+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/local/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/bowtie2-2.5.4/work.log
+ su pbulk -c '"$@"' make /opt/local/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/bowtie2-2.5.4/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for bowtie2-2.5.4.tar.gz
=> Checksum SHA512 OK for bowtie2-2.5.4.tar.gz
===> Installing dependencies for bowtie2-2.5.4
==========================================================================
The following variables will affect the build process of this package,
bowtie2-2.5.4.  Their current value is shown below:

        * PYTHON_VERSION_DEFAULT = 311

Based on these variables, the following variables have been set:

        * PYPACKAGE = python311

You may want to abort the process now with CTRL-C and change the value
of variables in the first group before continuing.  Be sure to run
`/opt/local/bin/bmake clean' after the changes.
==========================================================================
=> Tool dependency mktools-[0-9]*: found mktools-20220614
=> Tool dependency gmake>=3.81: found gmake-4.4.1
=> Tool dependency pax>=20040802: found pax-20210219
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency gcc13>=13.1.0: found gcc13-13.3.0
=> Build dependency simde>=0.7.2: found simde-0.8.2
=> Full dependency perl>=5.0: found perl-5.38.2
=> Full dependency gcc13-libs>=13.2.0: found gcc13-libs-13.3.0
=> Full dependency python311>=3.11.0: found python311-3.11.9nb1
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
===> Overriding tools for bowtie2-2.5.4
===> Extracting for bowtie2-2.5.4
===> Patching for bowtie2-2.5.4
=> Applying pkgsrc patches for bowtie2-2.5.4
=> Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/bowtie2/patches/patch-Makefile
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/bowtie2/patches/patch-Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile,v 1.6 2024/05/24 11:32:58 bacon Exp $
|
|# Respect pkgsrc env
|
|--- Makefile.orig	2021-12-17 01:48:49.470438839 +0000
|+++ Makefile
--------------------------
Patching file Makefile using Plan A...
Hunk #1 succeeded at 21.
Hunk #2 succeeded at 230 (offset 31 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.6 2024/05/24 11:32:58 bacon Exp $
|
|# Eliminate bash dependency
|
|--- scripts/bowtie2-hbb.sh.orig	2020-10-06 03:46:41.000000000 +0000
|+++ scripts/bowtie2-hbb.sh
--------------------------
Patching file scripts/bowtie2-hbb.sh using Plan A...
Hunk #1 succeeded at 11.
done
===> Creating toolchain wrappers for bowtie2-2.5.4
===> Configuring for bowtie2-2.5.4
=> Replacing python interpreter in bowtie2-build bowtie2-inspect.
=> Replacing Perl interpreter in scripts/*.pl bowtie2.
=> Replacing sh interpreter in scripts/bowtie2-hbb.sh.
=> Checking for portability problems in extracted files