+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=312 WRKLOG=/tmp/bulklog/stacks-2.60nb3/work.log
+ su pbulk -c '"$@"' make /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=312 WRKLOG=/tmp/bulklog/stacks-2.60nb3/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for stacks-2.60.tar.gz
=> Checksum SHA512 OK for stacks-2.60.tar.gz
===> Installing dependencies for stacks-2.60nb3
==========================================================================
The following variables will affect the build process of this package,
stacks-2.60nb3.  Their current value is shown below:

        * PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp
        * PYTHON_VERSION_DEFAULT = 312

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

        * BLAS_INCLUDES (not defined)
        * BLAS_LIBS = -lblas
        * BLAS_PC = blas
        * BLAS_TYPE = netlib
        * CBLAS_LIBS (not defined)
        * CBLAS_PC (not defined)
        * LAPACKE_LIBS (not defined)
        * LAPACKE_PC (not defined)
        * LAPACK_LIBS = -llapack -lblas
        * LAPACK_PC = lapack
        * PYPACKAGE = python312

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
`/usr/pkg/bin/bmake clean' after the changes.
==========================================================================
=> Tool dependency mktools-[0-9]*: found mktools-20220614
=> Tool dependency nbpatch-[0-9]*: found nbpatch-20151107
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Full dependency perl>=5.0: found perl-5.40.0nb1
=> Full dependency R>=4.2.0nb1: found R-4.4.2nb2
=> Full dependency python312>=3.12: found python312-3.12.8nb1
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
=> Full dependency blas>=3.9.0: found blas-3.12.0
=> Full dependency bzip2>=1.0.1: found bzip2-1.0.8
=> Full dependency lapack>=3.9.0: found lapack-3.12.0
=> Full dependency xz>=5.0.0: found xz-5.6.3
===> Overriding tools for stacks-2.60nb3
===> Extracting for stacks-2.60nb3
===> Patching for stacks-2.60nb3
=> Applying pkgsrc patches for stacks-2.60nb3
=> Verifying /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_Hwp.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_Hwp.cc
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_Hwp.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
|
|avoid ambiguous math functions
|
|--- src/Hwp.cc.orig	2020-06-24 17:47:53.000000000 +0000
|+++ src/Hwp.cc
--------------------------
Patching file src/Hwp.cc using Plan A...
Hunk #1 succeeded at 20.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_PopSum.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_PopSum.cc
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_PopSum.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
|
|avoid ambiguous math functions
|
|--- src/PopSum.cc.orig	2021-10-21 14:47:59.000000000 +0000
|+++ src/PopSum.cc
--------------------------
Patching file src/PopSum.cc using Plan A...
Hunk #1 succeeded at 20.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_Vcf.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_Vcf.cc
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_Vcf.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
|
|avoid ambiguous math functions
|
|--- src/Vcf.cc.orig	2021-06-28 20:21:30.000000000 +0000
|+++ src/Vcf.cc
--------------------------
Patching file src/Vcf.cc using Plan A...
Hunk #1 succeeded at 22.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_kmers.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_kmers.cc
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_kmers.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
|
|avoid ambiguous math functions
|
|--- src/kmers.cc.orig	2021-06-08 21:08:14.000000000 +0000
|+++ src/kmers.cc
--------------------------
Patching file src/kmers.cc using Plan A...
Hunk #1 succeeded at 23.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_smoothing__utils.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_smoothing__utils.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_smoothing__utils.h,v 1.1 2022/04/25 14:34:06 tnn Exp $
|
|avoid ambiguous math functions
|
|--- src/smoothing_utils.h.orig	2020-06-24 17:47:55.000000000 +0000
|+++ src/smoothing_utils.h
--------------------------
Patching file src/smoothing_utils.h using Plan A...
Hunk #1 succeeded at 24.
done
=> Verifying /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_utils.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/stacks/patches/patch-src_utils.cc
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_utils.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
|
|provide fallback declaration for ACCESSPERMS
|
|--- src/utils.cc.orig	2021-10-07 19:33:41.000000000 +0000
|+++ src/utils.cc
--------------------------
Patching file src/utils.cc using Plan A...
Hunk #1 succeeded at 401.
done
===> Creating toolchain wrappers for stacks-2.60nb3
===> Configuring for stacks-2.60nb3
=> Modifying GNU configure scripts to avoid --recheck
=> Replacing config-guess with pkgsrc versions
=> Replacing config-sub with pkgsrc versions
=> Replacing install-sh with pkgsrc version
=> Replacing Rscript interpreter in scripts/stacks-hist2d-loci-samples-coverage.
=> Replacing python interpreter in scripts/*.py scripts/stacks-integrate-alignments.
WARNING: [replace-interpreter] Skipping non-existent file "scripts/*.py".
=> Replacing bash interpreter in scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-dist-extract scripts/stacks-gdb scripts/stacks-samtools-tview.
INFO: [replace-interpreter] Nothing changed in scripts/stacks-gdb.
=> Replacing Perl interpreter in scripts/*.pl.
checking for a BSD-compatible install... /bin/install -c -o pbulk -g pbulk
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /home/pbulk/build/biology/stacks/work/.tools/bin/mkdir -p
checking for gawk... /bin/gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of c++... gcc3
checking for x86_64-redhat-linux-gcc... cc
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking dependency style of cc... gcc3
checking whether cc understands -c and -o together... yes
checking whether c++ supports C++11 features by default... yes
checking for x86_64-redhat-linux-ranlib... no
checking for ranlib... ranlib
checking for x86_64-redhat-linux-ar... no
checking for x86_64-redhat-linux-lib... no
checking for x86_64-redhat-linux-link... no
checking for ar... ar
checking the archiver (ar) interface... ar
checking for omp_set_num_threads in -lgomp... yes
checking for gzread in -lz... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... cc -E
checking for grep that handles long lines and -e... (cached) /bin/grep
checking for egrep... (cached) /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for cc option to support OpenMP... none needed
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether closedir returns void... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for clock_gettime... yes
checking for functional regular expressions... yes
checking for gawk... (cached) /bin/gawk
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating htslib/Makefile
config.status: creating config.h
config.status: executing depfiles commands