+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/subread-2.0.8/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/subread-2.0.8/work.log
=> Checksum BLAKE2s OK for subread-2.0.8-source.tar.gz
=> Checksum SHA512 OK for subread-2.0.8-source.tar.gz
===> Installing dependencies for subread-2.0.8
=> 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
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
===> Overriding tools for subread-2.0.8
===> Extracting for subread-2.0.8
===> Patching for subread-2.0.8
=> Applying pkgsrc patches for subread-2.0.8
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-HelperFunctions.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-HelperFunctions.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-HelperFunctions.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Use standard compiler macros
|
|--- HelperFunctions.c.orig	2024-07-25 00:30:10.000000000 +0000
|+++ HelperFunctions.c
--------------------------
Patching file HelperFunctions.c using Plan A...
Hunk #1 succeeded at 26.
Hunk #2 succeeded at 47.
Hunk #3 succeeded at 862.
Hunk #4 succeeded at 2721.
Hunk #5 succeeded at 2733.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-core-junction.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-core-junction.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-core-junction.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Portability
|
|--- core-junction.c.orig	2018-11-08 15:19:02 UTC
|+++ core-junction.c
--------------------------
Patching file core-junction.c using Plan A...
Hunk #1 succeeded at 22.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-gene-algorithms.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-gene-algorithms.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-gene-algorithms.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Use standard compiler macros
|
|--- gene-algorithms.c.orig	2024-07-25 00:30:10.000000000 +0000
|+++ gene-algorithms.c
--------------------------
Patching file gene-algorithms.c using Plan A...
Hunk #1 succeeded at 29.
Hunk #2 succeeded at 45.
Hunk #3 succeeded at 54.
Hunk #4 succeeded at 62.
Hunk #5 succeeded at 71.
Hunk #6 succeeded at 1378.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-input-files.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-input-files.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-input-files.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Use standard compiler macros
|
|--- input-files.c.orig	2024-07-26 04:36:04.000000000 +0000
|+++ input-files.c
--------------------------
Patching file input-files.c using Plan A...
Hunk #1 succeeded at 48.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-long-hashtable.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-long-hashtable.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-long-hashtable.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Use standard compiler macros
|
|--- long-hashtable.c.orig	2024-07-25 00:30:10.000000000 +0000
|+++ long-hashtable.c
--------------------------
Patching file long-hashtable.c using Plan A...
Hunk #1 succeeded at 21.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-longread-one_LRMsorted-hashtable.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-longread-one_LRMsorted-hashtable.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-longread-one_LRMsorted-hashtable.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Use standard compiler macros
|
|--- longread-one/LRMsorted-hashtable.c.orig	2018-11-08 14:47:43 UTC
|+++ longread-one/LRMsorted-hashtable.c
--------------------------
Patching file longread-one/LRMsorted-hashtable.c using Plan A...
Hunk #1 succeeded at 22.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-longread-one_Makefile
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-longread-one_Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-longread-one_Makefile,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Respect env
|
|--- longread-one/Makefile.orig	2024-07-25 00:35:55 UTC
|+++ longread-one/Makefile
--------------------------
Patching file longread-one/Makefile using Plan A...
Hunk #1 succeeded at 1.
Hunk #2 succeeded at 19.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-longread-one_longread-mapping.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-longread-one_longread-mapping.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-longread-one_longread-mapping.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Add FreeBSD support
|
|--- longread-one/longread-mapping.c.orig	2021-03-30 13:58:29 UTC
|+++ longread-one/longread-mapping.c
--------------------------
Patching file longread-one/longread-mapping.c using Plan A...
Hunk #1 succeeded at 30.
Hunk #2 succeeded at 227.
Hunk #3 succeeded at 248.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-read-repair.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-read-repair.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-read-repair.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Portability
|
|--- read-repair.c.orig	2018-11-08 15:20:06 UTC
|+++ read-repair.c
--------------------------
Patching file read-repair.c using Plan A...
Hunk #1 succeeded at 3.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-sambam-file.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-sambam-file.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-sambam-file.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Portability
|
|--- sambam-file.c.orig	2024-07-25 00:30:10.000000000 +0000
|+++ sambam-file.c
--------------------------
Patching file sambam-file.c using Plan A...
Hunk #1 succeeded at 30.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-sorted-hashtable.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-sorted-hashtable.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-sorted-hashtable.c,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Use standard compiler macros
|
|--- sorted-hashtable.c.orig	2018-11-08 03:33:50 UTC
|+++ sorted-hashtable.c
--------------------------
Patching file sorted-hashtable.c using Plan A...
Hunk #1 succeeded at 23.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-subread.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/subread/patches/patch-subread.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-subread.h,v 1.1 2025/01/20 17:29:59 bacon Exp $
|
|# Use standard compiler macros
|
|--- subread.h.orig	2024-07-25 00:30:10.000000000 +0000
|+++ subread.h
--------------------------
Patching file subread.h using Plan A...
Hunk #1 succeeded at 114.
done
===> Creating toolchain wrappers for subread-2.0.8
===> Configuring for subread-2.0.8
=> Checking for portability problems in extracted files