+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/canu-1.8nb12/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/canu-1.8nb12/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for canu-1.8.tar.gz
=> Checksum SHA512 OK for canu-1.8.tar.gz
===> Installing dependencies for canu-1.8nb12
=> Tool dependency mktools-[0-9]*: found mktools-20220614
=> Tool dependency gmake>=3.81: found gmake-4.3nb3
=> Tool dependency pax>=20040802: found pax-20210219
=> Tool dependency perl>=5.34.0: found perl-5.34.1
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency boost-headers-1.78.*: found boost-headers-1.78.0
=> Full dependency gnuplot>0: found gnuplot-5.4.2nb2
=> Full dependency boost-libs-1.78.*: found boost-libs-1.78.0nb2
=> Full dependency perl>=5.34.0<5.36.0: found perl-5.34.1
===> Overriding tools for canu-1.8nb12
===> Extracting for canu-1.8nb12
/usr/bin/chmod -R g-w /home/pbulk/build/biology/canu/work/canu-1.8
===> Patching for canu-1.8nb12
=> Applying pkgsrc patches for canu-1.8nb12
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/canu/patches/patch-Makefile
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/canu/patches/patch-Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile,v 1.1 2019/01/07 02:33:17 bacon Exp $
|
|# Template Makefile requires platform-specific defaults for each OS
|# To be sent upstream following commit
|
|--- Makefile.orig	2018-10-22 16:47:31.000000000 +0000
|+++ Makefile
--------------------------
Patching file Makefile using Plan A...
Hunk #1 succeeded at 545.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/canu/patches/patch-fastq-utilities_fastqSimulate_C
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/canu/patches/patch-fastq-utilities_fastqSimulate_C
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-fastq-utilities_fastqSimulate_C,v 1.1 2020/05/16 19:50:21 rillig Exp $
|
|fastq-utilities/fastqSimulate.C:796:31: error: 'UINT64_MAX' was not declared in this scope
|   uint64     numReads       = UINT64_MAX;  //  Number of reads to generate, constant
|
|AS_global.h must be included before the headers from the standard library
|to get the UINT64_MAX macro.
|
|--- fastq-utilities/fastqSimulate.C.orig	2018-10-22 16:47:31.000000000 +0000
|+++ fastq-utilities/fastqSimulate.C
--------------------------
Patching file fastq-utilities/fastqSimulate.C using Plan A...
Hunk #1 succeeded at 35.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/canu/patches/patch-pipelines_canu_Defaults.pm
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/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 1.1 2019/01/07 02:33:17 bacon Exp $
|
|# Add resource limits for SLURM
|# Upstream is considering a scheduler-independent approach to this feature
|
|--- pipelines/canu/Defaults.pm.orig	2018-06-22 08:20:52.000000000 +0000
|+++ pipelines/canu/Defaults.pm
--------------------------
Patching file pipelines/canu/Defaults.pm using Plan A...
Hunk #1 succeeded at 917 (offset 105 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/canu/patches/patch-pipelines_canu_Execution.pm
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/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 1.1 2019/01/07 02:33:17 bacon Exp $
|
|# 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
--------------------------
Patching file pipelines/canu/Execution.pm using Plan A...
Hunk #1 succeeded at 333 (offset 30 lines).
Hunk #2 succeeded at 750 (offset 60 lines).
Hunk #3 succeeded at 759 (offset 38 lines).
Hunk #4 succeeded at 965 (offset 65 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/canu/patches/patch-utility_objectStore.C
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/canu/patches/patch-utility_objectStore.C
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-utility_objectStore.C,v 1.1 2019/01/07 02:33:17 bacon Exp $
|
|# 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
--------------------------
Patching file utility/objectStore.C using Plan A...
Hunk #1 succeeded at 286.
done
===> Creating toolchain wrappers for canu-1.8nb12
===> Configuring for canu-1.8nb12
=> Substituting "jar" in pipelines/canu/OverlapMhap.pm
=> Substituting "optimize" in Makefile
=> Substituting "perl" in pipelines/canu.pl
=> Replacing Perl interpreter in *.pl */*.pl.
=> Checking for portability problems in extracted files