[package - 130releng-armv7-quarterly][biology/hyphy] Failed for hyphy-2.5.39 in build
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Date: Tue, 19 Jul 2022 04:45:05 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://beefy12.nyi.freebsd.org/data/130releng-armv7-quarterly/5f5560073285/logs/hyphy-2.5.39.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=5f5560073285
Log:
=>> Building biology/hyphy
build started at Tue Jul 19 04:44:21 UTC 2022
port directory: /usr/ports/biology/hyphy
package name: hyphy-2.5.39
building for: FreeBSD 130releng-armv7-quarterly-job-12 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 1300139 arm
maintained by: jrm@FreeBSD.org
Makefile ident:
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===> The following configuration options are available for hyphy-2.5.39:
AVX=off: Advanced vector extensions support
===> Use 'make config' to modify these settings
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--MAINTAINER--
jrm@FreeBSD.org
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--End CONFIGURE_ARGS--
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--End CONFIGURE_ENV--
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> hyphy-2.5.39 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.3.pkg
[130releng-armv7-quarterly-job-12] Installing pkg-1.18.3...
[130releng-armv7-quarterly-job-12] Extracting pkg-1.18.3: .......... done
===> hyphy-2.5.39 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of hyphy-2.5.39
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by hyphy-2.5.39 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by hyphy-2.5.39 for building
=> SHA256 Checksum OK for veg-hyphy-2.5.39_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by hyphy-2.5.39 for building
===> Extracting for hyphy-2.5.39
=> SHA256 Checksum OK for veg-hyphy-2.5.39_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for hyphy-2.5.39
===> Applying FreeBSD patches for hyphy-2.5.39 from /usr/ports/biology/hyphy/files
===========================================================================
=======================<phase: build-depends >============================
===> hyphy-2.5.39 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-3.23.2.pkg
[130releng-armv7-quarterly-job-12] Installing cmake-3.23.2...
[130releng-armv7-quarterly-job-12] `-- Installing curl-7.84.0...
[130releng-armv7-quarterly-job-12] | `-- Installing ca_root_nss-3.78...
[130releng-armv7-quarterly-job-12] | `-- Extracting ca_root_nss-3.78: .......... done
[130releng-armv7-quarterly-job-12] | `-- Installing libnghttp2-1.48.0...
[130releng-armv7-quarterly-job-12] | `-- Extracting libnghttp2-1.48.0: .......... done
[130releng-armv7-quarterly-job-12] | `-- Installing libpsl-0.21.1_4...
[130releng-armv7-quarterly-job-12] | | `-- Installing gettext-runtime-0.21...
[130releng-armv7-quarterly-job-12] | | `-- Installing indexinfo-0.3.1...
[130releng-armv7-quarterly-job-12] | | `-- Extracting indexinfo-0.3.1: .... done
[130releng-armv7-quarterly-job-12] | | `-- Extracting gettext-runtime-0.21: .......... done
[130releng-armv7-quarterly-job-12] | | `-- Installing libidn2-2.3.2...
[130releng-armv7-quarterly-job-12] | | `-- Installing libunistring-1.0...
[130releng-armv7-quarterly-job-12] | | `-- Extracting libunistring-1.0: .......... done
[130releng-armv7-quarterly-job-12] | | `-- Extracting libidn2-2.3.2: .......... done
[130releng-armv7-quarterly-job-12] | `-- Extracting libpsl-0.21.1_4: .......... done
[130releng-armv7-quarterly-job-12] | `-- Installing libssh2-1.10.0,3...
[130releng-armv7-quarterly-job-12] | `-- Extracting libssh2-1.10.0,3: .......... done
[130releng-armv7-quarterly-job-12] `-- Extracting curl-7.84.0: .......... done
[130releng-armv7-quarterly-job-12] `-- Installing expat-2.4.8...
[130releng-armv7-quarterly-job-12] `-- Extracting expat-2.4.8: .......... done
[130releng-armv7-quarterly-job-12] `-- Installing jsoncpp-1.9.5...
[130releng-armv7-quarterly-job-12] `-- Extracting jsoncpp-1.9.5: .......... done
[130releng-armv7-quarterly-job-12] `-- Installing libarchive-3.6.1,1...
[130releng-armv7-quarterly-job-12] | `-- Installing liblz4-1.9.3,1...
[130releng-armv7-quarterly-job-12] | `-- Extracting liblz4-1.9.3,1: .......... done
[130releng-armv7-quarterly-job-12] | `-- Installing zstd-1.5.2...
[130releng-armv7-quarterly-job-12] | `-- Extracting zstd-1.5.2: .......... done
[130releng-armv7-quarterly-job-12] `-- Extracting libarchive-3.6.1,1: .......... done
[130releng-armv7-quarterly-job-12] `-- Installing libuv-1.42.0...
[130releng-armv7-quarterly-job-12] `-- Extracting libuv-1.42.0: .......... done
[130releng-armv7-quarterly-job-12] `-- Installing rhash-1.4.3...
[130releng-armv7-quarterly-job-12] `-- Extracting rhash-1.4.3: .......... done
[130releng-armv7-quarterly-job-12] Extracting cmake-3.23.2: .......... done
=====
Message from ca_root_nss-3.78:
--
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-2.5.39 depends on file: /usr/local/bin/cmake - found
===> Returning to build of hyphy-2.5.39
===> hyphy-2.5.39 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.10.2,2.pkg
[130releng-armv7-quarterly-job-12] Installing ninja-1.10.2,2...
[130releng-armv7-quarterly-job-12] `-- Installing python39-3.9.13...
[130releng-armv7-quarterly-job-12] | `-- Installing libffi-3.4.2...
[130releng-armv7-quarterly-job-12] | `-- Extracting libffi-3.4.2: .......... done
[130releng-armv7-quarterly-job-12] | `-- Installing mpdecimal-2.5.1...
[130releng-armv7-quarterly-job-12] | `-- Extracting mpdecimal-2.5.1: .......... done
[130releng-armv7-quarterly-job-12] | `-- Installing readline-8.1.2...
[130releng-armv7-quarterly-job-12] | `-- Extracting readline-8.1.2: .......... done
[130releng-armv7-quarterly-job-12] `-- Extracting python39-3.9.13: .......... done
[130releng-armv7-quarterly-job-12] Extracting ninja-1.10.2,2: ........ done
=====
Message from python39-3.9.13:
--
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
===> hyphy-2.5.39 depends on executable: ninja - found
===> Returning to build of hyphy-2.5.39
===========================================================================
=======================<phase: lib-depends >============================
===> hyphy-2.5.39 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for hyphy-2.5.39
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/hyphy/work/.build
-- The C compiler identification is Clang 11.0.1
-- The CXX compiler identification is Clang 11.0.1
-- 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
-- Performing Test HAVE_SSE3_EXTENSIONS
-- Performing Test HAVE_SSE3_EXTENSIONS - Failed
-- Performing Test HAVE_NEON_EXTENSIONS
-- Performing Test HAVE_NEON_EXTENSIONS - Failed
Set compiler flags to -fsigned-char -O3
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
-- Found CURL: /usr/local/lib/libcurl.so (found version "7.84.0")
/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-2.5.39
[ 1% 1/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/parser2.cpp.o -MF CMakeFiles/hyphy.dir/src/core/parser2.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/parser2.cp
p.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/parser2.cpp
[ 3% 2/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o -MF CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/polynoml
.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/polynoml.cpp
[ 4% 3/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o -MF CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/simp
lelist.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/simplelist.cpp
[ 6% 4/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/site.cpp.o -MF CMakeFiles/hyphy.dir/src/core/site.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/site.cpp.o -c /w
rkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/site.cpp
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/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/stack.cpp
[ 9% 6/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o.d -o CMakeFiles/hyphy.dir/src/cor
e/string_buffer.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/string_buffer.cpp
[ 10% 7/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o -MF CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o.d -o CMakeFiles/hyphy
.dir/src/core/string_file_wrapper.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/string_file_wrapper.cpp
[ 12% 8/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/strings.cpp.o -MF CMakeFiles/hyphy.dir/src/core/strings.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/strings.cp
p.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/strings.cpp
[ 13% 9/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o -MF CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o.d -o CMakeFiles/hyphy.dir/src
/core/time_difference.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/time_difference.cpp
[ 15% 10/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/topology.cpp.o -MF CMakeFiles/hyphy.dir/src/core/topology.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/topolog
y.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/topology.cpp
[ 16% 11/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o -MF CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o.d -o CMakeFiles/hyphy.di
r/src/core/translation_table.cpp.o -c /wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/translation_table.cpp
[ 18% 12/66] /nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree.cpp.o -c /
wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/tree.cpp
FAILED: CMakeFiles/hyphy.dir/src/core/tree.cpp.o
/nxb-bin/usr/bin/c++ -D_HYPHY_LIBDIRECTORY_=\"/usr/local/share/hyphy\" -D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__ -D__HYPHYCURL__ -D__MP2__ -D__MP__ -D__UNIX__ -D__ZLIB__ -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/contrib -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/lib/Link -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/new/include -I/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/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 -w -g -Weffc++ -Wextra -Wall -std=c++14 -w -Wno-int-to-pointer-cast -MD -MT CMakeFiles/hyphy.dir/src/core/tree.cpp.o -MF CMakeFiles/hyphy.dir/src/core/tree.cpp.o.d -o CMakeFiles/hyphy.dir/src/core/tree.cpp.o -c /wrkdirs/usr/p
orts/biology/hyphy/work/hyphy-2.5.39/src/core/tree.cpp
/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/tree.cpp:2748:9: error: use of undeclared identifier 'parallel'
if (parallel.lLength) {
^
/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/tree.cpp:2758:28: error: use of undeclared identifier 'parallel'
for (id = 0; id < parallel.lLength; id++) {
^
/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/tree.cpp:2759:29: error: use of undeclared identifier 'parallel'
long matrixID = parallel.get (id);
^
/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/tree.cpp:2768:24: error: use of undeclared identifier 'serial'
for ( id = 0; id < serial.lLength; id++) {
^
/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.39/src/core/tree.cpp:2769:25: error: use of undeclared identifier 'serial'
long matrixID = serial.get (id);
^
5 errors generated.
ninja: build stopped: subcommand failed.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/hyphy