Date: Thu, 21 May 2020 19:13:39 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-powerpc64-default][science/py-MDAnalysis] Failed for py37-MDAnalysis-0.19.2_2 in build Message-ID: <202005211913.04LJDdLN007312@pylon.nyi.freebsd.org>
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Maintainer: yuri@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: head/science/py-MDAnalysis/Makefile 507372 2019-07-26 20:46:53Z gerald $ Log URL: http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p535193_s361019/logs/py37-MDAnalysis-0.19.2_2.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p535193_s361019 Log: =>> Building science/py-MDAnalysis build started at Thu May 21 19:09:23 UTC 2020 port directory: /usr/ports/science/py-MDAnalysis package name: py37-MDAnalysis-0.19.2_2 building for: FreeBSD head-powerpc64-default-job-01 13.0-CURRENT FreeBSD 13.0-CURRENT 1300094 powerpc maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/science/py-MDAnalysis/Makefile 507372 2019-07-26 20:46:53Z gerald $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300084 Jail OSVERSION: 1300094 Job Id: 01 !!! Jail is newer than host. (Jail: 1300094, Host: 1300084) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300094 UNAME_v=FreeBSD 13.0-CURRENT 1300094 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-powerpc64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-powerpc64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py37 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py37 ---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/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py37 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py37 HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py37 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py37/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py37 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py37 HOME=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py37 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-MDAnalysis/work-py37/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES 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=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -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/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=13.0 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-- 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 #### /usr/local/etc/poudriere.d/make.conf #### # 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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: powerpc64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: powerpc64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: powerpc64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 PPC_ABI=ELFv2 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300094 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 33554432 stack size (kbytes, -s) 524288 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) 1024 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 >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> py37-MDAnalysis-0.19.2_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.4.txz [head-powerpc64-default-job-01] Installing pkg-1.14.4... [head-powerpc64-default-job-01] Extracting pkg-1.14.4: .......... done ===> py37-MDAnalysis-0.19.2_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py37-MDAnalysis-0.19.2_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py37-MDAnalysis-0.19.2_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py37-MDAnalysis-0.19.2_2 for building => SHA256 Checksum OK for MDAnalysis-0.19.2.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py37-MDAnalysis-0.19.2_2 for building ===> Extracting for py37-MDAnalysis-0.19.2_2 => SHA256 Checksum OK for MDAnalysis-0.19.2.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for py37-MDAnalysis-0.19.2_2 ===> Applying FreeBSD patches for py37-MDAnalysis-0.19.2_2 ===> Cleanly applied FreeBSD patch(es) patch-setup.py =========================================================================== =======================<phase: build-depends >============================ ===> py37-MDAnalysis-0.19.2_2 depends on package: py37-numpy>=1.16,1<1.19,1 - not found ===> Installing existing package /packages/All/py37-numpy-1.16.5_5,1.txz [head-powerpc64-default-job-01] Installing py37-numpy-1.16.5_5,1... [head-powerpc64-default-job-01] `-- Installing gcc9-9.3.0_1... [head-powerpc64-default-job-01] | `-- Installing binutils-2.33.1_2,1... [head-powerpc64-default-job-01] | | `-- Installing gettext-runtime-0.20.2... [head-powerpc64-default-job-01] | | `-- Installing indexinfo-0.3.1... [head-powerpc64-default-job-01] | | `-- Extracting indexinfo-0.3.1: .... done [head-powerpc64-default-job-01] | | `-- Extracting gettext-runtime-0.20.2: .......... done <snip> 2 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -lpython3.7m -o build/lib.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/_transformations.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.freebsd-13.0-CURRENT-powerpc-3.7/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/usr/local/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.7m -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -funroll-loops In file included from MDAnalysis/lib/formats/libmdaxdr.c:618: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /usr/local/lib/python3.7/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:621: 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:622: 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:623: 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 -*- ^ 4 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/usr/local/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.7m -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -funroll-loops In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: 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:1107:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion] if ((float)maxint[0] - (float)minint[0] >= 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-int-float-conversion] (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1109:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion] (float)maxint[2] - (float)minint[2] >= 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:1594:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion] if ((float)maxint[0] - (float)minint[0] >= 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-int-float-conversion] (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1596:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-int-float-conversion] (float)maxint[2] - (float)minint[2] >= 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: warning: incompatible pointer types initializing 'unsigned int (*)(XDR *)' (aka 'unsigned int (*)(struct XDR *)') with an expression of type 'int64_t (XDR *)' (aka 'long (struct XDR *)') [-Wincompatible-pointer-types] xdrstdio_getpos, /* get offset in the stream */ ^~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile.c:2536:3: warning: incompatible 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-pointer-types] xdrstdio_setpos, /* set offset in the stream */ ^~~~~~~~~~~~~~~ 27 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/usr/local/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.7m -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -funroll-loops In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: 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/xdrfile_xtc.c:31: 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 -*- ^ 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/usr/local/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.7m -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -funroll-loops In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: 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/xdrfile_trr.c:39: 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/src/xdrfile_trr.c:78:14: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] if (slen != strlen(version) + 1) ~~~~ ^ ~~~~~~~~~~~~~~~~~~~ MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~ 4 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/usr/local/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.7m -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -funroll-loops In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: 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: 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/usr/local/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/lib/formats/include -IMDAnalysis/lib/formats -I/usr/local/include/python3.7m -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -funroll-loops In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: 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/xtc_seek.c:26: 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 -*- ^ 2 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/libmdaxdr.o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/xdrfile.o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/trr_seek.o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/local/lib -lpython3.7m -o build/lib.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/libmdaxdr.so building 'MDAnalysis.lib.formats.cython_util' 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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MDAnalysis/lib/formats/cython_util.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -funroll-loops In file included from MDAnalysis/lib/formats/cython_util.c:592: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /usr/local/lib/python3.7/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 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/cython_util.o -L/usr/local/lib -lpython3.7m -o build/lib.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/lib/formats/cython_util.so building 'MDAnalysis.analysis.encore.cutils' extension creating build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/analysis creating build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/analysis/encore 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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MDAnalysis/analysis/encore/cutils.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -funroll-loops In file included from MDAnalysis/analysis/encore/cutils.c:592: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /usr/local/lib/python3.7/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 -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/analysis/encore/cutils.o -L/usr/local/lib -lpython3.7m -o build/lib.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/analysis/encore/cutils.so building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension creating build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/analysis/encore/clustering creating build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/analysis/encore/clustering/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 -I/usr/local/lib/python3.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python3.7m -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -funroll-loops In file included from MDAnalysis/analysis/encore/clustering/affinityprop.c:598: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /usr/local/lib/python3.7/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 -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/python3.7/site-packages/numpy/core/include -IMDAnalysis/analysis/encore/clustering/include -I/usr/local/include/python3.7m -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.freebsd-13.0-CURRENT-powerpc-3.7/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -funroll-loops setup.py:118: DeprecationWarning: The SafeConfigParser class has been renamed to ConfigParser in Python 3.2. This alias will be removed in future versions. Use ConfigParser directly instead. self.config = configparser.SafeConfigParser() error: command 'cc' terminated by signal 4 *** Error code 1 Stop. make: stopped in /usr/ports/science/py-MDAnalysis
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