From e17c7410633b77aa4dff57012176e7bc102460bc Mon Sep 17 00:00:00 2001 From: Jason Bacon Date: Thu, 23 Jul 2020 09:24:12 -0500 Subject: [PATCH] samtools,bcftools: Use SUBST to properly patch test script --- bcftools/Makefile | 6 +++++ bcftools/distinfo | 1 - bcftools/patches/patch-test_test.pl | 42 ----------------------------- samtools/Makefile | 10 +++++-- samtools/distinfo | 1 - samtools/patches/patch-test_test.pl | 30 --------------------- 6 files changed, 14 insertions(+), 76 deletions(-) delete mode 100644 bcftools/patches/patch-test_test.pl delete mode 100644 samtools/patches/patch-test_test.pl diff --git a/bcftools/Makefile b/bcftools/Makefile index ba2eef4b79..0794f984b3 100644 --- a/bcftools/Makefile +++ b/bcftools/Makefile @@ -17,6 +17,12 @@ SUBST_STAGE.version= pre-configure SUBST_SED.version= -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|" SUBST_FILES.version= configure.ac +SUBST_CLASSES+= bash +SUBST_STAGE.bash= pre-configure +SUBST_SED.bash+= -e 's|/bin/bash|${PREFIX}/bin/bash|' +SUBST_SED.bash+= -e 's|\\/bin\\/bash|${PREFIX:S,/,\\\/,g}\\/bin\\/bash|' +SUBST_FILES.bash= test/test.pl + REPLACE_PERL+= misc/*.pl REPLACE_PERL+= misc/fix-broken-GATK-Double-vs-Integer REPLACE_PERL+= misc/plot-vcfstats diff --git a/bcftools/distinfo b/bcftools/distinfo index 3bfd9db0fd..fcd6846ef3 100644 --- a/bcftools/distinfo +++ b/bcftools/distinfo @@ -6,4 +6,3 @@ SHA512 (bcftools-1.10.2.tar.gz) = 12c004603db557ac69098e83ad3aaa5762b02b4718b79f Size (bcftools-1.10.2.tar.gz) = 2880994 bytes SHA1 (patch-Makefile) = 1f1397e9b0389a7b4fccc9eae87981e7ce1d7980 SHA1 (patch-misc_run-roh.pl) = 8a29ee7b1001af6670955f174ce4dbab31f05659 -SHA1 (patch-test_test.pl) = 5fc3896d9013a6d5caa24a4d3e6798905d1243e1 diff --git a/bcftools/patches/patch-test_test.pl b/bcftools/patches/patch-test_test.pl deleted file mode 100644 index ae6bd1a5dc..0000000000 --- a/bcftools/patches/patch-test_test.pl +++ /dev/null @@ -1,42 +0,0 @@ -$NetBSD$ - -# Portable bash path - ---- test/test.pl.orig 2020-07-21 20:47:32.977230067 +0000 -+++ test/test.pl -@@ -610,7 +610,7 @@ sub _cmd - else - { - # child -- exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!"); -+ exec('bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!"); - } - return ($? >> 8, join('',@out)); - } -@@ -622,7 +622,7 @@ sub _cmd3 - my $pid = fork(); - if ( !$pid ) - { -- exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o"); -+ exec('bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o"); - } - waitpid($pid,0); - -@@ -1063,7 +1063,7 @@ sub test_usage - my $command = $args{cmd}; - my $commandpath = $$opts{bin}."/".$command; - my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1"); -- if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; } -+ if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; } - - my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); - -@@ -1118,7 +1118,7 @@ sub test_usage_subcommand - my $subcommand = $args{subcmd}; - my $commandpath = $$opts{bin}."/".$command; - my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1"); -- if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; } -+ if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; } - - my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); - diff --git a/samtools/Makefile b/samtools/Makefile index 88b5b4d4a8..6ce10c2e42 100644 --- a/samtools/Makefile +++ b/samtools/Makefile @@ -14,8 +14,14 @@ GNU_CONFIGURE= yes SUBST_CLASSES+= version SUBST_STAGE.version= pre-configure -SUBST_SED.version= -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|" -SUBST_FILES.version= configure.ac +SUBST_SED.version+= -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|" +SUBST_FILES.version+= configure.ac + +SUBST_CLASSES+= bash +SUBST_STAGE.bash= pre-configure +SUBST_SED.bash+= -e "s|'bash'|'${PREFIX}/bin/bash'|" +SUBST_SED.bash+= -e 's|\\/bin\\/bash|${PREFIX:S,/,\\\/,g}\\/bin\\/bash|' +SUBST_FILES.bash+= test/test.pl REPLACE_PERL+= misc/*.pl REPLACE_PERL+= test/*.pl diff --git a/samtools/distinfo b/samtools/distinfo index 52cef73ca3..9376bd1e4d 100644 --- a/samtools/distinfo +++ b/samtools/distinfo @@ -5,4 +5,3 @@ RMD160 (samtools-1.10.tar.gz) = e8d91dfc0970a0faa85d45962f76f831af331007 SHA512 (samtools-1.10.tar.gz) = 7760a1e8a89780ac80053b136930a8ed0cc130b72c9f66cdc9c211e93b6bcc8923140e7caae9824c81caa4a2bfab3a14280e3e7d7245abeaa6f91f0f96123fda Size (samtools-1.10.tar.gz) = 4457760 bytes SHA1 (patch-Makefile) = 409ef37ff0730257d82989d866c8cba705e3ef8a -SHA1 (patch-test_test.pl) = 7dc29671de06bfa7adadee32538a31d34817579f diff --git a/samtools/patches/patch-test_test.pl b/samtools/patches/patch-test_test.pl deleted file mode 100644 index ac39ec79dd..0000000000 --- a/samtools/patches/patch-test_test.pl +++ /dev/null @@ -1,30 +0,0 @@ -$NetBSD$ - -# Portable bash path - ---- test/test.pl.orig 2019-12-06 16:40:42.000000000 +0000 -+++ test/test.pl -@@ -1,4 +1,4 @@ --#!/usr/bin/env perl -+#!/home/bacon/Pkgsrc/pkg/bin/perl - # - # Copyright (C) 2013-2019 Genome Research Ltd. - # -@@ -907,7 +907,7 @@ sub test_usage - my $command = $args{cmd}; - my $commandpath = $$opts{bin}."/".$command; - my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}"); -- if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; } -+ if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; } - - my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); - -@@ -965,7 +965,7 @@ sub test_usage_subcommand - my $commandpath = $$opts{bin}."/".$command; - my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}"); - -- if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; } -+ if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; } - - if ( $err =~ m/not.*implemented/is ) { failed($opts,msg=>$test,reason=>"subcommand indicates it is not implemented",expect_fail=>1); return; } -