+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/canu-2.2nb3/work.log
+ su pbulk -c '"$@"' make /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/canu-2.2nb3/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for canu-2.2.tar.xz
=> Checksum SHA512 OK for canu-2.2.tar.xz
===> Installing dependencies for canu-2.2nb3
=> Tool dependency mktools-[0-9]*: found mktools-20220614
=> Tool dependency nbpatch-[0-9]*: found nbpatch-20151107
=> Tool dependency pax>=20040802: found pax-20210219
=> Tool dependency perl>=5.38.0: found perl-5.38.2
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency boost-headers-1.84.*: found boost-headers-1.84.0
=> Build dependency gcc6>=6.5.0nb9: found gcc6-6.5.0nb9
=> Full dependency boost-libs-1.84.*: found boost-libs-1.84.0
=> Full dependency boost-libs>=1.84.0: found boost-libs-1.84.0
=> Full dependency perl>=5.38.0<5.39.0: found perl-5.38.2
===> Overriding tools for canu-2.2nb3
===> Extracting for canu-2.2nb3
/bin/chmod -R g-w /home/pbulk/build/biology/canu/work
===> Patching for canu-2.2nb3
=> Applying pkgsrc patches for canu-2.2nb3
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-Makefile
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile,v 1.4 2023/05/20 14:42:11 bacon Exp $
|
|# Portability
|
|--- Makefile.orig	2021-08-04 00:21:51.000000000 +0000
|+++ Makefile
--------------------------
Patching file Makefile using Plan A...
Hunk #1 succeeded at 418.
Hunk #2 succeeded at 497.
Hunk #3 succeeded at 540.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-pipelines_canu_Defaults.pm
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-pipelines_canu_Defaults.pm
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.4 2023/05/20 14:42:11 bacon Exp $
|
|# Better task limit control under slurm
|
|--- pipelines/canu/Defaults.pm.orig	2018-10-22 16:47:31 UTC
|+++ pipelines/canu/Defaults.pm
--------------------------
Patching file pipelines/canu/Defaults.pm using Plan A...
Hunk #1 succeeded at 888 (offset -29 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-pipelines_canu_Execution.pm
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-pipelines_canu_Execution.pm
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-pipelines_canu_Execution.pm,v 1.4 2023/05/20 14:42:11 bacon Exp $
|
|# Better task limit control under slurm
|
|--- pipelines/canu/Execution.pm.orig	2020-09-07 19:08:24 UTC
|+++ pipelines/canu/Execution.pm
--------------------------
Patching file pipelines/canu/Execution.pm using Plan A...
Hunk #1 succeeded at 779 (offset 17 lines).
Hunk #2 succeeded at 820 (offset 17 lines).
Hunk #3 succeeded at 1002 (offset 17 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.3 2023/05/20 14:42:11 bacon Exp $
|
|# Portability
|
|--- utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp.orig	2021-12-18 13:01:24 UTC
|+++ utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp
--------------------------
Patching file utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp using Plan A...
Hunk #1 succeeded at 25.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utility_src_utility_files.H
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utility_src_utility_files.H
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-utility_src_utility_files.H,v 1.3 2023/05/20 14:42:11 bacon Exp $
|
|# Portability
|
|--- utility/src/utility/files.H.orig	2021-12-17 20:57:15 UTC
|+++ utility/src/utility/files.H
--------------------------
Patching file utility/src/utility/files.H using Plan A...
Hunk #1 succeeded at 22.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utility_src_utility_logging.H
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utility_src_utility_logging.H
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-utility_src_utility_logging.H,v 1.3 2023/05/20 14:42:11 bacon Exp $
|
|# Portability
|
|--- utility/src/utility/logging.H.orig	2023-05-18 15:39:08.832210910 +0000
|+++ utility/src/utility/logging.H
--------------------------
Patching file utility/src/utility/logging.H using Plan A...
Hunk #1 succeeded at 20.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utility_src_utility_system.H
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utility_src_utility_system.H
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-utility_src_utility_system.H,v 1.3 2023/05/20 14:42:11 bacon Exp $
|
|# Portability
|
|--- utility/src/utility/system.H.orig	2021-12-17 20:57:47 UTC
|+++ utility/src/utility/system.H
--------------------------
Patching file utility/src/utility/system.H using Plan A...
Hunk #1 succeeded at 23.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utility_src_utility_types.H
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/canu/patches/patch-utility_src_utility_types.H
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-utility_src_utility_types.H,v 1.3 2023/05/20 14:42:11 bacon Exp $
|
|# Portability
|
|--- utility/src/utility/types.H.orig	2021-12-17 20:58:13 UTC
|+++ utility/src/utility/types.H
--------------------------
Patching file utility/src/utility/types.H using Plan A...
Hunk #1 succeeded at 55.
done
===> Creating toolchain wrappers for canu-2.2nb3
===> Configuring for canu-2.2nb3
=> Substituting "perl" in pipelines/canu.pl
=> Replacing Perl interpreter in bogart/*.pl pipelines/*.pl bogus/*.pl bogart-analysis/*.pl overlapBasedTrimming/*.pl overlapInCore-analysis/*.pl merTrim/*.pl erateEstimate/*.pl meryl/.pl fastq-utilities/*.pl *.pl.
WARNING: [replace-interpreter] Skipping non-existent file "bogus/*.pl".
WARNING: [replace-interpreter] Skipping non-existent file "bogart-analysis/*.pl".
WARNING: [replace-interpreter] Skipping non-existent file "overlapBasedTrimming/*.pl".
WARNING: [replace-interpreter] Skipping non-existent file "overlapInCore-analysis/*.pl".
WARNING: [replace-interpreter] Skipping non-existent file "merTrim/*.pl".
WARNING: [replace-interpreter] Skipping non-existent file "erateEstimate/*.pl".
WARNING: [replace-interpreter] Skipping non-existent file "meryl/.pl".
WARNING: [replace-interpreter] Skipping non-existent file "fastq-utilities/*.pl".
WARNING: [replace-interpreter] Skipping non-existent file "*.pl".
=> Checking for portability problems in extracted files