+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/kallisto-0.51.1/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/kallisto-0.51.1/work.log
WARNING: USE_CMAKE is deprecated; use devel/cmake/build.mk instead.
=> Checksum BLAKE2s OK for kallisto-0.51.1.tar.gz
=> Checksum SHA512 OK for kallisto-0.51.1.tar.gz
===> Installing dependencies for kallisto-0.51.1
=> Tool dependency autoconf>=2.50: found autoconf-2.72
=> Tool dependency cmake>=3.18: found cmake-3.31.1
=> 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
=> Full dependency hdf5>=1.8.11: found hdf5-1.12.2
=> Full dependency htslib>=1.21: found htslib-1.21nb3
=> Full dependency libaec>=1.0.4: found libaec-1.0.6
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
===> Overriding tools for kallisto-0.51.1
===> Extracting for kallisto-0.51.1
/bin/cp /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/files/kallisto-test /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1
/usr/bin/rm -rf /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/htslib
===> Patching for kallisto-0.51.1
=> Applying pkgsrc patches for kallisto-0.51.1
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-CMakeLists.txt
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-CMakeLists.txt
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-CMakeLists.txt,v 1.6 2024/09/20 00:03:15 bacon Exp $
|
|# Use external htslib
|
|--- CMakeLists.txt.orig	2024-07-20 19:07:27.000000000 +0000
|+++ CMakeLists.txt
--------------------------
Patching file CMakeLists.txt using Plan A...
Hunk #1 succeeded at 23.
Hunk #2 succeeded at 69.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.3 2024/09/20 00:03:15 bacon Exp $
|
|# Respect pkgsrc build flags
|
|--- ext/bifrost/CMakeLists.txt.orig	2024-07-23 11:56:13.172038229 +0000
|+++ ext/bifrost/CMakeLists.txt
--------------------------
Patching file ext/bifrost/CMakeLists.txt using Plan A...
Hunk #1 succeeded at 6.
Hunk #2 succeeded at 19.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_BitContainer.cpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ext_bifrost_src_BitContainer.cpp,v 1.3 2024/09/20 00:03:15 bacon Exp $
|
|# vfscanf() not found on NetBSD 9
|
|--- ext/bifrost/src/BitContainer.cpp.orig	2023-11-01 12:46:19.000000000 +0000
|+++ ext/bifrost/src/BitContainer.cpp
--------------------------
Patching file ext/bifrost/src/BitContainer.cpp using Plan A...
Hunk #1 succeeded at 1.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_ColorSet.cpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ext_bifrost_src_ColorSet.cpp,v 1.3 2024/09/20 00:03:15 bacon Exp $
|
|# vfscanf() not found on NetBSD 9
|
|--- ext/bifrost/src/ColorSet.cpp.orig	2023-11-03 12:48:11.435933052 +0000
|+++ ext/bifrost/src/ColorSet.cpp
--------------------------
Patching file ext/bifrost/src/ColorSet.cpp using Plan A...
Hunk #1 succeeded at 1.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_libpopcnt.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ext_bifrost_src_libpopcnt.h,v 1.3 2024/09/20 00:03:15 bacon Exp $
|
|# Use native popcnt
|
|--- ext/bifrost/src/libpopcnt.h.orig	2023-07-24 12:34:08.037669065 +0000
|+++ ext/bifrost/src/libpopcnt.h
--------------------------
Patching file ext/bifrost/src/libpopcnt.h using Plan A...
Hunk #1 succeeded at 32.
Hunk #2 succeeded at 586.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-ext_bifrost_src_strict__fstream.hpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ext_bifrost_src_strict__fstream.hpp,v 1.3 2024/09/20 00:03:15 bacon Exp $
|
|# Portability
|
|--- ext/bifrost/src/strict_fstream.hpp.orig	2023-06-27 10:45:00.000000000 +0000
|+++ ext/bifrost/src/strict_fstream.hpp
--------------------------
Patching file ext/bifrost/src/strict_fstream.hpp using Plan A...
Hunk #1 succeeded at 64.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_Bootstrap.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_Bootstrap.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_Bootstrap.h,v 1.3 2024/09/20 00:03:15 bacon Exp $
|
|# Portability
|
|--- src/Bootstrap.h.orig	2020-04-01 16:56:42 UTC
|+++ src/Bootstrap.h
--------------------------
Patching file src/Bootstrap.h using Plan A...
Hunk #1 succeeded at 1.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_CMakeLists.txt
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_CMakeLists.txt
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_CMakeLists.txt,v 1.6 2024/09/20 00:03:15 bacon Exp $
|
|# Use external htslib
|
|--- src/CMakeLists.txt.orig	2024-07-23 11:52:01.089699466 +0000
|+++ src/CMakeLists.txt
--------------------------
Patching file src/CMakeLists.txt using Plan A...
Hunk #1 succeeded at 3.
Hunk #2 succeeded at 17.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_kseq.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_kseq.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_kseq.h,v 1.4 2024/09/20 00:03:15 bacon Exp $
|
|# Portability
|
|--- src/kseq.h.orig	2019-11-04 16:28:52 UTC
|+++ src/kseq.h
--------------------------
Patching file src/kseq.h using Plan A...
Hunk #1 succeeded at 28 (offset -4 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_main.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/kallisto/patches/patch-src_main.cpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_main.cpp,v 1.3 2024/09/20 00:03:15 bacon Exp $
|
|# Portability
|
|--- src/main.cpp.orig	2023-11-01 12:46:19.000000000 +0000
|+++ src/main.cpp
--------------------------
Patching file src/main.cpp using Plan A...
Hunk #1 succeeded at 11.
done
===> Creating toolchain wrappers for kallisto-0.51.1
===> Configuring for kallisto-0.51.1
=> Substituting "test" in kallisto-test
=> Fixing CMAKE_MODULE_PATH in CMakeLists.txt
INFO: [subst.mk:cmake] Nothing changed in "CMakeLists.txt".
=> Checking for portability problems in extracted files
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- The C compiler identification is GNU 13.3.0
-- The CXX compiler identification is GNU 13.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /home/pbulk/build/biology/kallisto/work/.cwrapper/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/pbulk/build/biology/kallisto/work/.cwrapper/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS_CXX17
-- Performing Test COMPILER_SUPPORTS_CXX17 - Success
shared build
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found HDF5: /opt/pkg/lib/libhdf5.so;/opt/pkg/lib/libsz.so;/opt/pkg/lib/libz.so;/usr/lib/64/libdl.so;/usr/lib/64/libm.so (found version "1.12.2")
-- Found ZLIB: /opt/pkg/lib/libz.so (found version "1.3.1")
-- Configuring done (11.0s)
-- Generating done (0.1s)
-- Build files have been written to: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1
=> Rewrite cmake Dependencies files