[package - 130releng-armv7-quarterly][science/py-pymol] Failed for py39-pymol-2.4.0_6 in build/runaway
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Sun, 07 Aug 2022 05:02:46 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: http://ampere1.nyi.freebsd.org/data/130releng-armv7-quarterly/8662e656d870/logs/py39-pymol-2.4.0_6.log
Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=8662e656d870
Log:
=>> Building science/py-pymol
build started at Sun Aug 7 02:49:58 UTC 2022
port directory: /usr/ports/science/py-pymol
package name: py39-pymol-2.4.0_6
building for: FreeBSD 130releng-armv7-quarterly-job-13 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 1300139 arm
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400063
Jail OSVERSION: 1300139
Job Id: 13
---Begin Environment---
SHELL=/bin/csh
OSVERSION=1300139
UNAME_v=FreeBSD 13.0-RELEASE-p11 1300139
UNAME_r=13.0-RELEASE-p11
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
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-21-g883afb07
MASTERMNT=/usr/local/poudriere/data/.m/130releng-armv7-quarterly/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/130releng-armv7-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=130releng-armv7-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/130releng-armv7-quarterly/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=py39
DEPENDS_ARGS=
MAKE_ARGS= FLAVOR=py39
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for py39-pymol-2.4.0_6:
====> GUI (Graphical User Interface) support: you have to select exactly one of them
QT5=on: Qt 5 toolkit support
TK=off: Tk GUI toolkit support
===> Use 'make config' to modify these settings
---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-pymol/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-pymol/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-pymol/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-pymol/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-pymol/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-pymol/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/libdata/pkgconfig NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 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="i
nstall -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--
GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 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="" PYQT_APIDIR=share/PyQt5/3.9/qsci PYQT_DOCDIR=share/doc/PyQt5/3.9 PYQT_EXAMPLEDIR=share/examples/PyQt5/3.9 PYQT_SIPDIR=/usr/local/lib/python3.9/site-packages/PyQt5/bindings PYQT_DESIGNERDIR=/designer/PyQt5/3.9 PYQT_QMLDIR=/PyQt5/3.9 PYQT_SIPVERSION=6.5.1 PYQT_QSCIVERSION=2.13.2 PYQT_PYQTVERSION=5.15.6 OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py39-pymol" EXAMPLESDIR="share/examples/py39-pymol" DATADIR="share/py39-pymol" WWWDIR="www/py39-pymol" ETCDIR="etc/py39-pymol"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py39-pymol DOCSDIR=/usr/local/share/doc/py39-pymol EXAMPLESDIR=/usr/local/share/examples/py39-pymol WWWDIR=/usr/local/www/py39-pymol ETCDIR=/usr/local/etc/py39-pymol
--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 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--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 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=armv7
OPSYS=FreeBSD
_OSRELEASE=13.0-RELEASE-p11
OSREL=13.0
OSVERSION=1300139
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) 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) 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 PyMOL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py39-pymol-2.4.0_6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.3.pkg
[130releng-armv7-quarterly-job-13] Installing pkg-1.18.3...
[130releng-armv7-quarterly-job-13] Extracting pkg-1.18.3: .......... done
===> py39-pymol-2.4.0_6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-pymol-2.4.0_6
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License PyMOL accepted by the user
===> Fetching all distfiles required by py39-pymol-2.4.0_6 for building
===========================================================================
=======================<phase: checksum >============================
===> License PyMOL accepted by the user
===> Fetching all distfiles required by py39-pymol-2.4.0_6 for building
=> SHA256 Checksum OK for schrodinger-pymol-open-source-v2.4.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License PyMOL accepted by the user
===> Fetching all distfiles required by py39-pymol-2.4.0_6 for building
===> Extracting for py39-pymol-2.4.0_6
=> SHA256 Checksum OK for schrodinger-pymol-open-source-v2.4.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py39-pymol-2.4.0_6
===> Applying FreeBSD patches for py39-pymol-2.4.0_6 from /usr/ports/science/py-pymol/files
===========================================================================
=======================<phase: build-depends >============================
===> py39-pymol-2.4.0_6 depends on package: py39-numpy>=1.16,1<1.23,1 - not found
===> Installing existing package /packages/All/py39-numpy-1.22.4_1,1.pkg
[130releng-armv7-quarterly-job-13] Installing py39-numpy-1.22.4_1,1...
[130releng-armv7-quarterly-job-13] `-- Installing gcc11-11.3.0...
[130releng-armv7-quarterly-job-13] | `-- Installing binutils-2.37_2,1...
[130releng-armv7-quarterly-job-13] | | `-- Installing gettext-runtime-0.21...
[130releng-armv7-quarterly-job-13] | | `-- Installing indexinfo-0.3.1...
[130releng-armv7-quarterly-job-13] | | `-- Extracting indexinfo-0.3.1: .... done
[130releng-armv7-quarterly-job-13] | | `-- Extracting gettext-runtime-0.21: .......... done
[130releng-armv7-quarterly-job-13] | `-- Extracting binutils-2.37_2,1: .......... done
[130releng-armv7-quarterly-job-13] | `-- Installing gmp-6.2.1...
[130releng-armv7-quarterly-job-13] | `-- Extracting gmp-6.2.1: .......... done
[130releng-armv7-quarterly-job-13] | `-- Installing mpc-1.2.1...
[130releng-armv7-quarterly-job-13] | | `-- Installing mpfr-4.1.0_1...
<snip>
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer5/PyMOL.cpp -o build/temp.freebsd-13.0-RELEASE-p11-arm-cpython-39/layer5/PyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
1 warning generated.
In file included from layer2/Sculpt.cpp:29:
In file included from layer3/Editor.h:22:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectMesh.cpp -o build/temp.freebsd-13.0-RELEASE-p11-arm-cpython-39/layer2/ObjectMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
In file included from layer2/RepCylBond.cpp:26:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer5/main.cpp -o build/temp.freebsd-13.0-RELEASE-p11-arm-cpython-39/layer5/main.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
In file included from layer2/RepAngle.cpp:33:
In file included from layer2/CoordSet.h:25:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
1 warning generated.
1 warning generated.
In file included from layer2/CoordSet.cpp:29:
In file included from layer2/CoordSet.h:25:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
In file included from layer5/PyMOL.cpp:32:
In file included from layer3/Selector.h:24:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/PlugIOManager.cpp -o build/temp.freebsd-13.0-RELEASE-p11-arm-cpython-39/layer3/PlugIOManager.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
1 warning generated.
1 warning generated.
In file included from layer3/MoleculeExporter.cpp:22:
In file included from layer3/Selector.h:24:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
In file included from layer5/main.cpp:45:
In file included from layer1/P.h:22:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
layer5/PyMOL.cpp:1798:3: warning: 'PyEval_InitThreads' is deprecated [-Wdeprecated-declarations]
PyEval_InitThreads();
^
/usr/local/include/python3.9/ceval.h:130:1: note: 'PyEval_InitThreads' has been explicitly marked deprecated here
Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void);
^
/usr/local/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
In file included from layer2/ObjectMesh.cpp:35:
In file included from layer3/Executive.h:26:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer2/ObjectMolecule2.cpp -o build/temp.freebsd-13.0-RELEASE-p11-arm-cpython-39/layer2/ObjectMolecule2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
1 warning generated.
In file included from layer3/PlugIOManager.cpp:24:
In file included from layer3/PlugIOManager.h:22:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer4/Menu.cpp -o build/temp.freebsd-13.0-RELEASE-p11-arm-cpython-39/layer4/Menu.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
2 warnings generated.
1 warning generated.
In file included from layer2/ObjectMolecule2.cpp:31:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
In file included from layer4/Menu.cpp:26:
In file included from layer1/P.h:22:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
1 warning generated.
1 warning generated.
4 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/ExecutivePython.cpp -o build/temp.freebsd-13.0-RELEASE-p11-arm-cpython-39/layer3/ExecutivePython.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
1 warning generated.
1 warning generated.
In file included from layer3/ExecutivePython.cpp:1:
In file included from layer3/ExecutivePython.h:3:
In file included from layer3/Executive.h:26:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/freetype2 -I/usr/local/include/libxml2 -I/usr/local/include/python3.9 -c -MMD layer3/SelectorTmp.cpp -o build/temp.freebsd-13.0-RELEASE-p11-arm-cpython-39/layer3/SelectorTmp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
1 warning generated.
In file included from layer3/SelectorTmp.cpp:7:
In file included from layer3/Selector.h:24:
layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
^
PDBInfoRec
layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration
inline bool is_pqr_file() const {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration
} PDBInfoRec;
^
1 warning generated.
=>> Killing runaway build after 7200 seconds with no output