[package - 140amd64-default][science/py-MDAnalysis] Failed for py39-MDAnalysis-2.3.0_1 in build
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Date: Sat, 23 Mar 2024 11:26:12 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/beefy12/data/140amd64-default/1d9788d2de86/logs/py39-MDAnalysis-2.3.0_1.log
Build URL: https://pkg-status.freebsd.org/beefy12/build.html?mastername=140amd64-default&build=1d9788d2de86
Log:
=>> Building science/py-MDAnalysis
build started at Sat Mar 23 11:24:38 UTC 2024
port directory: /usr/ports/science/py-MDAnalysis
package name: py39-MDAnalysis-2.3.0_1
building for: FreeBSD 140amd64-default-job-07 14.0-RELEASE-p5 FreeBSD 14.0-RELEASE-p5 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1507 Aug 26 2023 /usr/ports/science/py-MDAnalysis/Makefile
Ports top last git commit: 1d9788d2de
Ports top unclean checkout: no
Port dir last git commit: 157c391cc1
Port dir unclean checkout: no
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Host OSVERSION: 1500006
Jail OSVERSION: 1400097
Job Id: 07
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yuri@FreeBSD.org
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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.
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max user processes (-u) 89999
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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-1.20.9_1.pkg
[140amd64-default-job-07] Installing pkg-1.20.9_1...
[140amd64-default-job-07] Extracting pkg-1.20.9_1: .......... 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
[140amd64-default-job-07] Installing py39-numpy-1.25.0_6,1...
[140amd64-default-job-07] `-- Installing gcc13-13.2.0_4...
[140amd64-default-job-07] | `-- Installing binutils-2.40_5,1...
[140amd64-default-job-07] | | `-- Installing gettext-runtime-0.22.3_1...
[140amd64-default-job-07] | | `-- Installing indexinfo-0.3.1...
[140amd64-default-job-07] | | `-- Extracting indexinfo-0.3.1: .... done
[140amd64-default-job-07] | | `-- Extracting gettext-runtime-0.22.3_1: .......... done
[140amd64-default-job-07] | | `-- Installing zstd-1.5.5_1...
[140amd64-default-job-07] | | `-- Installing liblz4-1.9.4_1,1...
[140amd64-default-job-07] | | `-- Extracting liblz4-1.9.4_1,1: .......... done
[140amd64-default-job-07] | | `-- Extracting zstd-1.5.5_1: .......... done
[140amd64-default-job-07] | `-- Extracting binutils-2.40_5,1: .......... done
[140amd64-default-job-07] | `-- Installing gmp-6.3.0...
[140amd64-default-job-07] | `-- Extracting gmp-6.3.0: .......... done
[140amd64-default-job-07] | `-- Installing mpc-1.3.1_1...
[140amd64-default-job-07] | | `-- Installing mpfr-4.2.1,1...
[140amd64-default-job-07] | | `-- Extracting mpfr-4.2.1,1: .......... done
[140amd64-default-job-07] | `-- Extracting mpc-1.3.1_1: ......... done
[140amd64-default-job-07] `-- Extracting gcc13-13.2.0_4: .......... done
[140amd64-default-job-07] `-- Installing openblas-0.3.25,2...
[140amd64-default-job-07] `-- Extracting openblas-0.3.25,2: .......... done
[140amd64-default-job-07] `-- Installing py39-setuptools-63.1.0_1...
[140amd64-default-job-07] | `-- Installing python39-3.9.18_2...
[140amd64-default-job-07] | | `-- 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-p5-amd64-cpython-39/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -o build/lib.freebsd-14.0-RELEASE-p5-amd64-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-p5-amd64-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-p5-amd64-cpython-39/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -o build/lib.freebsd-14.0-RELEASE-p5-amd64-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-p5-amd64-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-p5-amd64-cpython-39/MDAnalysis/lib/qcprot.o -L/usr/local/lib -o build/lib.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/qcprot.cpython-39.so
building 'MDAnalysis.lib._transformations' extension
creating build/temp.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/src
creating build/temp.freebsd-14.0-RELEASE-p5-amd64-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-p5-amd64-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-p5-amd64-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -o build/lib.freebsd-14.0-RELEASE-p5-amd64-cpython-39/MDAnalysis/lib/_transformations.cpython-39.so
building 'MDAnalysis.lib.formats.libmdaxdr' extension
creating build/temp.freebsd-14.0-RELEASE-p5-amd64-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-p5-amd64-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-p5-amd64-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-p5-amd64-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