+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/hisat2-2.2.1nb4/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/hisat2-2.2.1nb4/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for hisat2-2.2.1.tar.gz
=> Checksum SHA512 OK for hisat2-2.2.1.tar.gz
===> Installing dependencies for hisat2-2.2.1nb4
==========================================================================
The following variables will affect the build process of this package,
hisat2-2.2.1nb4.  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 perl>=5.0: found perl-5.38.2
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency simde>=0.7.2: found simde-0.7.2
=> Full dependency python311>=3.11.0: found python311-3.11.8
===> Overriding tools for hisat2-2.2.1nb4
===> Extracting for hisat2-2.2.1nb4
===> Patching for hisat2-2.2.1nb4
=> Applying pkgsrc patches for hisat2-2.2.1nb4
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-Makefile
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile,v 1.2 2023/05/17 21:55:34 bacon Exp $
|
|# Respect env
|
|--- Makefile.orig	2020-07-24 20:07:54.000000000 +0000
|+++ Makefile
--------------------------
Patching file Makefile using Plan A...
Hunk #1 succeeded at 23.
Hunk #2 succeeded at 57.
Hunk #3 succeeded at 152.
Hunk #4 succeeded at 231.
Hunk #5 succeeded at 267.
Hunk #6 succeeded at 497.
Hunk #7 succeeded at 510.
Hunk #8 succeeded at 534.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-aligner__sw.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-aligner__sw.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-aligner__sw.h,v 1.1 2023/05/17 21:55:34 bacon Exp $
|
|# Support non-x86
|
|--- aligner_sw.h.orig	2020-07-24 20:07:54.000000000 +0000
|+++ aligner_sw.h
--------------------------
Patching file aligner_sw.h using Plan A...
Hunk #1 succeeded at 66.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-hisat2
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-hisat2
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-hisat2,v 1.3 2023/05/17 21:55:34 bacon Exp $
|
|# Support BSD, etc.
|
|--- hisat2.orig	2018-11-07 21:43:32 UTC
|+++ hisat2
--------------------------
Patching file hisat2 using Plan A...
Hunk #1 succeeded at 45.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-processor__support.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-processor__support.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-processor__support.h,v 1.2 2023/05/17 21:55:34 bacon Exp $
|
|# Support non-x86
|
|--- processor_support.h.orig	2020-07-24 20:07:54 UTC
|+++ processor_support.h
--------------------------
Patching file processor_support.h using Plan A...
Hunk #1 succeeded at 12.
Hunk #2 succeeded at 52.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-sse__util.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/hisat2/patches/patch-sse__util.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-sse__util.h,v 1.1 2023/05/17 21:55:34 bacon Exp $
|
|# Support non-x86
|
|--- sse_util.h.orig	2020-07-24 20:07:54.000000000 +0000
|+++ sse_util.h
--------------------------
Patching file sse_util.h using Plan A...
Hunk #1 succeeded at 20.
done
/usr/bin/mv /home/pbulk/build/biology/hisat2/work/hisat2-2.2.1/VERSION /home/pbulk/build/biology/hisat2/work/hisat2-2.2.1/HISAT2_VERSION
===> Creating toolchain wrappers for hisat2-2.2.1nb4
===> Configuring for hisat2-2.2.1nb4
=> Replacing python interpreter in *.py scripts/*.py hisat2-build hisat2-inspect.
=> Replacing bash interpreter in scripts/*.sh.
=> Replacing Perl interpreter in hisat2 scripts/*.sh scripts/*.pl scripts/*.py.
INFO: [replace-interpreter] Nothing changed in scripts/make_a_thaliana_tair.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_b_taurus_UMD3.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_bdgp6.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_bdgp6_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_canFam2.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_ce10.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_dm6.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_e_coli.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch37.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch37_snp.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch37_snp_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch37_snp_tran_ercc.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch37_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch38.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_rep.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_snp.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_snp_rep.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_snp_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_snp_tran_ercc.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grcm38.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grcm38_snp.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grcm38_snp_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_grcm38_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_hg19.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_hg38.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_hg38_allsnp.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_hg38_snp.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_hg38_snp_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_mm10.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_mm9.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_r64.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_r64_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_rn4.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_rn6.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_rnor6.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_rnor6_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_sc3.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_wbcel235.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_wbcel235_tran.sh.
INFO: [replace-interpreter] Nothing changed in scripts/make_zm3_snp_tran_ercc.sh.
INFO: [replace-interpreter] Nothing changed in scripts/sa.py.
INFO: [replace-interpreter] Nothing changed in scripts/validate_repeat.py.
=> Checking for portability problems in extracted files