[package - 140arm64-quarterly][science/py-MDAnalysis] Failed for py39-MDAnalysis-2.3.0_1 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Fri, 03 May 2024 14:00:09 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/ampere1/data/140arm64-quarterly/1658bffbb679/logs/py39-MDAnalysis-2.3.0_1.log
Build URL:      https://pkg-status.freebsd.org/ampere1/build.html?mastername=140arm64-quarterly&build=1658bffbb679
Log:

=>> Building science/py-MDAnalysis
build started at Fri May  3 13:58:22 UTC 2024
port directory: /usr/ports/science/py-MDAnalysis
package name: py39-MDAnalysis-2.3.0_1
building for: FreeBSD 140arm64-quarterly-job-04 14.0-RELEASE-p6 FreeBSD 14.0-RELEASE-p6 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 1507 Apr 14 01:02 /usr/ports/science/py-MDAnalysis/Makefile
Ports top last git commit: 1658bffbb
Ports top unclean checkout: no
Port dir last git commit: 1b931669d
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1400097
Job Id: 04

---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400097
UNAME_v=FreeBSD 14.0-RELEASE-p6
UNAME_r=14.0-RELEASE-p6
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.1-30-g79e3edcd
MASTERMNT=/usr/local/poudriere/data/.m/140arm64-quarterly/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/140arm64-quarterly/04/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=140arm64-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/140arm64-quarterly/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.1-30-g79e3edcd
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---

---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=py39
MAKE_ARGS= FLAVOR=py39
---End Poudriere Port Flags/Env---

---Begin OPTIONS List---
---End OPTIONS List---

--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39  XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39  XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.cache  HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39  XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39  XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.cache  HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local  LOCALBASE=/usr/local  CC="cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -fno-strict-aliasing "  CPP="cpp" CPPFLAGS=""  LDFLAGS=" -s -fstack-protector-strong " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing  " BSD_INSTALL_PROGRAM="ins
tall  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 0644"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444"
--End MAKE_ENV--

--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python3.9  PYTHON_LIBDIR=lib/python3.9  PYTHON_PLATFORM=freebsd14  PYTHON_SITELIBDIR=lib/python3.9/site-packages  PYTHON_SUFFIX=39  PYTHON_EXT_SUFFIX=.cpython-39  PYTHON_VER=3.9  PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/MDAnalysis"  EXAMPLESDIR="share/examples/MDAnalysis"  DATADIR="share/MDAnalysis"  WWWDIR="www/MDAnalysis"  ETCDIR="etc/MDAnalysis"
--End PLIST_SUB--

--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.9  PYTHON_LIBDIR=/usr/local/lib/python3.9  PYTHON_PLATFORM=freebsd14  PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages  PYTHON_SUFFIX=39  PYTHON_EXT_SUFFIX=.cpython-39  PYTHON_VER=3.9  PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/MDAnalysis DOCSDIR=/usr/local/share/doc/MDAnalysis EXAMPLESDIR=/usr/local/share/examples/MDAnalysis  WWWDIR=/usr/local/www/MDAnalysis ETCDIR=/usr/local/etc/MDAnalysis
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
####  ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure.  It currently retries the same
# failed mirror and then fails rather then trying another.  It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  1048576
stack size              (kbytes, -s)  1048576
core file size      (512-blocks, -c)  unlimited
max memory size         (kbytes, -m)  unlimited
locked memory           (kbytes, -l)  unlimited
max user processes              (-u)  89999
open files                      (-n)  8192
virtual mem size        (kbytes, -v)  unlimited
swap limit              (kbytes, -w)  unlimited
socket buffer size       (bytes, -b)  unlimited
pseudo-terminals                (-p)  unlimited
kqueues                         (-k)  unlimited
umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   py39-MDAnalysis-2.3.0_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.21.2.pkg
[140arm64-quarterly-job-04] Installing pkg-1.21.2...
[140arm64-quarterly-job-04] Extracting pkg-1.21.2: .......... done
===>   py39-MDAnalysis-2.3.0_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of py39-MDAnalysis-2.3.0_1
===========================================================================
=======================<phase: fetch-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch          >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by py39-MDAnalysis-2.3.0_1 for building
===========================================================================
=======================<phase: checksum       >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by py39-MDAnalysis-2.3.0_1 for building
=> SHA256 Checksum OK for MDAnalysis-2.3.0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract        >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by py39-MDAnalysis-2.3.0_1 for building
===>  Extracting for py39-MDAnalysis-2.3.0_1
=> SHA256 Checksum OK for MDAnalysis-2.3.0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch          >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  Patching for py39-MDAnalysis-2.3.0_1
===>  Applying FreeBSD patches for py39-MDAnalysis-2.3.0_1 from /usr/ports/science/py-MDAnalysis/files
===========================================================================
=======================<phase: build-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   py39-MDAnalysis-2.3.0_1 depends on package: py39-numpy>=1.16,1<1.26,1 - not found
===>   Installing existing package /packages/All/py39-numpy-1.25.0_6,1.pkg
[140arm64-quarterly-job-04] Installing py39-numpy-1.25.0_6,1...
[140arm64-quarterly-job-04] `-- Installing gcc13-13.2.0_4...
[140arm64-quarterly-job-04] |   `-- Installing binutils-2.40_5,1...
[140arm64-quarterly-job-04] |   | `-- Installing gettext-runtime-0.22.5...
[140arm64-quarterly-job-04] |   |   `-- Installing indexinfo-0.3.1...
[140arm64-quarterly-job-04] |   |   `-- Extracting indexinfo-0.3.1: .... done
[140arm64-quarterly-job-04] |   | `-- Extracting gettext-runtime-0.22.5: .......... done
[140arm64-quarterly-job-04] |   | `-- Installing zstd-1.5.6...
[140arm64-quarterly-job-04] |   |   `-- Installing liblz4-1.9.4_1,1...
[140arm64-quarterly-job-04] |   |   `-- Extracting liblz4-1.9.4_1,1: .......... done
[140arm64-quarterly-job-04] |   | `-- Extracting zstd-1.5.6: .......... done
[140arm64-quarterly-job-04] |   `-- Extracting binutils-2.40_5,1: .......... done
[140arm64-quarterly-job-04] |   `-- Installing gmp-6.3.0...
[140arm64-quarterly-job-04] |   `-- Extracting gmp-6.3.0: .......... done
[140arm64-quarterly-job-04] |   `-- Installing mpc-1.3.1_1...
[140arm64-quarterly-job-04] |   | `-- Installing mpfr-4.2.1,1...
[140arm64-quarterly-job-04] |   | `-- Extracting mpfr-4.2.1,1: .......... done
[140arm64-quarterly-job-04] |   `-- Extracting mpc-1.3.1_1: ......... done
[140arm64-quarterly-job-04] `-- Extracting gcc13-13.2.0_4: .......... done
[140arm64-quarterly-job-04] `-- Installing openblas-0.3.25,2...
[140arm64-quarterly-job-04] `-- Extracting openblas-0.3.25,2: .......... done
[140arm64-quarterly-job-04] `-- Installing py39-setuptools-63.1.0_1...
[140arm64-quarterly-job-04] |   `-- Installing python39-3.9.18_2...
[140arm64-quarterly-job-04] |   | `-- Installing libffi-3.4.4_1...
<snip>
      #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
                                 ^
3 warnings generated.
cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -o build/lib.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/c_distances.cpython-39.so
building 'MDAnalysis.lib.c_distances_openmp' extension
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -DPARALLEL -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/include -I/usr/local/include/python3.9 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/c_distances_openmp.c:797:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
1 warning generated.
cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -o build/lib.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39.so -fopenmp
building 'MDAnalysis.lib.qcprot' extension
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MDAnalysis/lib/qcprot.c -o build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/qcprot.c:780:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
MDAnalysis/lib/qcprot.c:2385:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
    for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
                        ~~~~~~~~~ ^ ~~~~~~~~~
MDAnalysis/lib/qcprot.c:2593:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
    for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
                        ~~~~~~~~~ ^ ~~~~~~~~~
3 warnings generated.
cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/qcprot.o -L/usr/local/lib -o build/lib.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/qcprot.cpython-39.so
building 'MDAnalysis.lib._transformations' extension
creating build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/src
creating build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/src/transformations
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/src/transformations/transformations.c:73:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
MDAnalysis/lib/src/transformations/transformations.c:2122:35: warning: 'PyUnicode_GetSize' is deprecated [-Wdeprecated-declarations]
    if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) {
                                  ^
/usr/local/include/python3.9/unicodeobject.h:177:1: note: 'PyUnicode_GetSize' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize(
^
/usr/local/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                     ^
2 warnings generated.
cc -shared -s -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -o build/lib.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/_transformations.cpython-39.so
building 'MDAnalysis.lib.formats.libmdaxdr' extension
creating build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/formats/src
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/include/python3.9 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/libmdaxdr.c:807:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from MDAnalysis/lib/formats/libmdaxdr.c:816:
/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
 /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
 ^
In file included from MDAnalysis/lib/formats/libmdaxdr.c:817:
/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: '/*' within block comment [-Wcomment]
 /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
 ^
In file included from MDAnalysis/lib/formats/libmdaxdr.c:818:
/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment]
 /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
 ^
MDAnalysis/lib/formats/libmdaxdr.c:28469:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
                    CYTHON_FALLTHROUGH;
                    ^
MDAnalysis/lib/formats/libmdaxdr.c:400:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
      #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
                                 ^
MDAnalysis/lib/formats/libmdaxdr.c:28480:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
                    CYTHON_FALLTHROUGH;
                    ^
MDAnalysis/lib/formats/libmdaxdr.c:400:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
      #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
                                 ^
MDAnalysis/lib/formats/libmdaxdr.c:29345:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
                    CYTHON_FALLTHROUGH;
                    ^
MDAnalysis/lib/formats/libmdaxdr.c:400:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
      #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
                                 ^
MDAnalysis/lib/formats/libmdaxdr.c:29356:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
                    CYTHON_FALLTHROUGH;
                    ^
MDAnalysis/lib/formats/libmdaxdr.c:400:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
      #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
                                 ^
8 warnings generated.
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/include/python3.9 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/trr_seek.c:30:
/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
 /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
 ^
In file included from MDAnalysis/lib/formats/src/trr_seek.c:31:
/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment]
 /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
 ^
2 warnings generated.
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats -I/usr/local/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.freebsd-14.0-RELEASE-p6-arm64-cpython-39/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile.c:62:
/wrkdirs/usr/ports/science/py-MDAnalysis/work-py39/MDAnalysis-2.3.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
 /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
 ^
MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
    while (size >= num && num_of_bits < 32)
           ~~~~ ^  ~~~
MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
    while (bytes[num_of_bytes] >= num)
           ~~~~~~~~~~~~~~~~~~~ ^  ~~~
MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
    if (num_of_bits >= num_of_bytes * 8)
        ~~~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
                for (i = 0; i < num_of_bytes; i++)
                            ~ ^ ~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
                for (i = 0; i < num_of_bytes-1; i++)
                            ~ ^ ~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
                if (lastbits < num_of_bits)
                    ~~~~~~~~ ^ ~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
        if(size3>xfp->buf1size)
           ~~~~~^~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
        maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
                  ~~~~~~~^~~~
MDAnalysis/lib/formats/src/xdrfile.c:1012:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
        if(size3>xfp->buf1size)
           ~~~~~^~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1109:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion]
                (float)maxint[2] - (float)minint[2] >= INT_MAX-2) {
                                                    ~~ ~~~~~~~^~
MDAnalysis/lib/formats/src/xdrfile.c:1108:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion]
                (float)maxint[1] - (float)minint[1] >= INT_MAX-2 ||
                                                    ~~ ~~~~~~~^~
MDAnalysis/lib/formats/src/xdrfile.c:1107:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion]
        if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 ||
                                                ~~ ~~~~~~~^~
MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
        while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
               ~~~~~~~~ ^ ~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
        maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
                  ~~~~~~~^~~~
MDAnalysis/lib/formats/src/xdrfile.c:1273:8: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
        if(tmp==(unsigned int)buf2[0])
           ~~~^ ~~~~~~~~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1313:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
        if(size3>xfp->buf1size)
           ~~~~~^~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
        maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
                  ~~~~~~~^~~~
MDAnalysis/lib/formats/src/xdrfile.c:1504:10: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
        if(size3>xfp->buf1size) {
           ~~~~~^~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1596:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion]
                (float)maxint[2] - (float)minint[2] >= INT_MAX-2) {
                                                    ~~ ~~~~~~~^~
MDAnalysis/lib/formats/src/xdrfile.c:1595:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion]
                (float)maxint[1] - (float)minint[1] >= INT_MAX-2 ||
                                                    ~~ ~~~~~~~^~
MDAnalysis/lib/formats/src/xdrfile.c:1594:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion]
        if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 ||
                                                ~~ ~~~~~~~^~
MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
        while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
               ~~~~~~~~ ^ ~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
        maxidx = (LASTIDX<tmp) ? LASTIDX : tmp;
                  ~~~~~~~^~~~
MDAnalysis/lib/formats/src/xdrfile.c:1734:8: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
        if(tmp==(unsigned int)buf2[0])
           ~~~^ ~~~~~~~~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:2535:3: error: incompatible function pointer types initializing 'unsigned int (*)(XDR *)' (aka 'unsigned int (*)(struct XDR *)') with an expression of type 'int64_t (XDR *)' (aka 'long (struct XDR *)') [-Wincompatible-function-pointer-types]
                xdrstdio_getpos,                /* get offset in the stream */
                ^~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:2536:3: error: incompatible function pointer types initializing 'int (*)(XDR *, unsigned int)' (aka 'int (*)(struct XDR *, unsigned int)') with an expression of type 'int (XDR *, int64_t, int)' (aka 'int (struct XDR *, long, int)') [-Wincompatible-function-pointer-types]
                xdrstdio_setpos,                /* set offset in the stream */
                ^~~~~~~~~~~~~~~
25 warnings and 2 errors generated.
error: command '/usr/bin/cc' failed with exit code 1
*** Error code 1

Stop.
make: stopped in /usr/ports/science/py-MDAnalysis