+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/sra-tools-3.0.6nb2/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/sra-tools-3.0.6nb2/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for outpaddling-ncbi-vdb-38972fc.tar.gz
=> Checksum SHA512 OK for outpaddling-ncbi-vdb-38972fc.tar.gz
=> Checksum BLAKE2s OK for sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz
=> Checksum SHA512 OK for sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz
===> Installing dependencies for sra-tools-3.0.6nb2
==========================================================================
The following variables will affect the build process of this package,
sra-tools-3.0.6nb2. 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 cmake>=3.18: found cmake-3.28.3
=> Tool dependency mktools-[0-9]*: found mktools-20220614
=> 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 python311>=3.11.0: found python311-3.11.8
=> Full dependency libxml2>=2.10.4nb3: found libxml2-2.12.4
=> Full dependency hdf5>=1.8.11: found hdf5-1.12.2
=> Full dependency zstd>=1.3.6: found zstd-1.5.5
===> Overriding tools for sra-tools-3.0.6nb2
===> Extracting for sra-tools-3.0.6nb2
===> Patching for sra-tools-3.0.6nb2
=> Applying pkgsrc patches for sra-tools-3.0.6nb2
=> 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 1.1 2023/08/29 00:00:25 bacon Exp $
|
|# static standard libs are not standard nor easy to install on Alma Linux
|
|--- build/env.cmake.orig 2023-08-13 18:06:02.445968665 +0000
|+++ build/env.cmake
--------------------------
Patching file build/env.cmake using Plan A...
Hunk #1 succeeded at 555.
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 1.1 2023/08/29 00:00:25 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 1.1 2023/08/29 00:00:25 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-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 1.1 2023/08/29 00:00:25 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 578.
done
===> Creating toolchain wrappers for sra-tools-3.0.6nb2
===> Configuring for sra-tools-3.0.6nb2
=> 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-984f1493e8612cd59a269569bf8c06e25e4e604c/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON ..
-- The C compiler identification is GNU 13.2.0
-- The CXX compiler identification is GNU 13.2.0
-- 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=3.0.6
CMake Error at build/env.cmake:90 (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 in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools
*** Error code 1
Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/sra-tools