diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
| commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
| tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch | |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch')
| -rw-r--r-- | sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch | 108 |
1 files changed, 108 insertions, 0 deletions
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch new file mode 100644 index 000000000000..783d0530aa7a --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch @@ -0,0 +1,108 @@ +* Fix ancient perl 4 modules that are long gone. +* Fix perl shebangs to be portable and usable on Prefix. +See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ + +--- a/squid/Testsuite/bug-1-sfetch-paths ++++ b/squid/Testsuite/bug-1-sfetch-paths +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test for bug #1: sfetch/SSI path bug. + # sfetch can't follow paths out of current directory if it's using +--- a/squid/Testsuite/x-base-afetch ++++ b/squid/Testsuite/x-base-afetch +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-alistat ++++ b/squid/Testsuite/x-base-alistat +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-seqstat ++++ b/squid/Testsuite/x-base-seqstat +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-sfetch ++++ b/squid/Testsuite/x-base-sfetch +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-shuffle ++++ b/squid/Testsuite/x-base-shuffle +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-sindex ++++ b/squid/Testsuite/x-base-sindex +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/squid/Testsuite/x-base-sreformat ++++ b/squid/Testsuite/x-base-sreformat +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use testsuite; + +--- a/testsuite/sqc ++++ b/testsuite/sqc +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # sqc + # quality control script for exercising code, regression testing, +@@ -176,12 +176,11 @@ + # SRE, Tue Aug 6 11:16:39 2002 + # CVS $Id: sqc,v 1.3 2003/01/05 23:40:57 eddy Exp $ + +-require "getopts.pl"; +-require "importenv.pl"; ++use Getopt::Std; + + # Parse our command line + # +-&Getopts('mp:r:v'); ++getopts('mp:r:v'); + if ($opt_m) { $do_memtest = 1; } + if ($opt_p) { push @prepdirs, $opt_p; } + if ($opt_r) { push @olddirs, $opt_r; } +@@ -506,7 +505,7 @@ + # + sub tempname { + my ($dir, $name, $suffix); +- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} ++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} + + foreach $suffix ("aa".."zz") { + $name = "$dir"."sre".$suffix.$$; +--- a/testsuite/test1-conversion.pl ++++ b/testsuite/test1-conversion.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test hmmconvert. + # |