[package - main-armv6-default][science/arbor] Failed for arbor-0.8_1 in build
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Date: Tue, 13 Dec 2022 14:07:21 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy8/data/main-armv6-default/p762ba391cbeb_s4e240e55d8/logs/arbor-0.8_1.log
Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=p762ba391cbeb_s4e240e55d8
Log:
=>> Building science/arbor
build started at Tue Dec 13 14:03:45 UTC 2022
port directory: /usr/ports/science/arbor
package name: arbor-0.8_1
building for: FreeBSD main-armv6-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400074 arm
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400074
Job Id: 10
!!! Jail is newer than host. (Jail: 1400074, Host: 1400073) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for arbor-0.8_1:
NATIVE=off: Use native optimization (-march=native)
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
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--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/arbor DOCSDIR=/usr/local/share/doc/arbor EXAMPLESDIR=/usr/local/share/examples/arbor WWWDIR=/usr/local/www/arbor ETCDIR=/usr/local/etc/arbor
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> arbor-0.8_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[main-armv6-default-job-10] Installing pkg-1.18.4...
[main-armv6-default-job-10] Extracting pkg-1.18.4: .......... done
===> arbor-0.8_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of arbor-0.8_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
<snip>
===> arbor-0.8_1 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.2.12.pkg
[main-armv6-default-job-10] Installing bash-5.2.12...
[main-armv6-default-job-10] `-- Installing gettext-runtime-0.21.1...
[main-armv6-default-job-10] | `-- Installing indexinfo-0.3.1...
[main-armv6-default-job-10] | `-- Extracting indexinfo-0.3.1: .... done
[main-armv6-default-job-10] `-- Extracting gettext-runtime-0.21.1: .......... done
[main-armv6-default-job-10] `-- Installing readline-8.2.0...
[main-armv6-default-job-10] `-- Extracting readline-8.2.0: .......... done
[main-armv6-default-job-10] Extracting bash-5.2.12: .......... done
===> arbor-0.8_1 depends on executable: bash - found
===> Returning to build of arbor-0.8_1
===> arbor-0.8_1 depends on package: libfmt>0 - not found
===> Installing existing package /packages/All/libfmt-8.1.1.pkg
[main-armv6-default-job-10] Installing libfmt-8.1.1...
[main-armv6-default-job-10] Extracting libfmt-8.1.1: .......... done
===> arbor-0.8_1 depends on package: libfmt>0 - found
===> Returning to build of arbor-0.8_1
===> arbor-0.8_1 depends on package: nlohmann-json>0 - not found
===> Installing existing package /packages/All/nlohmann-json-3.11.2.pkg
[main-armv6-default-job-10] Installing nlohmann-json-3.11.2...
[main-armv6-default-job-10] Extracting nlohmann-json-3.11.2: .......... done
===> arbor-0.8_1 depends on package: nlohmann-json>0 - found
===> Returning to build of arbor-0.8_1
===> arbor-0.8_1 depends on package: random123>0 - not found
===> Installing existing package /packages/All/random123-1.14.0.5.pkg
[main-armv6-default-job-10] Installing random123-1.14.0.5...
[main-armv6-default-job-10] Extracting random123-1.14.0.5: .......... done
===> arbor-0.8_1 depends on package: random123>0 - found
===> Returning to build of arbor-0.8_1
===> arbor-0.8_1 depends on package: py39-svgwrite>0 - not found
===> Installing existing package /packages/All/py39-svgwrite-1.4.3.pkg
[main-armv6-default-job-10] Installing py39-svgwrite-1.4.3...
[main-armv6-default-job-10] `-- Installing py39-setuptools-63.1.0...
[main-armv6-default-job-10] | `-- Installing python39-3.9.15_1...
[main-armv6-default-job-10] | | `-- Installing libffi-3.4.4...
[main-armv6-default-job-10] | | `-- Extracting libffi-3.4.4: .......... done
[main-armv6-default-job-10] | | `-- Installing mpdecimal-2.5.1...
[main-armv6-default-job-10] | | `-- Extracting mpdecimal-2.5.1: .......... done
[main-armv6-default-job-10] | `-- Extracting python39-3.9.15_1: .......... done
[main-armv6-default-job-10] `-- Extracting py39-setuptools-63.1.0: .......... done
[main-armv6-default-job-10] Extracting py39-svgwrite-1.4.3: .......... done
=====
Message from python39-3.9.15_1:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> arbor-0.8_1 depends on package: py39-svgwrite>0 - found
===> Returning to build of arbor-0.8_1
===> arbor-0.8_1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.24.3_2.pkg
[main-armv6-default-job-10] Installing cmake-core-3.24.3_2...
[main-armv6-default-job-10] `-- Installing expat-2.5.0...
[main-armv6-default-job-10] `-- Extracting expat-2.5.0: .......... done
[main-armv6-default-job-10] `-- Installing jsoncpp-1.9.5...
[main-armv6-default-job-10] `-- Extracting jsoncpp-1.9.5: .......... done
[main-armv6-default-job-10] `-- Installing libuv-1.44.2...
[main-armv6-default-job-10] `-- Extracting libuv-1.44.2: .......... done
[main-armv6-default-job-10] `-- Installing rhash-1.4.3...
[main-armv6-default-job-10] `-- Extracting rhash-1.4.3: .......... done
[main-armv6-default-job-10] Extracting cmake-core-3.24.3_2: .......... done
===> arbor-0.8_1 depends on file: /usr/local/bin/cmake - found
===> Returning to build of arbor-0.8_1
===> arbor-0.8_1 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.11.1,2.pkg
[main-armv6-default-job-10] Installing ninja-1.11.1,2...
[main-armv6-default-job-10] Extracting ninja-1.11.1,2: ........ done
===> arbor-0.8_1 depends on executable: ninja - found
===> Returning to build of arbor-0.8_1
===> arbor-0.8_1 depends on file: /usr/local/bin/python3.9 - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for arbor-0.8_1
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/arbor/work/.build
-- The C compiler identification is Clang 14.0.5
-- The CXX compiler identification is Clang 14.0.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /nxb-bin/usr/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: /nxb-bin/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found nlohmann_json: /usr/local/share/cmake/nlohmann_json/nlohmann_jsonConfig.cmake (found version "3.11.2")
-- Found Random123: /usr/local/include
The git submodule for google-benchmark_sub is not available.
To check out all submodules use the following commands:
git submodule init
git submodule update
Or download submodules recursively when checking out:
git clone --recursive https://github.com/arbor-sim/arbor.git
The git submodule for googletest_sub is not available.
To check out all submodules use the following commands:
git submodule init
git submodule update
Or download submodules recursively when checking out:
git clone --recursive https://github.com/arbor-sim/arbor.git
-- Found Python3: /usr/local/bin/python3.9 (found suitable version "3.9.15", minimum required is "3.7.0") found components: Interpreter
-- PYTHON_EXECUTABLE: /usr/local/bin/python3.9
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
Catalogue name: dummy
Catalogue mechanisms: dummy
Extra cxx files:
Catalogue sources: /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/test/unit/dummy
Catalogue output: /wrkdirs/usr/ports/science/arbor/work/.build/test/unit/generated/dummy
Arbor cxx flags: $<$<BUILD_INTERFACE:$<COMPILE_LANGUAGE:CXX>>:-fvisibility=hidden>;$<$<BUILD_INTERFACE:$<COMPILE_LANGUAGE:CUDA>>:-Xcompiler=-fvisibility=hidden>
Arbor cxx compiler:
Current cxx compiler: /nxb-bin/usr/bin/c++
Catalogue name: ou
Catalogue mechanisms: ornstein_uhlenbeck
Extra cxx files:
Catalogue sources: /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/example/ornstein_uhlenbeck
Catalogue output: /wrkdirs/usr/ports/science/arbor/work/.build/example/ornstein_uhlenbeck/generated/ou
Arbor cxx flags: $<$<BUILD_INTERFACE:$<COMPILE_LANGUAGE:CXX>>:-fvisibility=hidden>;$<$<BUILD_INTERFACE:$<COMPILE_LANGUAGE:CUDA>>:-Xcompiler=-fvisibility=hidden>
Arbor cxx compiler:
Current cxx compiler: /nxb-bin/usr/bin/c++
-- Failed to locate sphinx-build executable (missing: SPHINX_EXECUTABLE)
-- Found PY_svgwrite: /usr/local/lib/python3.9/site-packages/svgwrite
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
BOOST_PYTHON_SUFFIX
CMAKE_COLOR_MAKEFILE
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
FETCHCONTENT_FULLY_DISCONNECTED
Python_ADDITIONAL_VERSIONS
-- Build files have been written to: /wrkdirs/usr/ports/science/arbor/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for arbor-0.8_1
[ 0% 1/173] cd /wrkdirs/usr/ports/science/arbor/work/.build/arbor/include && true
[ 1% 2/173] cd /wrkdirs/usr/ports/science/arbor/work/.build/arbor/include && /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/arbor/include/git-source-id 0.8.0 none RELEASE > version.hpp-test
[ 1% 3/173] cd /wrkdirs/usr/ports/science/arbor/work/.build/arbor/include && /usr/local/bin/cmake -E copy_if_different version.hpp-test arbor/version.hpp
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[ 15% 26/173] /nxb-bin/usr/bin/c++ -DFMT_HEADER_ONLY=1 -Dlibmodcc_EXPORTS_STATIC -I/wrkdirs/usr/ports/science/arbor/work/arbor-0.8/modcc -I/wrkdirs/usr/ports/science/arbor/work/.build/modcc/include -I/wrkdirs/usr/ports/science/arbor/work/arbor-0.8/arbor/include -I/wrkdirs/usr/ports/science/arbor/work/.build/arbor/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIC -Wall -Wno-missing-braces -Wno-potentially-evaluated-expression -Wno-unused-function -Wno-unused-local-typedef -Wno-format-security -std=c++17 -MD -MT modcc/CMakeFiles/libmodcc.dir/printer/printerutil.cpp.o -MF modcc/CMakeFiles/libmodcc.dir/printer/printerutil.cpp.o.d -o modcc/CMakeFiles/libmodcc.dir/printer/printerutil.cpp.o -c /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/modcc/printer/printerutil.cpp
[ 15% 27/173] : && /usr/local/bin/cmake -E rm -f lib/libmodcc.a && /nxb-bin/usr/bin/llvm-ar qc lib/libmodcc.a modcc/CMakeFiles/libmodcc.dir/astmanip.cpp.o modcc/CMakeFiles/libmodcc.dir/blocks.cpp.o modcc/CMakeFiles/libmodcc.dir/errorvisitor.cpp.o modcc/CMakeFiles/libmodcc.dir/expression.cpp.o modcc/CMakeFiles/libmodcc.dir/functionexpander.cpp.o modcc/CMakeFiles/libmodcc.dir/functioninliner.cpp.o modcc/CMakeFiles/libmodcc.dir/procinliner.cpp.o modcc/CMakeFiles/libmodcc.dir/lexer.cpp.o modcc/CMakeFiles/libmodcc.dir/kineticrewriter.cpp.o modcc/CMakeFiles/libmodcc.dir/linearrewriter.cpp.o modcc/CMakeFiles/libmodcc.dir/module.cpp.o modcc/CMakeFiles/libmodcc.dir/parser.cpp.o modcc/CMakeFiles/libmodcc.dir/solvers.cpp.o modcc/CMakeFiles/libmodcc.dir/symdiff.cpp.o modcc/CMakeFiles/libmodcc.dir/symge.cpp.o modcc/CMakeFiles/libmodcc.dir/token.cpp.o modcc/CMakeFiles/libmodcc.dir/io/prefixbuf.cpp.o modcc/CMakeFiles/libmodcc.dir/printer/cexpr_emit.cpp.o modcc/CMakeFiles/libmodcc.dir/printer/cprin
ter.cpp.o modcc/CMakeFiles/libmodcc.dir/printer/marks.cpp.o modcc/CMakeFiles/libmodcc.dir/printer/gpuprinter.cpp.o modcc/CMakeFiles/libmodcc.dir/printer/infoprinter.cpp.o modcc/CMakeFiles/libmodcc.dir/printer/printerutil.cpp.o && /nxb-bin/usr/bin/llvm-ranlib lib/libmodcc.a && :
[ 16% 28/173] /nxb-bin/usr/bin/c++ -DFMT_HEADER_ONLY=1 -I/wrkdirs/usr/ports/science/arbor/work/arbor-0.8/modcc -I/wrkdirs/usr/ports/science/arbor/work/.build/modcc/include -I/wrkdirs/usr/ports/science/arbor/work/arbor-0.8/arbor/include -I/wrkdirs/usr/ports/science/arbor/work/.build/arbor/include -I/wrkdirs/usr/ports/science/arbor/work/arbor-0.8/ext/tinyopt/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fPIE -Wall -Wno-missing-braces -Wno-potentially-evaluated-expression -Wno-unused-function -Wno-unused-local-typedef -Wno-format-security -std=c++17 -MD -MT modcc/CMakeFiles/modcc.dir/modcc.cpp.o -MF modcc/CMakeFiles/modcc.dir/modcc.cpp.o.d -o modcc/CMakeFiles/modcc.dir/modcc.cpp.o -c /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/modcc/modcc.cpp
In file included from /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/modcc/modcc.cpp:8:
/wrkdirs/usr/ports/science/arbor/work/arbor-0.8/ext/tinyopt/include/tinyopt/tinyopt.h:894:18: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if (c==EOF) break;
~^ ~~~
1 warning generated.
[ 16% 29/173] : && /nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fstack-protector-strong modcc/CMakeFiles/modcc.dir/modcc.cpp.o -o bin/modcc lib/libmodcc.a && :
[ 17% 30/173] cd /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms && /wrkdirs/usr/ports/science/arbor/work/.build/bin/modcc -t cpu -N arb -c bbp -o /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/CaDynamics_E2.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Ca_HVA.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Ca_LVAst.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Ih.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Im.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/K_Pst.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/K_Tst.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Nap_Et2.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/NaTa_t.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/NaTs2_t.mod /wrkdirs/usr/ports/science/ar
bor/work/arbor-0.8/mechanisms/bbp/SK_E2.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/SKv3_1.mod
FAILED: mechanisms/generated/bbp/bbp_catalogue.cpp mechanisms/generated/bbp/CaDynamics_E2_cpu.cpp mechanisms/generated/bbp/Ca_HVA_cpu.cpp mechanisms/generated/bbp/Ca_LVAst_cpu.cpp mechanisms/generated/bbp/Ih_cpu.cpp mechanisms/generated/bbp/Im_cpu.cpp mechanisms/generated/bbp/K_Pst_cpu.cpp mechanisms/generated/bbp/K_Tst_cpu.cpp mechanisms/generated/bbp/Nap_Et2_cpu.cpp mechanisms/generated/bbp/NaTa_t_cpu.cpp mechanisms/generated/bbp/NaTs2_t_cpu.cpp mechanisms/generated/bbp/SK_E2_cpu.cpp mechanisms/generated/bbp/SKv3_1_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/bbp_catalogue.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/CaDynamics_E2_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/Ca_HVA_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/Ca_LVAst_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/Ih_cpu.cpp /wrkdirs/usr/ports/science/arbor/w
ork/.build/mechanisms/generated/bbp/Im_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/K_Pst_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/K_Tst_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/Nap_Et2_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/NaTa_t_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/NaTs2_t_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/SK_E2_cpu.cpp /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp/SKv3_1_cpu.cpp
cd /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms && /wrkdirs/usr/ports/science/arbor/work/.build/bin/modcc -t cpu -N arb -c bbp -o /wrkdirs/usr/ports/science/arbor/work/.build/mechanisms/generated/bbp /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/CaDynamics_E2.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Ca_HVA.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Ca_LVAst.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Ih.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Im.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/K_Pst.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/K_Tst.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/Nap_Et2.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/NaTa_t.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/NaTs2_t.mod /wrkdirs/usr/ports/science/arbor/work/arbor
-0.8/mechanisms/bbp/SK_E2.mod /wrkdirs/usr/ports/science/arbor/work/arbor-0.8/mechanisms/bbp/SKv3_1.mod
qemu: uncaught target signal 11 (Segmentation fault) - core dumped
ninja: build stopped: subcommand failed.
*** Error code 1
Stop.
make: stopped in /usr/ports/science/arbor