[package - 130releng-armv7-quarterly][science/py-pymol] Failed for py39-pymol-2.4.0_6 in build/runaway

From: <pkg-fallout_at_FreeBSD.org>
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: 
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Host OSVERSION: 1400063
Jail OSVERSION: 1300139
Job Id: 13

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=======================<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