+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=312 WRKLOG=/tmp/bulklog/sra-tools-3.2.0nb1/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=312 WRKLOG=/tmp/bulklog/sra-tools-3.2.0nb1/work.log
=> Checksum BLAKE2s OK for ncbi-ncbi-vdb-3.2.0.tar.gz
=> Checksum SHA512 OK for ncbi-ncbi-vdb-3.2.0.tar.gz
=> Checksum BLAKE2s OK for sra-tools-3.2.0.tar.gz
=> Checksum SHA512 OK for sra-tools-3.2.0.tar.gz
===> Installing dependencies for sra-tools-3.2.0nb1
==========================================================================
The following variables will affect the build process of this package,
sra-tools-3.2.0nb1. Their current value is shown below:
* PYTHON_VERSION_DEFAULT = 312
Based on these variables, the following variables have been set:
* 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
`/opt/pkg/bin/bmake clean' after the changes.
==========================================================================
=> Tool dependency cmake>=3.18: found cmake-3.31.7nb2
=> Tool dependency bison>=1.0: found bison-3.8.2nb1
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Full dependency hdf5>=1.8.11: found hdf5-1.14.6
=> Full dependency libxml2>=2.14.2nb1: found libxml2-2.14.2nb2
=> Full dependency python312>=3.12.0: found python312-3.12.10nb1
=> Full dependency zstd>=1.3.6: found zstd-1.5.7
=> Full dependency gettext-lib>=0.22: found gettext-lib-0.22.5
=> Full dependency libiconv>=1.9.1: found libiconv-1.17
=> Full dependency libaec>=1.0.4: found libaec-1.1.3
=> Full dependency xz>=5.0.0: found xz-5.8.1
=> Full dependency zlib>=1.1.4: found zlib-1.3.1
===> Overriding tools for sra-tools-3.2.0nb1
===> Extracting for sra-tools-3.2.0nb1
===> Patching for sra-tools-3.2.0nb1
=> Applying pkgsrc patches for sra-tools-3.2.0nb1
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-build_env.cmake
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-build_env.cmake
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-build_env.cmake,v 1.3 2025/02/02 14:25:34 bacon Exp $
|
|# static standard libs are not standard nor easy to install on Alma Linux
|
|--- build/env.cmake.orig 2025-01-29 20:24:37.167226512 +0000
|+++ build/env.cmake
--------------------------
Patching file build/env.cmake using Plan A...
Hunk #1 succeeded at 574.
Hunk #2 succeeded at 582.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-libs_kxml_xml.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-libs_kxml_xml.c
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-libs_kxml_xml.c,v 1.1 2025/04/25 07:37:15 wiz Exp $
|
|libxml2 2.14 compatibility.
|
|--- libs/kxml/xml.c.orig 2025-04-25 07:35:01.143677606 +0000
|+++ libs/kxml/xml.c
--------------------------
Patching file libs/kxml/xml.c using Plan A...
Hunk #1 succeeded at 171.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c,v 1.3 2025/02/02 14:25:34 bacon Exp $
|
|# Add NetBSD pthread_main_np() stand-in
|
|--- ncbi-vdb/libs/kproc/bsd/sysmgr.c.orig 2023-08-15 12:41:59.000000000 +0000
|+++ ncbi-vdb/libs/kproc/bsd/sysmgr.c
--------------------------
Patching file ncbi-vdb/libs/kproc/bsd/sysmgr.c using Plan A...
Hunk #1 succeeded at 30.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ngs_ngs-java_CMakeLists.txt,v 1.3 2025/02/02 14:25:34 bacon Exp $
|
|# Disable java
|
|--- ngs/ngs-java/CMakeLists.txt.orig 2023-08-13 21:46:05.343038455 +0000
|+++ ngs/ngs-java/CMakeLists.txt
--------------------------
Patching file ngs/ngs-java/CMakeLists.txt using Plan A...
Hunk #1 succeeded at 99.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ngs_ngs-python_examples_CMakeLists.txt,v 1.2 2025/02/02 14:25:34 bacon Exp $
|
|# Canonicalize python examples dir
|
|--- ngs/ngs-python/examples/CMakeLists.txt.orig 2024-11-18 12:08:54.646596198 +0000
|+++ ngs/ngs-python/examples/CMakeLists.txt
--------------------------
Patching file ngs/ngs-python/examples/CMakeLists.txt using Plan A...
Hunk #1 succeeded at 53 (offset -1 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-ngs_ngs-sdk_examples_CMakeLists.txt,v 1.2 2025/02/02 14:25:35 bacon Exp $
|
|# Canonicalize examples dir
|
|--- ngs/ngs-sdk/examples/CMakeLists.txt.orig 2024-11-18 12:10:46.495627136 +0000
|+++ ngs/ngs-sdk/examples/CMakeLists.txt
--------------------------
Patching file ngs/ngs-sdk/examples/CMakeLists.txt using Plan A...
Hunk #1 succeeded at 62.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-tools_external_driver-tool_sratools.cpp,v 1.3 2025/02/02 14:25:35 bacon Exp $
|
|# Add NetBSD pthread_main_np() stand-in
|
|--- tools/external/driver-tool/sratools.cpp.orig 2023-08-15 12:51:29.845642918 +0000
|+++ tools/external/driver-tool/sratools.cpp
--------------------------
Patching file tools/external/driver-tool/sratools.cpp using Plan A...
Hunk #1 succeeded at 580 (offset 2 lines).
done
===> Creating toolchain wrappers for sra-tools-3.2.0nb1
===> Configuring for sra-tools-3.2.0nb1
=> Substituting "binpath" in tools/external/driver-tool/file-path.posix.cpp
=> Substituting "etcdir" in ncbi-vdb/libs/kfg/config.c
=> Substituting "submoddir" in CMakeLists.txt
cd /home/pbulk/build/biology/sra-tools/work/sra-tools-3.2.0/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON ..
-- 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/sra-tools/work/.cwrapper/bin/cc - 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/sra-tools/work/.cwrapper/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at build/env.cmake:32 (cmake_policy):
The OLD behavior for policy CMP0115 will be removed from a future version
of CMake.
The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.
Call Stack (most recent call first):
CMakeLists.txt:78 (include)
VERSION=3.2.0
CMake Error at build/env.cmake:92 (message):
unknown OS SunOS
Call Stack (most recent call first):
CMakeLists.txt:78 (include)
-- Configuring incomplete, errors occurred!
*** Error code 1
Stop.
bmake[1]: stopped making "configure" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools
*** Error code 1
Stop.
bmake: stopped making "configure" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools