id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4132 "Build fails ""no such option: --extra-index-url""" Tom Goddard Greg Couch "Looks like your change to handling of ChimeraX.exe options broke the Linux build. Here is where the build from scratch failed installing bundle arrays. make -C arrays build make[5]: Entering directory '/home/goddard/ucsf/chimerax/src/bundles/arrays' ../../../ChimeraX.app/bin/ChimeraX --nogui --safemode --exit --cmd ""devel install . user false exit true noDeps true"" INFO: Executing: devel install . user false exit true noDeps true Warning: Can't read registry to find the necessary compiler setting Make sure that Python modules winreg, win32api or win32con are installed. C compiler: gcc -pipe -fPIC -std=gnu99 -fstack-protector-strong -DUSE_DYLD_GLOBAL_NAMESPACE -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -O3 -Wall -D_FORTIFY=2 -fstack-protector-strong -fPIC compile options: '-std=c++11 -DDYNAMIC_LIBRARY=1 -I/home/goddard/ucsf/chimerax/src/bundles/arrays/../../../ChimeraX.app/include -I/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/numpy/core/include -I/home/goddard/ucsf/chimerax/ChimeraX.app/include/python3.8 -c' gcc: _arrays/refcount.cpp gcc: _arrays/rcarray.cpp gcc: _arrays/pythonarray.cpp cc1plus: warning: command line option ‘-std=gnu99’ is valid for C/ObjC but not for C++ cc1plus: warning: command line option ‘-std=gnu99’ is valid for C/ObjC but not for C++ cc1plus: warning: command line option ‘-std=gnu99’ is valid for C/ObjC but not for C++ _arrays/refcount.cpp: In copy constructor ‘Reference_Count::Reference_Count(const Reference_Count&)’: _arrays/refcount.cpp:45:28: warning: ‘*.Reference_Count::ref_count’ is used uninitialized in this function [-Wuninitialized] 45 | decrement_reference_count(ref_count); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ creating src/lib c++ -pipe -fPIC -std=gnu99 -fdebug-prefix-map=/home/goddard/ucsf/chimerax/build=. -fstack-protector-strong -I/home/goddard/ucsf/chimerax/build/include -L/home/goddard/ucsf/chimerax/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -pthread -shared -O3 -Wall -Wextra -D_FORTIFY=2 -Wl,-rpath,$ORIGIN/lib _arrays/pythonarray.o _arrays/rcarray.o _arrays/refcount.o -L/home/goddard/ucsf/chimerax/src/bundles/arrays/../../../ChimeraX.app/lib -o src/lib/libarrays.so running build running build_py creating build creating build/lib.linux-x86_64-3.8 creating build/lib.linux-x86_64-3.8/chimerax creating build/lib.linux-x86_64-3.8/chimerax/arrays copying src/__init__.py -> build/lib.linux-x86_64-3.8/chimerax/arrays creating build/lib.linux-x86_64-3.8/chimerax/arrays/include creating build/lib.linux-x86_64-3.8/chimerax/arrays/include/arrays copying src/include/arrays/pythonarray.h -> build/lib.linux-x86_64-3.8/chimerax/arrays/include/arrays copying src/include/arrays/rcarray.h -> build/lib.linux-x86_64-3.8/chimerax/arrays/include/arrays copying src/include/arrays/refcount.h -> build/lib.linux-x86_64-3.8/chimerax/arrays/include/arrays copying src/include/arrays/imex.h -> build/lib.linux-x86_64-3.8/chimerax/arrays/include/arrays creating build/lib.linux-x86_64-3.8/chimerax/arrays/lib copying src/lib/libarrays.so -> build/lib.linux-x86_64-3.8/chimerax/arrays/lib running build_ext building 'chimerax.arrays._arrays' extension C compiler: gcc -pipe -fPIC -std=gnu99 -fstack-protector-strong -DUSE_DYLD_GLOBAL_NAMESPACE -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -O3 -Wall -D_FORTIFY=2 -fstack-protector-strong -fPIC creating build/temp.linux-x86_64-3.8 creating build/temp.linux-x86_64-3.8/_arrays compile options: '-DMAJOR_VERSION=0 -DMINOR_VERSION=1 -I/home/goddard/ucsf/chimerax/src/bundles/arrays/../../../ChimeraX.app/include -Isrc/include -I/home/goddard/ucsf/chimerax/ChimeraX.app/include/python3.8 -c' extra options: '-std=c++11' gcc: _arrays/load_arrays.cpp cc1plus: warning: command line option ‘-std=gnu99’ is valid for C/ObjC but not for C++ c++ -pipe -fPIC -std=gnu99 -fdebug-prefix-map=/home/goddard/ucsf/chimerax/build=. -fstack-protector-strong -I/home/goddard/ucsf/chimerax/build/include -L/home/goddard/ucsf/chimerax/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -pthread -shared -O3 -Wall -Wextra -D_FORTIFY=2 build/temp.linux-x86_64-3.8/_arrays/load_arrays.o -L/home/goddard/ucsf/chimerax/src/bundles/arrays/../../../ChimeraX.app/lib -Lsrc/lib -L/home/goddard/ucsf/chimerax/build/lib -larrays -o build/lib.linux-x86_64-3.8/chimerax/arrays/_arrays.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN/lib running bdist_wheel installing to build/bdist.linux-x86_64/wheel running install running install_lib running build_ext creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/chimerax creating build/bdist.linux-x86_64/wheel/chimerax/arrays creating build/bdist.linux-x86_64/wheel/chimerax/arrays/include creating build/bdist.linux-x86_64/wheel/chimerax/arrays/include/arrays copying build/lib.linux-x86_64-3.8/chimerax/arrays/include/arrays/refcount.h -> build/bdist.linux-x86_64/wheel/chimerax/arrays/include/arrays copying build/lib.linux-x86_64-3.8/chimerax/arrays/include/arrays/pythonarray.h -> build/bdist.linux-x86_64/wheel/chimerax/arrays/include/arrays copying build/lib.linux-x86_64-3.8/chimerax/arrays/include/arrays/imex.h -> build/bdist.linux-x86_64/wheel/chimerax/arrays/include/arrays copying build/lib.linux-x86_64-3.8/chimerax/arrays/include/arrays/rcarray.h -> build/bdist.linux-x86_64/wheel/chimerax/arrays/include/arrays copying build/lib.linux-x86_64-3.8/chimerax/arrays/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/arrays copying build/lib.linux-x86_64-3.8/chimerax/arrays/_arrays.cpython-38-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/chimerax/arrays creating build/bdist.linux-x86_64/wheel/chimerax/arrays/lib copying build/lib.linux-x86_64-3.8/chimerax/arrays/lib/libarrays.so -> build/bdist.linux-x86_64/wheel/chimerax/arrays/lib running install_egg_info running egg_info creating ChimeraX_Arrays.egg-info writing ChimeraX_Arrays.egg-info/PKG-INFO writing dependency_links to ChimeraX_Arrays.egg-info/dependency_links.txt writing top-level names to ChimeraX_Arrays.egg-info/top_level.txt writing manifest file 'ChimeraX_Arrays.egg-info/SOURCES.txt' reading manifest file 'ChimeraX_Arrays.egg-info/SOURCES.txt' writing manifest file 'ChimeraX_Arrays.egg-info/SOURCES.txt' Copying ChimeraX_Arrays.egg-info to build/bdist.linux-x86_64/wheel/ChimeraX_Arrays-1.0-py3.8.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/ChimeraX_Arrays-1.0.dist-info/WHEEL creating 'dist/ChimeraX_Arrays-1.0-cp38-cp38-manylinux_2_31_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'chimerax/arrays/__init__.py' adding 'chimerax/arrays/_arrays.cpython-38-x86_64-linux-gnu.so' adding 'chimerax/arrays/include/arrays/imex.h' adding 'chimerax/arrays/include/arrays/pythonarray.h' adding 'chimerax/arrays/include/arrays/rcarray.h' adding 'chimerax/arrays/include/arrays/refcount.h' adding 'chimerax/arrays/lib/libarrays.so' adding 'ChimeraX_Arrays-1.0.dist-info/METADATA' adding 'ChimeraX_Arrays-1.0.dist-info/WHEEL' adding 'ChimeraX_Arrays-1.0.dist-info/top_level.txt' adding 'ChimeraX_Arrays-1.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Distribution is in ./dist/ChimeraX_Arrays-1.0-cp38-cp38-manylinux_2_31_x86_64.whl INFO: Executing: toolshed install ./dist/ChimeraX_Arrays-1.0-cp38-cp38-manylinux_2_31_x86_64.whl userOnly false noDeps true Traceback (most recent call last): File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/toolshed_utils/__init__.py"", line 495, in _pip_install results = _run_pip(command, logger) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/toolshed_utils/__init__.py"", line 546, in _run_pip raise RuntimeError(s) RuntimeError: Usage: /home/goddard/ucsf/chimerax/src/bundles/arrays/../../../ChimeraX.app/bin/ChimeraX -m pip [options] no such option: --extra-index-url During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/core/commands/devel.py"", line 162, in _run unbound_method(bb, *args, **kw) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/bundle_builder/bundle_builder.py"", line 118, in make_install run(session, cmd) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/core/commands/toolshed.py"", line 301, in toolshed_install ts.install_bundle(bundles, logger, **kw) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/core/toolshed/__init__.py"", line 898, in install_bundle _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/toolshed_utils/__init__.py"", line 237, in _install_bundle results = _pip_install( File ""/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/toolshed_utils/__init__.py"", line 498, in _pip_install raise UserError(str(e)) chimerax.core.errors.UserError: Usage: /home/goddard/ucsf/chimerax/src/bundles/arrays/../../../ChimeraX.app/bin/ChimeraX -m pip [options] no such option: --extra-index-url 0.00% done: Initializing core 50.00% done: Initializing bundles make[5]: *** [../Makefile.bundle:49: install] Error 1 make[5]: Leaving directory '/home/goddard/ucsf/chimerax/src/bundles/arrays' make[4]: *** [/home/goddard/ucsf/chimerax/mk/subdir.make:63: arrays.build] Error 2 make[4]: Leaving directory '/home/goddard/ucsf/chimerax/src/bundles' make[3]: *** [Makefile:68: install] Error 2 make[3]: Leaving directory '/home/goddard/ucsf/chimerax/src/bundles' make[2]: *** [/home/goddard/ucsf/chimerax/mk/subdir.make:25: bundles.install] Error 2 make[2]: Leaving directory '/home/goddard/ucsf/chimerax/src' make[1]: *** [Makefile:35: install] Error 2 make[1]: Leaving directory '/home/goddard/ucsf/chimerax' make: *** [Makefile:110: build-from-scratch] Error 2 " defect closed moderate Build System fixed all ChimeraX