[package - main-amd64-default][biology/hyphy] Failed for hyphy-2.5.32 in build
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Date: Wed, 17 Nov 2021 01:52:16 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: jrm@FreeBSD.org
Log URL: http://beefy18.nyi.freebsd.org/data/main-amd64-default/p5718aa5f2a8f_s9b8eb1c5b6/logs/hyphy-2.5.32.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=p5718aa5f2a8f_s9b8eb1c5b6
Log:
=>> Building biology/hyphy
build started at Wed Nov 17 01:52:07 UTC 2021
port directory: /usr/ports/biology/hyphy
package name: hyphy-2.5.32
building for: FreeBSD main-amd64-default-job-11 14.0-CURRENT FreeBSD 14.0-CURRENT 1400042 amd64
maintained by: jrm@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400008
Jail OSVERSION: 1400042
Job Id: 11
!!! Jail is newer than host. (Jail: 1400042, Host: 1400008) !!!
!!! 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 hyphy-2.5.32:
AVX=off: Advanced vector extensions support
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jrm@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hyphy/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hyphy/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hyphy/work/.cache HOME=/wrkdirs/usr/ports/biology/hyphy/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hyphy/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
--End CONFIGURE_ENV--
--MAKE_ENV--
NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hyphy/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hyphy/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/hyphy/work/.cache HOME=/wrkdirs/usr/ports/biology/hyphy/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hyphy/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/hyphy/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644"
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--End resource limits--
=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> hyphy-2.5.32 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5.pkg
[main-amd64-default-job-11] Installing pkg-1.17.5...
[main-amd64-default-job-11] Extracting pkg-1.17.5: .......... done
===> hyphy-2.5.32 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of hyphy-2.5.32
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by hyphy-2.5.32 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by hyphy-2.5.32 for building
=> SHA256 Checksum OK for veg-hyphy-2.5.32_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by hyphy-2.5.32 for building
===> Extracting for hyphy-2.5.32
=> SHA256 Checksum OK for veg-hyphy-2.5.32_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for hyphy-2.5.32
===========================================================================
=======================<phase: build-depends >============================
===> hyphy-2.5.32 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-3.21.4_1.pkg
[main-amd64-default-job-11] Installing cmake-3.21.4_1...
[main-amd64-default-job-11] `-- Installing curl-7.79.1...
[main-amd64-default-job-11] | `-- Installing ca_root_nss-3.71...
[main-amd64-default-job-11] | `-- Extracting ca_root_nss-3.71: ........ done
[main-amd64-default-job-11] | `-- Installing libnghttp2-1.46.0...
[main-amd64-default-job-11] | `-- Extracting libnghttp2-1.46.0: .......... done
[main-amd64-default-job-11] | `-- Installing libssh2-1.9.0_3,3...
[main-amd64-default-job-11] | `-- Extracting libssh2-1.9.0_3,3: .......... done
[main-amd64-default-job-11] `-- Extracting curl-7.79.1: .......... done
[main-amd64-default-job-11] `-- Installing expat-2.4.1...
[main-amd64-default-job-11] `-- Extracting expat-2.4.1: .......... done
[main-amd64-default-job-11] `-- Installing jsoncpp-1.9.5...
[main-amd64-default-job-11] `-- Extracting jsoncpp-1.9.5: .......... done
[main-amd64-default-job-11] `-- Installing libarchive-3.5.1,1...
[main-amd64-default-job-11] | `-- Installing liblz4-1.9.3,1...
[main-amd64-default-job-11] | `-- Extracting liblz4-1.9.3,1: .......... done
[main-amd64-default-job-11] `-- Extracting libarchive-3.5.1,1: .......... done
[main-amd64-default-job-11] `-- Installing libuv-1.42.0...
[main-amd64-default-job-11] `-- Extracting libuv-1.42.0: .......... done
[main-amd64-default-job-11] `-- Installing rhash-1.4.2...
[main-amd64-default-job-11] | `-- Installing gettext-runtime-0.21...
[main-amd64-default-job-11] | | `-- Installing indexinfo-0.3.1...
[main-amd64-default-job-11] | | `-- Extracting indexinfo-0.3.1: .... done
[main-amd64-default-job-11] | `-- Extracting gettext-runtime-0.21: .......... done
[main-amd64-default-job-11] `-- Extracting rhash-1.4.2: .......... done
[main-amd64-default-job-11] Extracting cmake-3.21.4_1: .......... done
=====
Message from ca_root_nss-3.71:
--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.
Assessment and verification of trust is the complete responsibility of the
system administrator.
This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.
This enables SSL Certificate Verification by client software without manual
intervention.
If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.
* /etc/ssl/cert.pem
* /usr/local/etc/ssl/cert.pem
* /usr/local/openssl/cert.pem
===> hyphy-2.5.32 depends on file: /usr/local/bin/cmake - found
===> Returning to build of hyphy-2.5.32
===> hyphy-2.5.32 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.10.2,2.pkg
[main-amd64-default-job-11] Installing ninja-1.10.2,2...
[main-amd64-default-job-11] `-- Installing python38-3.8.12_1...
[main-amd64-default-job-11] | `-- Installing libffi-3.3_1...
[main-amd64-default-job-11] | `-- Extracting libffi-3.3_1: .......... done
[main-amd64-default-job-11] | `-- Installing mpdecimal-2.5.1...
[main-amd64-default-job-11] | `-- Extracting mpdecimal-2.5.1: .......... done
[main-amd64-default-job-11] | `-- Installing readline-8.1.1...
[main-amd64-default-job-11] | `-- Extracting readline-8.1.1: .......... done
[main-amd64-default-job-11] `-- Extracting python38-3.8.12_1: .......... done
[main-amd64-default-job-11] Extracting ninja-1.10.2,2: ........ done
=====
Message from python38-3.8.12_1:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py38-gdbm databases/py-gdbm@py38
py38-sqlite3 databases/py-sqlite3@py38
py38-tkinter x11-toolkits/py-tkinter@py38
===> hyphy-2.5.32 depends on executable: ninja - found
===> Returning to build of hyphy-2.5.32
===========================================================================
=======================<phase: lib-depends >============================
===> hyphy-2.5.32 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for hyphy-2.5.32
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/hyphy/work/.build
-- The C compiler identification is Clang 13.0.0
-- The CXX compiler identification is Clang 13.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /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: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_SSE3_EXTENSIONS
-- Performing Test HAVE_SSE3_EXTENSIONS - Success
-- Performing Test HAVE_NEON_EXTENSIONS
-- Performing Test HAVE_NEON_EXTENSIONS - Failed
Set compiler flags to -fsigned-char -O3 -msse3
-- Found OpenMP_C: -fopenmp=libomp (found version "5.0")
-- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0")
-- Found OpenMP: TRUE (found version "5.0")
-- Found CURL: /usr/local/lib/libcurl.so (found version "7.79.1")
/usr/local/lib/libcurl.so
-- Found ZLIB: /usr/lib/libz.so (found suitable version "1.2.11", minimum required is "1.2.9")
Node not installed; API documentation will not be generated
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_COLOR_MAKEFILE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
THREADS_HAVE_PTHREAD_ARG
-- Build files have been written to: /wrkdirs/usr/ports/biology/hyphy/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for hyphy-2.5.32
[ 1% 2/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/contrib/SQLite-3.8.2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -MF CMakeFiles/hyphy.dir/src/core/_hyE
xecutionContext.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/_hyExecutionContext.cpp
[ 3% 3/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/contrib/SQLite-3.8.2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.
o.d -o CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/alignment.cpp
FAILED: CMakeFiles/hyphy.dir/src/core/alignment.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/contrib/SQLite-3.8.2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/alignment.cpp.o -MF CMakeFiles/hyphy.dir/src/core/alignment.cpp.o.d -o CMake
Files/hyphy.dir/src/core/alignment.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/alignment.cpp
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/alignment.cpp:44:
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/alignment.h:44:
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/likefunc.h:44:
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/category.h:44:
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/batchlan.h:47:
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/dataset.h:47:
/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/function_templates.h:160:15: error: duplicate directives 'unroll_count(8)' and '#pragma unroll(4)'
#pragma GCC unroll 4
^
1 error generated.
[ 4% 3/66] /usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/contrib/SQLite-3.8.2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associa
tive_list.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/associative_list.cpp
FAILED: CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o
/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D_SLKP_USE_SSE_INTRINSICS -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/contrib/SQLite-3.8.2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fsigned-char -O3 -msse3 -w -g -fopenmp=libomp -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -MF CMakeFiles/hyphy.dir/src/core/associative_list.cp
p.o.d -o CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/associative_list.cpp
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/associative_list.cpp:62:
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/global_object_lists.h:42:
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/dataset_filter.h:44:
In file included from /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/dataset.h:47:
/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.32/src/core/include/function_templates.h:160:15: error: duplicate directives 'unroll_count(8)' and '#pragma unroll(4)'
#pragma GCC unroll 4
^
1 error generated.
ninja: build stopped: subcommand failed.
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/hyphy