[package - main-amd64-default][science/py-pymol] Failed for py39-pymol-2.4.0_7 in build
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Date: Fri, 11 Nov 2022 10:15:30 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://beefy18.nyi.freebsd.org/data/main-amd64-default/p97fda7e3a598_s813c5b75e6/logs/py39-pymol-2.4.0_7.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=p97fda7e3a598_s813c5b75e6
Log:
=>> Building science/py-pymol
build started at Fri Nov 11 10:14:39 UTC 2022
port directory: /usr/ports/science/py-pymol
package name: py39-pymol-2.4.0_7
building for: FreeBSD main-amd64-default-job-06 14.0-CURRENT FreeBSD 14.0-CURRENT 1400073 amd64
maintained by: yuri@FreeBSD.org
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===> The following configuration options are available for py39-pymol-2.4.0_7:
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=======================<phase: check-sanity >============================
===> License PyMOL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py39-pymol-2.4.0_7 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[main-amd64-default-job-06] Installing pkg-1.18.4...
[main-amd64-default-job-06] Extracting pkg-1.18.4: .......... done
===> py39-pymol-2.4.0_7 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-pymol-2.4.0_7
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License PyMOL accepted by the user
===> Fetching all distfiles required by py39-pymol-2.4.0_7 for building
===========================================================================
=======================<phase: checksum >============================
===> License PyMOL accepted by the user
===> Fetching all distfiles required by py39-pymol-2.4.0_7 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_7 for building
===> Extracting for py39-pymol-2.4.0_7
=> 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_7
===> Applying FreeBSD patches for py39-pymol-2.4.0_7 from /usr/ports/science/py-pymol/files
===========================================================================
=======================<phase: build-depends >============================
===> py39-pymol-2.4.0_7 depends on package: py39-numpy>=1.16,1<1.24,1 - not found
===> Installing existing package /packages/All/py39-numpy-1.23.4,1.pkg
[main-amd64-default-job-06] Installing py39-numpy-1.23.4,1...
[main-amd64-default-job-06] `-- Installing gcc11-11.3.0_5...
[main-amd64-default-job-06] | `-- Installing binutils-2.39,1...
[main-amd64-default-job-06] | | `-- Installing gettext-runtime-0.21...
[main-amd64-default-job-06] | | `-- Installing indexinfo-0.3.1...
[main-amd64-default-job-06] | | `-- Extracting indexinfo-0.3.1: .... done
[main-amd64-default-job-06] | | `-- Extracting gettext-runtime-0.21: .......... done
<snip>
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.
2 warnings generated.
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__))
^
1 warning generated.
1 warning generated.
In file included from layer1/Rep.cpp:27:
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.
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/RepCylBond.cpp -o build/temp.freebsd-14.0-CURRENT-amd64-cpython-39/layer2/RepCylBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
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-14.0-CURRENT-amd64-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 layer1/ScenePicking.cpp:10:
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.
2 warnings generated.
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.
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 layer1/Shaker.cpp -o build/temp.freebsd-14.0-CURRENT-amd64-cpython-39/layer1/Shaker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
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/CoordSet.cpp -o build/temp.freebsd-14.0-CURRENT-amd64-cpython-39/layer2/CoordSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
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-14.0-CURRENT-amd64-cpython-39/layer2/ObjectMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
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.
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;
^
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;
^
1 warning generated.
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 layer2/ObjectMolecule2.cpp -o build/temp.freebsd-14.0-CURRENT-amd64-cpython-39/layer2/ObjectMolecule2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
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-14.0-CURRENT-amd64-cpython-39/layer4/Menu.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
1 warning 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;
^
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.
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-14.0-CURRENT-amd64-cpython-39/layer3/ExecutivePython.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3
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.
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 layer3/SelectorTmp.cpp -o build/temp.freebsd-14.0-CURRENT-amd64-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.
error: command '/usr/bin/c++' failed with exit code 1
Exception ignored in: <function Pool.__del__ at 0x857bbbe50>
Traceback (most recent call last):
File "/usr/local/lib/python3.9/multiprocessing/pool.py", line 268, in __del__
File "/usr/local/lib/python3.9/multiprocessing/queues.py", line 377, in put
File "/usr/local/lib/python3.9/multiprocessing/connection.py", line 205, in send_bytes
File "/usr/local/lib/python3.9/multiprocessing/connection.py", line 405, in _send_bytes
AttributeError: 'NoneType' object has no attribute 'pack'
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-pymol