+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/bedtools-2.31.1/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/bedtools-2.31.1/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for bedtools-2.31.1.tar.gz
=> Checksum SHA512 OK for bedtools-2.31.1.tar.gz
===> Installing dependencies for bedtools-2.31.1
==========================================================================
The following variables will affect the build process of this package,
bedtools-2.31.1.  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/pkg/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 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
=> Full dependency bzip2>=1.0.3: found bzip2-1.0.8
=> Full dependency xz>=5.0.0: found xz-5.6.1nb100
=> Full dependency python311>=3.11.0: found python311-3.11.9
===> Overriding tools for bedtools-2.31.1
===> Extracting for bedtools-2.31.1
===> Patching for bedtools-2.31.1
=> Applying pkgsrc patches for bedtools-2.31.1
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools/patches/patch-Makefile
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools/patches/patch-Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile,v 1.3 2023/11/08 16:46:44 bacon Exp $
|
|# Portability, respect env
|
|--- Makefile.orig	2023-11-08 15:05:30.454330622 +0000
|+++ Makefile
--------------------------
Patching file Makefile using Plan A...
Hunk #1 succeeded at 4.
Hunk #2 succeeded at 21.
Hunk #3 succeeded at 43.
Hunk #4 succeeded at 158.
Hunk #5 succeeded at 200.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_utils_BamTools_include_SamHeader.hpp,v 1.1 2021/02/08 01:49:25 bacon Exp $
|
|# Silence compiler warnings
|
|--- src/utils/BamTools/include/SamHeader.hpp.orig	2021-01-24 16:15:06 UTC
|+++ src/utils/BamTools/include/SamHeader.hpp
--------------------------
Patching file src/utils/BamTools/include/SamHeader.hpp using Plan A...
Hunk #1 succeeded at 7.
Hunk #2 succeeded at 30.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools/patches/patch-src_utils_htslib_Makefile
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools/patches/patch-src_utils_htslib_Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_utils_htslib_Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
|
|# Respect pkgsrc env
|
|--- src/utils/htslib/Makefile.orig	2021-01-23 19:33:26.000000000 +0000
|+++ src/utils/htslib/Makefile
--------------------------
Patching file src/utils/htslib/Makefile using Plan A...
Hunk #1 succeeded at 22.
Hunk #2 succeeded at 33.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools/patches/patch-test_test.sh
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools/patches/patch-test_test.sh
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-test_test.sh,v 1.1 2021/02/08 01:49:25 bacon Exp $
|
|# Warning for impending failed tests
|
|--- test/test.sh.orig	2021-02-07 19:54:21.793084552 +0000
|+++ test/test.sh
--------------------------
Patching file test/test.sh using Plan A...
Hunk #1 succeeded at 1.
done
===> Creating toolchain wrappers for bedtools-2.31.1
ERROR: gettext-lib>=0.22 is not installed; can't buildlink files.
*** Error code 1

Stop.
bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools
*** Error code 1

Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/bedtools