+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/bwa-0.7.17nb7/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/bwa-0.7.17nb7/work.log
=> Checksum BLAKE2s OK for bwa-0.7.17.tar.gz
=> Checksum SHA512 OK for bwa-0.7.17.tar.gz
===> Installing dependencies for bwa-0.7.17nb7
=> Tool dependency gmake>=3.81: found gmake-4.4.1
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency simde>=0.7.2: found simde-0.8.2
=> Full dependency perl>=5.0: found perl-5.42.0
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
===> Overriding tools for bwa-0.7.17nb7
===> Extracting for bwa-0.7.17nb7
===> Patching for bwa-0.7.17nb7
=> Applying pkgsrc patches for bwa-0.7.17nb7
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bwa/patches/patch-Makefile
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bwa/patches/patch-Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile,v 1.3 2023/05/18 14:05:15 bacon Exp $
|
|# Respect env, add librt for NetBSD
|
|--- Makefile.orig	2017-10-23 17:10:17.000000000 +0000
|+++ Makefile
--------------------------
Patching file Makefile using Plan A...
Hunk #1 succeeded at 1.
Hunk #2 succeeded at 12.
Hunk #3 succeeded at 30.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bwa/patches/patch-kopen.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bwa/patches/patch-kopen.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-kopen.c,v 1.4 2023/05/18 14:05:15 bacon Exp $
|
|# Add includes for getting timevals and select prototype into scope.
|
|--- kopen.c.orig	2017-10-23 17:10:17.000000000 +0000
|+++ kopen.c
--------------------------
Patching file kopen.c using Plan A...
Hunk #1 succeeded at 12.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bwa/patches/patch-ksw.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bwa/patches/patch-ksw.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ksw.c,v 1.1 2023/05/18 14:05:15 bacon Exp $
|
|# Use SIMDE to support non-x86 architectures
|
|--- ksw.c.orig	2017-10-23 17:10:17.000000000 +0000
|+++ ksw.c
--------------------------
Patching file ksw.c using Plan A...
Hunk #1 succeeded at 26.
done
===> Creating toolchain wrappers for bwa-0.7.17nb7
===> Configuring for bwa-0.7.17nb7
=> Replacing Perl interpreter in *.pl.
=> Checking for portability problems in extracted files