+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/stacks-2.60nb2/work.log
+ su pbulk -c '"$@"' make /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/stacks-2.60nb2/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-2.60nb2
==========================================================================
The following variables will affect the build process of this package,
stacks-2.60nb2. Their current value is shown below:
* PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp
* PYTHON_VERSION_DEFAULT = 310
Based on these variables, the following variables have been set:
* BLAS_INCLUDES (not defined)
* BLAS_LIBS = -lblas
* BLAS_TYPE = netlib
* CBLAS_LIBS = -lcblas -lblas
* LAPACKE_LIBS = -llapacke -llapack -lblas
* LAPACK_LIBS = -llapack -lblas
* PYPACKAGE = python310
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-5.36.0
=> Full dependency python310>=3.10.0: found python310-3.10.9
=> Full dependency R>=4.2.0nb1: found R-4.2.0nb3
=> Full dependency zlib>=1.2.3: found zlib-1.2.13
===> Overriding tools for stacks-2.60nb2
===> Extracting for stacks-2.60nb2
===> Patching for stacks-2.60nb2
=> Applying pkgsrc patches for stacks-2.60nb2
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/stacks/patches/patch-src_Hwp.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-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-el7-trunk-x86_64/biology/stacks/patches/patch-src_kmers.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-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-el7-trunk-x86_64/biology/stacks/patches/patch-src_PopSum.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-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-el7-trunk-x86_64/biology/stacks/patches/patch-src_smoothing__utils.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-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-el7-trunk-x86_64/biology/stacks/patches/patch-src_utils.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-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
=> Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/stacks/patches/patch-src_Vcf.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-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
===> Creating toolchain wrappers for stacks-2.60nb2
===> Configuring for stacks-2.60nb2
=> 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 portability problems in extracted files
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... no
configure: error: in `/home/pbulk/build/biology/stacks/work/stacks-2.60':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
*** Error code 77
Stop.
bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/stacks
*** Error code 1
Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/stacks