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vsearch: Add Makefile.am patch
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Fri Dec 17 16:07:28 2021 -0600
Changeset: ffa86d735910feda45bdf4a5c453d93f54ab0c62
Modified Files:
canu/Makefile
canu/distinfo
Added Files:
vsearch/patch-src_Makefile.am
Removed Files:
canu/patches/patch-pipelines_canu_Execution.pm
canu/patches/patch-utility_objectStore.C
Log Message:
vsearch: Add Makefile.am patch
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ffa86d735910feda45bdf4a5c453d93f54ab0c62
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
canu/Makefile | 8 +--
canu/distinfo | 8 +--
canu/patches/patch-pipelines_canu_Execution.pm | 83 --------------------------
canu/patches/patch-utility_objectStore.C | 19 ------
vsearch/patch-src_Makefile.am | 22 +++++++
5 files changed, 26 insertions(+), 114 deletions(-)
diffs:
diff --git a/canu/Makefile b/canu/Makefile
index 910a06ef4f..09cb2bda65 100644
--- a/canu/Makefile
+++ b/canu/Makefile
@@ -1,6 +1,6 @@
# $NetBSD$
-DISTNAME= canu-1.8
+DISTNAME= canu-2.2
CATEGORIES= biology java
MASTER_SITES= ${MASTER_SITE_GITHUB:=marbl/}
GITHUB_TAG= v${PKGVERSION_NOREV}
@@ -23,11 +23,6 @@ SUBST_SED.optimize+= -e 's|-fexpensive-optimizations||g'
SUBST_SED.optimize+= -e 's|-finline-functions||g'
SUBST_FILES.optimize+= ${WRKSRC}/Makefile
-SUBST_CLASSES+= jar
-SUBST_STAGE.jar= pre-configure
-SUBST_SED.jar+= -e 's|\\$$bin/mhap-|${PREFIX}/${JAVAJARDIR}/mhap-|g'
-SUBST_FILES.jar+= ${WRKSRC}/pipelines/canu/OverlapMhap.pm
-
SUBST_CLASSES+= perl
SUBST_STAGE.perl= pre-configure
SUBST_SED.perl+= -e 's|$$FindBin::RealBin/../lib/site_perl|${PREFIX}/${SITE_PERL_REL}|g'
@@ -52,7 +47,6 @@ USE_LANGUAGES= c c++
USE_JAVA= run
USE_JAVA2= 8
USE_TOOLS+= gmake pax perl
-GCC_REQD+= 4.8
WRKSRC= ${WRKDIR}/canu-${PKGVERSION_NOREV}/src
MAKE_ENV+= DESTDIR=${WRKSRC}
diff --git a/canu/distinfo b/canu/distinfo
index 1df32bf424..d277a05c0c 100644
--- a/canu/distinfo
+++ b/canu/distinfo
@@ -1,9 +1,7 @@
$NetBSD$
-RMD160 (canu-1.8.tar.gz) = 78d4872b4034f526037ce225c699debd910bd586
-SHA512 (canu-1.8.tar.gz) = 650bc96675f371596f8e7748d4ab2d229f0262bf84cee8fed59af43d534d76095a72e4ba0b4a5ce9f561992268c317964cda2f6c89ee514f4920e2ba47fbc86c
-Size (canu-1.8.tar.gz) = 2465314 bytes
+BLAKE2s (canu-2.2.tar.gz) = ecb7c025c7cd24d90403844ac9d62bc4245fe1b63efb8bc18354542f1920a679
+SHA512 (canu-2.2.tar.gz) = 9c4389994857bdd8c75d6e1b6e9f5bba765d89716b3cc037ae8066b62fddd0c7028ce10ecdaacc762c641ea96831b95dcef07e0a27e09afe758377e1900b2694
+Size (canu-2.2.tar.gz) = 2068564 bytes
SHA1 (patch-Makefile) = aa83003677cbb12558e438c776402ec48df0598d
SHA1 (patch-pipelines_canu_Defaults.pm) = 55a4631d86abb1881b0cc997514d44c536209ea6
-SHA1 (patch-pipelines_canu_Execution.pm) = fbb080c06ea5d2393d1835a61771715d2aef0274
-SHA1 (patch-utility_objectStore.C) = c8407de79abbaf296f027f704080cc7e878b85f4
diff --git a/canu/patches/patch-pipelines_canu_Execution.pm b/canu/patches/patch-pipelines_canu_Execution.pm
deleted file mode 100644
index 195f5a685b..0000000000
--- a/canu/patches/patch-pipelines_canu_Execution.pm
+++ /dev/null
@@ -1,83 +0,0 @@
-$NetBSD$
-
-# Add resource limits for SLURM
-# Upstream is considering a scheduler-independent approach to this feature
-
---- pipelines/canu/Execution.pm.orig 2018-06-22 08:20:52.000000000 +0000
-+++ pipelines/canu/Execution.pm
-@@ -303,10 +303,6 @@ sub skipStage ($$@) {
- sub getInstallDirectory () {
- my $installDir = $FindBin::RealBin;
-
-- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
-- $installDir = $1;
-- }
--
- return($installDir);
- }
-
-@@ -694,8 +690,8 @@ sub submitScript ($$) {
-
-
-
--sub buildGridArray ($$$$) {
-- my ($name, $bgn, $end, $opt) = @_;
-+sub buildGridArray (@) {
-+ my ( $name, $bgn, $end, $opt, $thr ) = @_;
- my $off = 0;
-
- # In some grids (SGE) this is the maximum size of an array job.
-@@ -725,8 +721,42 @@ sub buildGridArray ($$$$) {
- $off = "-F \"$off\"";
- }
-
-- $opt =~ s/ARRAY_NAME/$name/g; # Replace ARRAY_NAME with 'job name'
-- $opt =~ s/ARRAY_JOBS/$bgn-$end/g; # Replace ARRAY_JOBS with 'bgn-end'
-+ if( $opt =~ m/(ARRAY_NAME)/ )
-+ {
-+ $opt =~ s/$1/$name/; # Replace ARRAY_NAME with 'job name'
-+ }
-+ elsif( $opt =~ m/(ARRAY_JOBS)/ )
-+ {
-+ $opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end'
-+
-+ if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
-+ {
-+ if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
-+ {
-+ $opt .= '%' . int( getGlobal( 'slurmCormhapCoreLimit' ) / $thr );
-+ }
-+ elsif( $name =~ m/^ovb_/i && defined getGlobal( 'slurmOvbCoreLimit' ) )
-+ {
-+ $opt .= '%' . getGlobal( 'slurmOvbCoreLimit' );
-+ }
-+ elsif( $name =~ m/^ovs_/i && defined getGlobal( 'slurmOvsCoreLimit' ) )
-+ {
-+ $opt .= '%' . getGlobal( 'slurmOvsCoreLimit' );
-+ }
-+ elsif( $name =~ m/^red_/i && defined getGlobal( 'slurmRedCoreLimit' ) )
-+ {
-+ $opt .= '%' . int( getGlobal( 'slurmRedCoreLimit' ) / $thr );
-+ }
-+ elsif( defined getGlobal( 'slurmArrayTaskLimit' ) )
-+ {
-+ $opt .= '%' . getGlobal( 'slurmArrayTaskLimit' );
-+ }
-+ elsif( defined getGlobal( 'slurmArrayCoreLimit' ) )
-+ {
-+ $opt .= '%' . int( getGlobal( 'slurmArrayCoreLimit' ) / $thr );
-+ }
-+ }
-+ }
-
- return($opt, $off);
- }
-@@ -870,7 +900,7 @@ sub buildGridJob ($$$$$$$$$) {
- my $jobNameT = makeUniqueJobName($jobType, $asm);
-
- my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));
-- my ($arrayOpt, $arrayOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayOption"));
-+ my ( $arrayOpt, $arrayOff ) = buildGridArray( $jobNameT, $bgnJob, $endJob, getGlobal( "gridEngineArrayOption" ), $thr );
-
- my $outputOption = buildOutputOption($path, $script);
-
diff --git a/canu/patches/patch-utility_objectStore.C b/canu/patches/patch-utility_objectStore.C
deleted file mode 100644
index 3300c4d56f..0000000000
--- a/canu/patches/patch-utility_objectStore.C
+++ /dev/null
@@ -1,19 +0,0 @@
-$NetBSD$
-
-# NetBSD does not provide WEXITED
-# Empty bitmask should suffice in this case
-
---- utility/objectStore.C.orig 2018-12-23 01:57:06.000000000 +0000
-+++ utility/objectStore.C
-@@ -286,6 +286,11 @@ fetchFromObjectStore(char *requested) {
- // Otherwise, we're still the parent, so wait for the (-1 == any) child
- // process to terminate.
-
-+// NetBSD does not provide WEXITED so send empty bitmask
-+#ifdef __NetBSD__
-+#define WEXITED 0
-+#endif
-+
- waitpid(-1, &err, WEXITED);
-
- if ((WIFEXITED(err)) &&
diff --git a/vsearch/patch-src_Makefile.am b/vsearch/patch-src_Makefile.am
new file mode 100644
index 0000000000..abf66190db
--- /dev/null
+++ b/vsearch/patch-src_Makefile.am
@@ -0,0 +1,22 @@
+$NetBSD$
+
+# Respect build env
+
+--- src/Makefile.am.orig 2019-04-30 11:57:32 UTC
++++ src/Makefile.am
+@@ -1,12 +1,12 @@
+ bin_PROGRAMS = $(top_builddir)/bin/vsearch
+
+ if TARGET_PPC
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+ if TARGET_AARCH64
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=armv8-a+simd -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ endif
+ endif
+
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