samtools,bcftools: Use SUBST to properly patch test script
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1c1c9244d6
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e17c741063
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@ -17,6 +17,12 @@ SUBST_STAGE.version= pre-configure
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SUBST_SED.version= -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
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SUBST_FILES.version= configure.ac
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SUBST_CLASSES+= bash
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SUBST_STAGE.bash= pre-configure
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SUBST_SED.bash+= -e 's|/bin/bash|${PREFIX}/bin/bash|'
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SUBST_SED.bash+= -e 's|\\/bin\\/bash|${PREFIX:S,/,\\\/,g}\\/bin\\/bash|'
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SUBST_FILES.bash= test/test.pl
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REPLACE_PERL+= misc/*.pl
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REPLACE_PERL+= misc/fix-broken-GATK-Double-vs-Integer
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REPLACE_PERL+= misc/plot-vcfstats
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@ -6,4 +6,3 @@ SHA512 (bcftools-1.10.2.tar.gz) = 12c004603db557ac69098e83ad3aaa5762b02b4718b79f
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Size (bcftools-1.10.2.tar.gz) = 2880994 bytes
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SHA1 (patch-Makefile) = 1f1397e9b0389a7b4fccc9eae87981e7ce1d7980
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SHA1 (patch-misc_run-roh.pl) = 8a29ee7b1001af6670955f174ce4dbab31f05659
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SHA1 (patch-test_test.pl) = 5fc3896d9013a6d5caa24a4d3e6798905d1243e1
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@ -1,42 +0,0 @@
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$NetBSD$
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# Portable bash path
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--- test/test.pl.orig 2020-07-21 20:47:32.977230067 +0000
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+++ test/test.pl
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@@ -610,7 +610,7 @@ sub _cmd
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else
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{
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# child
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- exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
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+ exec('bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
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}
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return ($? >> 8, join('',@out));
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}
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@@ -622,7 +622,7 @@ sub _cmd3
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my $pid = fork();
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if ( !$pid )
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{
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- exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o");
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+ exec('bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o");
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}
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waitpid($pid,0);
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@@ -1063,7 +1063,7 @@ sub test_usage
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my $command = $args{cmd};
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my $commandpath = $$opts{bin}."/".$command;
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my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
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- if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
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+ if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
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my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
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@@ -1118,7 +1118,7 @@ sub test_usage_subcommand
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my $subcommand = $args{subcmd};
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my $commandpath = $$opts{bin}."/".$command;
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my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");
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- if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
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+ if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; }
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my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
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@ -14,8 +14,14 @@ GNU_CONFIGURE= yes
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SUBST_CLASSES+= version
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SUBST_STAGE.version= pre-configure
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SUBST_SED.version= -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
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SUBST_FILES.version= configure.ac
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SUBST_SED.version+= -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
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SUBST_FILES.version+= configure.ac
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SUBST_CLASSES+= bash
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SUBST_STAGE.bash= pre-configure
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SUBST_SED.bash+= -e "s|'bash'|'${PREFIX}/bin/bash'|"
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SUBST_SED.bash+= -e 's|\\/bin\\/bash|${PREFIX:S,/,\\\/,g}\\/bin\\/bash|'
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SUBST_FILES.bash+= test/test.pl
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REPLACE_PERL+= misc/*.pl
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REPLACE_PERL+= test/*.pl
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@ -5,4 +5,3 @@ RMD160 (samtools-1.10.tar.gz) = e8d91dfc0970a0faa85d45962f76f831af331007
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SHA512 (samtools-1.10.tar.gz) = 7760a1e8a89780ac80053b136930a8ed0cc130b72c9f66cdc9c211e93b6bcc8923140e7caae9824c81caa4a2bfab3a14280e3e7d7245abeaa6f91f0f96123fda
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Size (samtools-1.10.tar.gz) = 4457760 bytes
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SHA1 (patch-Makefile) = 409ef37ff0730257d82989d866c8cba705e3ef8a
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SHA1 (patch-test_test.pl) = 7dc29671de06bfa7adadee32538a31d34817579f
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@ -1,30 +0,0 @@
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$NetBSD$
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# Portable bash path
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--- test/test.pl.orig 2019-12-06 16:40:42.000000000 +0000
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+++ test/test.pl
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@@ -1,4 +1,4 @@
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-#!/usr/bin/env perl
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+#!/home/bacon/Pkgsrc/pkg/bin/perl
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#
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# Copyright (C) 2013-2019 Genome Research Ltd.
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#
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@@ -907,7 +907,7 @@ sub test_usage
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my $command = $args{cmd};
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my $commandpath = $$opts{bin}."/".$command;
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my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}");
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- if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
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+ if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
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my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
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@@ -965,7 +965,7 @@ sub test_usage_subcommand
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my $commandpath = $$opts{bin}."/".$command;
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my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}");
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- if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
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+ if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
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if ( $err =~ m/not.*implemented/is ) { failed($opts,msg=>$test,reason=>"subcommand indicates it is not implemented",expect_fail=>1); return; }
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