++++++ |
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.../librg-utils-perl-1.0.43-r1.ebuild | 59 ++++++++ |
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2 files changed, 219 insertions(+) |
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|
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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 |
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new file mode 100644 |
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index 00000000000..3042d3af577 |
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--- /dev/null |
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+++ b/dev-perl/librg-utils-perl/files/librg-utils-perl-1.0.43-defined-array.patch |
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@@ -0,0 +1,160 @@ |
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+From 73e9e3126de1ac485462284fd1d97cb2ea3b09e8 Mon Sep 17 00:00:00 2001 |
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+From: Kent Fredric <kentnl@g.o> |
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+Date: Mon, 30 Oct 2017 03:36:42 +1300 |
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+Subject: Fix deprecated use of defined(@array) |
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+ |
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+--- |
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+ lib/RG/Utils/Conv_hssp2saf.pm | 4 ++-- |
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+ lib/RG/Utils/Copf.pm | 14 +++++++------- |
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+ lib/RG/Utils/Hssp_filter.pm | 14 +++++++------- |
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+ 3 files changed, 16 insertions(+), 16 deletions(-) |
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+ |
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+diff --git a/lib/RG/Utils/Conv_hssp2saf.pm b/lib/RG/Utils/Conv_hssp2saf.pm |
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+index 20bd803..f4a309e 100644 |
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+--- a/lib/RG/Utils/Conv_hssp2saf.pm |
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++++ b/lib/RG/Utils/Conv_hssp2saf.pm |
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+@@ -604,7 +604,7 @@ sub hsspRdAli { |
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+ # of all numbers wanted (i.e. = $want[M]) |
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+ undef @ptr_numFin2numWant; # $ptr[M]= N : see previous, the other way around! |
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+ |
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+- $#want=0 if (! defined @want); |
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++ $#want=0 if (!@want); |
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+ $LreadAll=0; |
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+ # ------------------------------ |
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+ # digest input |
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+@@ -657,7 +657,7 @@ sub hsspRdAli { |
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+ # sort the array |
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+ @wantNum= sort bynumber (@wantNum); |
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+ # too many wanted |
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+- if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ |
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++ if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ |
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+ $#tmp=0; |
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+ foreach $want (@wantNum){ |
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+ if ($want <= $locNum[$#locNum]){ |
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+diff --git a/lib/RG/Utils/Copf.pm b/lib/RG/Utils/Copf.pm |
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+index eb43700..c132f90 100644 |
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+--- a/lib/RG/Utils/Copf.pm |
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++++ b/lib/RG/Utils/Copf.pm |
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+@@ -2112,7 +2112,7 @@ sub brIniSet { |
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+ $par{$kwd}=$par{"dirOut"}.$par{$kwd} if (-d $par{"dirOut"});}} |
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+ # ------------------------------ |
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+ # push array of output files |
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+- $#fileOut=0 if (! defined @fileOut); |
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++ $#fileOut=0 if (!@fileOut); |
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+ foreach $kwd (@kwdFileOut){ |
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+ push(@fileOut,$par{$kwd});} |
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+ # ------------------------------ |
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+@@ -2240,7 +2240,7 @@ sub brIniWrt { |
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+ printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}} |
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+ # ------------------------------ |
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+ # input files |
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+- if (defined @fileIn && $#fileIn>1){ |
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++ if (@fileIn && $#fileIn>1){ |
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+ # get dirs |
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+ $#tmpdir=0; undef %tmpdir; |
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+ foreach $file (@fileIn){ |
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+@@ -2262,10 +2262,10 @@ sub brIniWrt { |
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+ $tmp=$fileIn[$it2]; $tmp=~s/^.*\///g; |
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+ printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;} |
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+ print $fhTraceLocSbr "\n";}} |
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+- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ |
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++ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ |
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+ $tmp=0; |
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+ $tmp=$fileIn if (defined $fileIn && $fileIn); |
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+- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1); |
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++ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1); |
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+ print $fhTraceLocSbr "--- \n"; |
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+ printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;} |
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+ print $fhTraceLocSbr "--- \n"; |
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+@@ -4737,7 +4737,7 @@ sub getSysARCH { |
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+ # ------------------------------ |
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+ # (1) find in arguments passed |
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+ # ------------------------------ |
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+-# if (defined @argLoc && $#argLoc > 0) { |
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++# if (@argLoc && $#argLoc > 0) { |
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+ # foreach $arg (@argLoc) { |
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+ # if ($arg=~/^ARCH=(\S+)/i) { |
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+ # $archFound=$1; |
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+@@ -5022,7 +5022,7 @@ sub hsspRdAli { |
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+ # of all numbers wanted (i.e. = $want[M]) |
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+ undef @ptr_numFin2numWant; # $ptr[M]= N : see previous, the other way around! |
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+ |
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+- $#want=0 if (! defined @want); |
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++ $#want=0 if (!@want); |
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+ $LreadAll=0; |
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+ # ------------------------------ |
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+ # digest input |
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+@@ -5075,7 +5075,7 @@ sub hsspRdAli { |
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+ # sort the array |
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+ @wantNum= sort bynumber (@wantNum); |
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+ # too many wanted |
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+- if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ |
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++ if (@wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){ |
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+ $#tmp=0; |
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+ foreach $want (@wantNum){ |
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+ if ($want <= $locNum[$#locNum]){ |
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+diff --git a/lib/RG/Utils/Hssp_filter.pm b/lib/RG/Utils/Hssp_filter.pm |
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+index 0172713..1e31573 100644 |
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+--- a/lib/RG/Utils/Hssp_filter.pm |
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++++ b/lib/RG/Utils/Hssp_filter.pm |
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+@@ -1436,7 +1436,7 @@ sub brIniSet { |
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+ $par{"$kwd"}=$par{"dirOut"}.$par{"$kwd"} if (-d $par{"dirOut"});}} |
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+ # ------------------------------ |
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+ # push array of output files |
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+- $#fileOut=0 if (! defined @fileOut); |
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++ $#fileOut=0 if (!@fileOut); |
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+ foreach $kwd (@kwdFileOut){ |
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+ push(@fileOut,$par{"$kwd"});} |
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+ # ------------------------------ |
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+@@ -1564,7 +1564,7 @@ sub brIniWrt { |
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+ printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{"$kwd"};}} |
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+ # ------------------------------ |
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+ # input files |
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+- if (defined @fileIn && $#fileIn>1){ |
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++ if (@fileIn && $#fileIn>1){ |
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+ # get dirs |
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+ $#tmpdir=0; undef %tmpdir; |
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+ foreach $file (@fileIn){ |
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+@@ -1586,10 +1586,10 @@ sub brIniWrt { |
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+ $tmp=$fileIn[$it2]; $tmp=~s/^.*\///g; |
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+ printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;} |
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+ print $fhTraceLocSbr "\n";}} |
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+- elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ |
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++ elsif ((@fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){ |
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+ $tmp=0; |
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+ $tmp=$fileIn if (defined $fileIn && $fileIn); |
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+- $tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1); |
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++ $tmp=$fileIn[1] if (! $tmp && @fileIn && $#fileIn==1); |
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+ print $fhTraceLocSbr "--- \n"; |
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+ printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;} |
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+ print $fhTraceLocSbr "--- \n"; |
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+@@ -1816,7 +1816,7 @@ sub getSysARCH { |
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+ # ------------------------------ |
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+ # (1) find in arguments passed |
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+ # ------------------------------ |
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+- if (defined @argLoc && $#argLoc > 0) { |
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++ if (@argLoc && $#argLoc > 0) { |
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+ foreach $arg (@argLoc) { |
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+ if ($arg=~/^ARCH=(\S+)/i) { |
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+ $archFound=$1; |
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+@@ -2318,7 +2318,7 @@ sub hsspFilterMarkFile { |
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+ # check arguments |
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+ return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc); |
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+ return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc); |
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+- return(0,"*** $sbrName: not def \@takeLoc!") if (! defined @takeLoc || $#takeLoc<1); |
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++ return(0,"*** $sbrName: not def \@takeLoc!") if (! @takeLoc || $#takeLoc<1); |
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+ return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc); |
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+ # open files |
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+ &open_file("$fhinLoc","$fileInLoc") || |
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+@@ -2371,7 +2371,7 @@ sub hsspGetFile { |
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+ $#dir2=$Lok=0; |
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+ return(0,"no input file") if (! defined $fileInLoc); |
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+ $chainLoc="";$idLoc=$fileInLoc;$idLoc=~s/^.*\///g; |
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+- $#dir=0 if (! defined @dir); |
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++ $#dir=0 if (!@dir); |
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+ $Lscreen=0 if (! defined $Lscreen); |
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+ # passed dir instead of Lscreen |
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+ if (-d $Lscreen) { @dir=($Lscreen,@dir); |
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+-- |
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+2.14.3 |
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+ |
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|
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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 |
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new file mode 100644 |
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index 00000000000..88b8d7cf6e0 |
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--- /dev/null |
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+++ b/dev-perl/librg-utils-perl/librg-utils-perl-1.0.43-r1.ebuild |
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@@ -0,0 +1,59 @@ |
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+# Copyright 1999-2017 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=6 |
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+ |
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+inherit perl-module |
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+ |
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+DESCRIPTION="Parsers and format conversion utilities used by (e.g.) profphd" |
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+HOMEPAGE="http://rostlab.org/" |
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+SRC_URI="ftp://rostlab.org/librg-utils-perl/${P}.tar.gz" |
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+ |
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+SLOT="0" |
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+LICENSE="GPL-2" |
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+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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+IUSE="" |
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+ |
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+RDEPEND=" |
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+ dev-perl/List-MoreUtils" |
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+DEPEND="${RDEPEND} |
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+ sci-libs/profphd-utils |
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+ dev-perl/Module-Build |
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+" |
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+PATCHES=("${FILESDIR}/${P}-defined-array.patch") |
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+src_configure() { |
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+ econf |
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+ perl-module_src_configure |
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+} |
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+ |
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+src_install() { |
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+ rm mat/Makefile* || die |
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+ perl-module_src_install |
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+ insinto /usr/share/${PN} |
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+ doins -r mat |
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+ exeinto /usr/share/${PN} |
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+ doexe *.pl dbSwiss |
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+ doman blib/libdoc/* |
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+} |
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+src_test() { |
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+ local MODULES=( |
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+ "RG::Utils::Conv_hssp2saf" |
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+ "RG::Utils::Hssp_filter" |
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+ "RG::Utils::Copf" |
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+ ) |
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+ local failed=() |
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+ for dep in "${MODULES[@]}"; do |
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+ ebegin "Compile testing ${dep}" |
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+ perl -Mblib="${S}" -M"${dep} ()" -e1 |
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+ eend $? || failed+=( "$dep" ) |
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+ done |
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+ if [[ ${failed[@]} ]]; then |
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+ echo |
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+ eerror "One or more modules failed compile:"; |
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+ for dep in "${failed[@]}"; do |
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+ eerror " ${dep}" |
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+ done |
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+ die "Failing due to module compilation errors"; |
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+ fi |
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+ perl-module_src_test |
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+} |
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