[package - 143i386-default][science/py-MDAnalysis] Failed for py311-MDAnalysis-2.10.0 in build
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Date: Mon, 04 May 2026 00:18:24 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/beefy18/data/143i386-default/f2e7c7e4ce40/logs/py311-MDAnalysis-2.10.0.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=143i386-default&build=f2e7c7e4ce40
Log:
=>> Building science/py-MDAnalysis
build started at Mon May 4 00:17:39 UTC 2026
port directory: /usr/ports/science/py-MDAnalysis
package name: py311-MDAnalysis-2.10.0
building for: FreeBSD 143i386-default-job-11 14.3-RELEASE-p13 FreeBSD 14.3-RELEASE-p13 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1604 May 3 01:01 /usr/ports/science/py-MDAnalysis/Makefile
Ports top last git commit: f2e7c7e4ce40de869ee2ee619e9b3c03f8ea0c6c
Ports top unclean checkout: no
Port dir last git commit: aa2d73ac0e813bc6a541044efa8cd903119b1792
Port dir unclean checkout: no
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Job Id: 11
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--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
===> py311-MDAnalysis-2.10.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.7.5.pkg
[143i386-default-job-11] Installing pkg-2.7.5...
[143i386-default-job-11] Extracting pkg-2.7.5: .......... done
===> py311-MDAnalysis-2.10.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py311-MDAnalysis-2.10.0
===========================================================================
=======================<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 py311-MDAnalysis-2.10.0 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 py311-MDAnalysis-2.10.0 for building
=> SHA256 Checksum OK for mdanalysis-2.10.0.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 py311-MDAnalysis-2.10.0 for building
===> Extracting for py311-MDAnalysis-2.10.0
=> SHA256 Checksum OK for mdanalysis-2.10.0.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 py311-MDAnalysis-2.10.0
===> Applying FreeBSD patches for py311-MDAnalysis-2.10.0 from /usr/ports/science/py-MDAnalysis/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-MDAnalysis-2.10.0 depends on package: py311-cython>=0.28 - not found
===> Installing existing package /packages/All/py311-cython-3.2.4.pkg
[143i386-default-job-11] Installing py311-cython-3.2.4...
[143i386-default-job-11] `-- Installing python311-3.11.15_2...
[143i386-default-job-11] | `-- Installing gettext-runtime-1.0...
[143i386-default-job-11] | | `-- Installing indexinfo-0.3.1_1...
[143i386-default-job-11] | | `-- Extracting indexinfo-0.3.1_1: .... done
[143i386-default-job-11] | `-- Extracting gettext-runtime-1.0: .......... done
[143i386-default-job-11] | `-- Installing libffi-3.5.1...
[143i386-default-job-11] | `-- Extracting libffi-3.5.1: .......... done
[143i386-default-job-11] | `-- Installing mpdecimal-4.0.1...
[143i386-default-job-11] | `-- Extracting mpdecimal-4.0.1: .......... done
[143i386-default-job-11] | `-- Installing readline-8.3.3...
[143i386-default-job-11] | `-- Extracting readline-8.3.3: .......... done
[143i386-default-job-11] `-- Extracting python311-3.11.15_2: .......... done
[143i386-default-job-11] Extracting py311-cython-3.2.4: .......... done
=====
Message from python311-3.11.15_2:
--
<snip>
creating build/lib.freebsd-14.3-RELEASE-p13-i386-cpython-311/doc/sphinx/source/documentation_pages/lib/formats
copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.freebsd-14.3-RELEASE-p13-i386-cpython-311/doc/sphinx/source/documentation_pages/lib/formats
copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.freebsd-14.3-RELEASE-p13-i386-cpython-311/doc/sphinx/source/documentation_pages/lib/formats
running build_ext
building 'MDAnalysis.lib.formats.libdcd' extension
creating build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311
creating build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis
creating build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib
creating build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/formats
cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/formats/libdcd.o -std=c11 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/libdcd.c:1159:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.11/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
In file included from MDAnalysis/lib/formats/libdcd.c:1166:
MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;
| ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~
2 warnings generated.
cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/formats/libdcd.o -L/usr/local/lib -o build/lib.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/formats/libdcd.cpython-311.so
building 'MDAnalysis.lib.c_distances' extension
cc -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/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/c_distances.c -o build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/c_distances.o -std=c11 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/c_distances.c:1161:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.11/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
1 warning generated.
cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -o build/lib.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/c_distances.cpython-311.so
building 'MDAnalysis.lib.c_distances_openmp' extension
cc -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/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c11 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/c_distances_openmp.c:1170:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.11/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
1 warning generated.
cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -o build/lib.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/c_distances_openmp.cpython-311.so -fopenmp
building 'MDAnalysis.lib.qcprot' extension
cc -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/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/qcprot.c -o build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/qcprot.o -std=c11 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/qcprot.c:1153:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.11/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
MDAnalysis/lib/qcprot.c:20858:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
20858 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ~~~~~~~~~ ^ ~~~~~~~~~
MDAnalysis/lib/qcprot.c:21066:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
21066 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ~~~~~~~~~ ^ ~~~~~~~~~
MDAnalysis/lib/qcprot.c:21497:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
21497 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ~~~~~~~~~ ^ ~~~~~~~~~
MDAnalysis/lib/qcprot.c:21705:35: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
21705 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
| ~~~~~~~~~ ^ ~~~~~~~~~
5 warnings generated.
cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/qcprot.o -L/usr/local/lib -o build/lib.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/qcprot.cpython-311.so
building 'MDAnalysis.lib._transformations' extension
creating build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/src
creating build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/src/transformations
cc -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/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/src/transformations/transformations.o -std=c11 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/src/transformations/transformations.c:73:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.11/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
1 warning generated.
cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -o build/lib.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/_transformations.cpython-311.so
building 'MDAnalysis.lib.formats.libmdaxdr' extension
creating build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/formats/src
cc -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-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/formats/libmdaxdr.o -std=c11 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1180:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.11/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1186:
MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
| ^
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1187:
MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: '/*' within block comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
| ^
In file included from MDAnalysis/lib/formats/libmdaxdr.c:1188:
MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
| ^
4 warnings generated.
cc -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-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/formats/src/trr_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/trr_seek.c:30:
/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
5 | /* -*- 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-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
| ^
2 warnings generated.
cc -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-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/include/python3.11 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.freebsd-14.3-RELEASE-p13-i386-cpython-311/MDAnalysis/lib/formats/src/xdrfile.o -std=c11 -O3 -funroll-loops -fsigned-zeros
In file included from MDAnalysis/lib/formats/src/xdrfile.c:62:
/wrkdirs/usr/ports/science/py-MDAnalysis/work-py311/mdanalysis-2.10.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment]
5 | /* -*- 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]
501 | 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]
547 | 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]
656 | 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]
658 | 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]
666 | 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]
706 | 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]
816 | if(size3>xfp->buf1size)
| ~~~~~^~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
868 | 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]
1012 | 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]
1109 | (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]
1108 | (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]
1107 | 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 int' [-Wsign-compare]
1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff)
| ~~~~~~~~ ^ ~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
1141 | 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]
1273 | 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]
1313 | if(size3>xfp->buf1size)
| ~~~~~^~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
1368 | 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]
1504 | 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]
1596 | (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]
1595 | (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]
1594 | 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 int' [-Wsign-compare]
1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) {
| ~~~~~~~~ ^ ~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
1624 | 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]
1734 | if(tmp==(unsigned int)buf2[0])
| ~~~^ ~~~~~~~~~~~~~~~~~~~~~
MDAnalysis/lib/formats/src/xdrfile.c:2536:3: error: incompatible function pointer types initializing 'off_t (*)(XDR *, off_t, int)' (aka 'long long (*)(struct XDR *, long long, int)') with an expression of type 'int (XDR *, int64_t, int)' (aka 'int (struct XDR *, long long, int)') [-Wincompatible-function-pointer-types]
2536 | xdrstdio_setpos, /* set offset in the stream */
| ^~~~~~~~~~~~~~~
25 warnings and 1 error generated.
error: command '/usr/bin/cc' failed with exit code 1
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-MDAnalysis