chrissciwilliams
commented
6 months ago Thanks for the error log; it's a big help!
The key lines look to be: TypeError: '>=' not supported between instances of 'NoneType' and 'int': File "/usr/local/MolProbity/modules/cctbx_project/libtbx/SConscript", line 644: if (env_etc.gcc_version >= 40400 and determine_cpp0x_flag()):
It looks like the env_etc.gcc_versionvariable is not being set properly. Do you have gcc on your machine? -Christopher Williams ---Richardson Lab, Duke University
On Wed, Jan 10, 2024 at 8:49 AM Vcald @.***> wrote:
I get this failure when trying to install the last git version of MolProbity:
./install_via_bootstrap.sh 12 ++++++++++ creating build directories ... fatal: destination path 'geostd' already exists and is not an empty directory. fatal: destination path 'mon_lib' already exists and is not an empty directory. fatal: destination path 'rotarama_data' already exists and is not an empty directory. fatal: destination path 'cablam_data' already exists and is not an empty directory. --2024-01-10 14:48:01-- https://github.com/rlabduke/reference_data/raw/master/Top8000/rama_z/top8000_rama_z_dict.pkl Resolving github.com (github.com)... 140.82.121.4 Connecting to github.com (github.com)|140.82.121.4|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://raw.githubusercontent.com/rlabduke/reference_data/master/Top8000/rama_z/top8000_rama_z_dict.pkl [following] --2024-01-10 14:48:01-- https://raw.githubusercontent.com/rlabduke/reference_data/master/Top8000/rama_z/top8000_rama_z_dict.pkl Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 2606:50c0:8002::154, 2606:50c0:8003::154, 2606:50c0:8001::154, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|2606:50c0:8002::154|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1117603 (1.1M) [application/octet-stream] Saving to: ‘rama_z/top8000_rama_z_dict.pkl’
rama_z/top8000_rama_z_dict.pkl 100%[===========================================================================================>] 1.07M --.-KB/s in 0.1s
2024-01-10 14:48:02 (9.10 MB/s) - ‘rama_z/top8000_rama_z_dict.pkl’ saved [1117603/1117603]
--2024-01-10 14:48:02-- https://github.com/cctbx/cctbx_project/raw/master/libtbx/auto_build/bootstrap.py Resolving github.com (github.com)... 140.82.121.4 Connecting to github.com (github.com)|140.82.121.4|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py [following] --2024-01-10 14:48:02-- https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 2606:50c0:8003::154, 2606:50c0:8002::154, 2606:50c0:8000::154, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|2606:50c0:8003::154|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 106584 (104K) [text/plain] Saving to: ‘bootstrap.py’
bootstrap.py 100%[===========================================================================================>] 104.09K --.-KB/s in 0.04s
2024-01-10 14:48:02 (2.74 MB/s) - ‘bootstrap.py’ saved [106584/106584] /usr/local/MolProbity/bootstrap.py:455: SyntaxWarning: invalid escape sequence '\s' if re.match('remote\s=', line.strip()): /usr/local/MolProbity/bootstrap.py:457: SyntaxWarning: invalid escape sequence '\s' if re.match('rebase\s=', line.strip()): Performing actions: hot update base build Installing base packages using: /usr/bin/python modules/cctbx_project/libtbx/auto_build/install_conda.py --builder=molprobity --python=37 ===== Running in modules/cbflib: git pull --rebase Already up to date. ===== Running in modules/cctbx_project: git pull --rebase Already up to date. ===== Running in modules/cctbx_project: /usr/bin/python libtbx/version.py Writing files containing version information for cctbx_project Wrote /usr/local/MolProbity/modules/cctbx_project/libtbx/../../cctbx_project/cctbx_version.txt Wrote /usr/local/MolProbity/modules/cctbx_project/libtbx/../../cctbx_project/cctbx_version.h Wrote /usr/local/MolProbity/modules/cctbx_project/libtbx/../../cctbx_project/setup.py
===== Running in modules/ccp4io: git pull --rebase Already up to date. ===== Running in modules/ccp4io_adaptbx: git pull --rebase Already up to date. ===== Running in modules/annlib: git pull --rebase Already up to date. ===== Running in modules/annlib_adaptbx: git pull --rebase Already up to date. ===== Running in modules/tntbx: git pull --rebase Already up to date. ===== Running in ./molprobity: git pull --rebase Already up to date. ===== Running in modules/reduce: git pull --rebase Already up to date. ===== Running in modules/probe: git pull --rebase Already up to date.
removing .pyc files in /usr/local/MolProbity/modules, walk? True removed 57 files ===== Running in .: base Base conda installation: /usr/local/MolProbity/mc3 The environment is newer than the environment file. Skipping update. ===== Running in build: run configure.py Python: 3.7.16 "/usr/local/MolProbity/build/../conda_base/bin/python" Compiler: default Build mode: release Warning level: 0 Precompiled Headers: False Static libraries: False Static exe: False Scan Boost headers: False Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Enable OpenMP if possible: False Boost threads enabled: True Enable CUDA: False Enable KOKKOS: False Use conda: True Use opt_resources if available: False Use environment flags: False Enable C++11: False command_version_suffix: None Relocatable paths anchored at: /usr/local/MolProbity/build Top-down list of all modules involved: mmtbx "/usr/local/MolProbity/modules/cctbx_project/mmtbx" probe "/usr/local/MolProbity/modules/probe" reduce "/usr/local/MolProbity/modules/reduce" iotbx "/usr/local/MolProbity/modules/cctbx_project/iotbx" cbflib+adaptbx "/usr/local/MolProbity/modules/cbflib" "/usr/local/MolProbity/modules/cctbx_project/cbflib_adaptbx" ccp4io+adaptbx "/usr/local/MolProbity/modules/ccp4io" "/usr/local/MolProbity/modules/ccp4io_adaptbx" smtbx "/usr/local/MolProbity/modules/cctbx_project/smtbx" ucif "/usr/local/MolProbity/modules/cctbx_project/ucif" cctbx "/usr/local/MolProbity/modules/cctbx_project/cctbx" scitbx "/usr/local/MolProbity/modules/cctbx_project/scitbx" fable "/usr/local/MolProbity/modules/cctbx_project/fable" cma_es "/usr/local/MolProbity/modules/cctbx_project/cma_es" omptbx "/usr/local/MolProbity/modules/cctbx_project/omptbx" boost+adaptbx "/usr/local/MolProbity/modules/cctbx_project/boost" "/usr/local/MolProbity/modules/cctbx_project/boost_adaptbx" tbxx "/usr/local/MolProbity/modules/cctbx_project/tbxx" chiltbx "/usr/local/MolProbity/modules/cctbx_project/chiltbx" libtbx "/usr/local/MolProbity/modules/cctbx_project/libtbx" Creating files in build directory: "/usr/local/MolProbity/build" dispatcher_include_template.sh dispatcher_head.sh setpaths.sh setpaths.csh setpaths_all.sh setpaths_all.csh setpaths_debug.sh unsetpaths.sh setpaths_debug.csh unsetpaths.csh SConstruct Makefile run_tests.csh Processing: "/usr/local/MolProbity/modules/cctbx_project/libtbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/fable/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/scitbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/cctbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/smtbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/cbflib_adaptbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/iotbx/command_line" Processing: "/usr/local/MolProbity/modules/reduce/command_line" Processing: "/usr/local/MolProbity/modules/probe/command_line" Ignored: [Errno 2] No such file or directory: '/usr/local/MolProbity/build/probe/exe/probe' Ignored: [Errno 2] No such file or directory: '/usr/local/MolProbity/build/probe/exe/probe' Processing: "/usr/local/MolProbity/modules/cctbx_project/mmtbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/libtbx/libtbx_refresh.py" Processing: "/usr/local/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" Processing: "/usr/local/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" Generating C++ header files in: "/usr/local/MolProbity/build/include/scitbx/array_family" Generating C++ files in: "/usr/local/MolProbity/build/include/scitbx/array_family/boost_python" Using fable to convert scitbx/lbfgs.f Updating entry points for scitbx 1 entries for entry point pytest_randomly.random_seeder Processing: "/usr/local/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" Generating C++ files in: "/usr/local/MolProbity/build/cctbx/eltbx" Generating C++ files in: "/usr/local/MolProbity/build/include/cctbx/boost_python" Processing: "/usr/local/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" Generating C++ files in: "/usr/local/MolProbity/build/include/smtbx/boost_python" Processing: "/usr/local/MolProbity/modules/cctbx_project/cbflib_adaptbx/libtbx_refresh.py" Copying to lib: "/usr/local/MolProbity/modules/cbflib/pycbf/pycbf.py" Processing: "/usr/local/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" Using fable to convert iotbx/pdb/hybrid_36_f.f Writing: iotbx/pdb/hybrid_36_fem.cpp Processing: "/usr/local/MolProbity/modules/reduce/libtbx_refresh.py" Processing: "/usr/local/MolProbity/modules/probe/libtbx_refresh.py" Processing: "/usr/local/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" Done. ===== Running in build: save configure command ===== Running in build: permit execution of config_modules.sh ===== Running in build: Writing additional setup scripts for conda. Base conda installation: /usr/local/MolProbity/mc3 conda_setpaths.sh has been written successfully. conda_unsetpaths.sh has been written successfully. conda_setpaths.csh has been written successfully. conda_unsetpaths.csh has been written successfully. ===== Running in build: libtbx.scons scons: Reading SConscript files ... TypeError: '>=' not supported between instances of 'NoneType' and 'int': File "/usr/local/MolProbity/build/SConstruct", line 6: SConscript("libtbx/SConscript") File "/usr/local/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 660: return method(*args, *kw) File "/usr/local/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 597: return _SConscript(self.fs, files, **subst_kw) File "/usr/local/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 285: exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals) File "/usr/local/MolProbity/modules/cctbx_project/libtbx/SConscript", line 644: if (env_etc.gcc_version >= 40400 and determine_cpp0x_flag()): usr+sys time: 0.08 seconds wall clock time: 0.10 seconds Process failed with return code 2 ++++++++++ MolProbity configure.sh finished. ++++++++++ Run molprobity/setup.sh to complete installation.
Any hint?
— Reply to this email directly, view it on GitHub https://github.com/rlabduke/MolProbity/issues/30, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACLEREDWW3FDRAML4SODKKLYN2L63AVCNFSM6AAAAABBU2MPPCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TINBRHEYTONQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Vcald
Nate-Dinger
I get this failure when trying to install the last git version of MolProbity:
./install_via_bootstrap.sh 12 ++++++++++ creating build directories ... fatal: destination path 'geostd' already exists and is not an empty directory. fatal: destination path 'mon_lib' already exists and is not an empty directory. fatal: destination path 'rotarama_data' already exists and is not an empty directory. fatal: destination path 'cablam_data' already exists and is not an empty directory. --2024-01-10 14:48:01-- https://github.com/rlabduke/reference_data/raw/master/Top8000/rama_z/top8000_rama_z_dict.pkl Resolving github.com (github.com)... 140.82.121.4 Connecting to github.com (github.com)|140.82.121.4|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://raw.githubusercontent.com/rlabduke/reference_data/master/Top8000/rama_z/top8000_rama_z_dict.pkl [following] --2024-01-10 14:48:01-- https://raw.githubusercontent.com/rlabduke/reference_data/master/Top8000/rama_z/top8000_rama_z_dict.pkl Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 2606:50c0:8002::154, 2606:50c0:8003::154, 2606:50c0:8001::154, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|2606:50c0:8002::154|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1117603 (1.1M) [application/octet-stream] Saving to: ‘rama_z/top8000_rama_z_dict.pkl’
rama_z/top8000_rama_z_dict.pkl 100%[===========================================================================================>] 1.07M --.-KB/s in 0.1s
2024-01-10 14:48:02 (9.10 MB/s) - ‘rama_z/top8000_rama_z_dict.pkl’ saved [1117603/1117603]
--2024-01-10 14:48:02-- https://github.com/cctbx/cctbx_project/raw/master/libtbx/auto_build/bootstrap.py Resolving github.com (github.com)... 140.82.121.4 Connecting to github.com (github.com)|140.82.121.4|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py [following] --2024-01-10 14:48:02-- https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 2606:50c0:8003::154, 2606:50c0:8002::154, 2606:50c0:8000::154, ... Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|2606:50c0:8003::154|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 106584 (104K) [text/plain] Saving to: ‘bootstrap.py’
bootstrap.py 100%[===========================================================================================>] 104.09K --.-KB/s in 0.04s
2024-01-10 14:48:02 (2.74 MB/s) - ‘bootstrap.py’ saved [106584/106584]
/usr/local/MolProbity/bootstrap.py:455: SyntaxWarning: invalid escape sequence '\s' if re.match('remote\s=', line.strip()): /usr/local/MolProbity/bootstrap.py:457: SyntaxWarning: invalid escape sequence '\s' if re.match('rebase\s=', line.strip()): Performing actions: hot update base build Installing base packages using: /usr/bin/python modules/cctbx_project/libtbx/auto_build/install_conda.py --builder=molprobity --python=37 ===== Running in modules/cbflib: git pull --rebase Already up to date. ===== Running in modules/cctbx_project: git pull --rebase Already up to date. ===== Running in modules/cctbx_project: /usr/bin/python libtbx/version.py Writing files containing version information for cctbx_project
Wrote /usr/local/MolProbity/modules/cctbx_project/libtbx/../../cctbx_project/cctbx_version.txt Wrote /usr/local/MolProbity/modules/cctbx_project/libtbx/../../cctbx_project/cctbx_version.h Wrote /usr/local/MolProbity/modules/cctbx_project/libtbx/../../cctbx_project/setup.py
===== Running in modules/ccp4io: git pull --rebase Already up to date. ===== Running in modules/ccp4io_adaptbx: git pull --rebase Already up to date. ===== Running in modules/annlib: git pull --rebase Already up to date. ===== Running in modules/annlib_adaptbx: git pull --rebase Already up to date. ===== Running in modules/tntbx: git pull --rebase Already up to date. ===== Running in ./molprobity: git pull --rebase Already up to date. ===== Running in modules/reduce: git pull --rebase Already up to date. ===== Running in modules/probe: git pull --rebase Already up to date.
removing .pyc files in /usr/local/MolProbity/modules, walk? True removed 57 files ===== Running in .: base Base conda installation: /usr/local/MolProbity/mc3 The environment is newer than the environment file. Skipping update. ===== Running in build: run configure.py Python: 3.7.16 "/usr/local/MolProbity/build/../conda_base/bin/python" Compiler: default Build mode: release Warning level: 0 Precompiled Headers: False Static libraries: False Static exe: False Scan Boost headers: False Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Enable OpenMP if possible: False Boost threads enabled: True Enable CUDA: False Enable KOKKOS: False Use conda: True Use opt_resources if available: False Use environment flags: False Enable C++11: False command_version_suffix: None Relocatable paths anchored at: /usr/local/MolProbity/build Top-down list of all modules involved: mmtbx "/usr/local/MolProbity/modules/cctbx_project/mmtbx" probe "/usr/local/MolProbity/modules/probe" reduce "/usr/local/MolProbity/modules/reduce" iotbx "/usr/local/MolProbity/modules/cctbx_project/iotbx" cbflib+adaptbx "/usr/local/MolProbity/modules/cbflib" "/usr/local/MolProbity/modules/cctbx_project/cbflib_adaptbx" ccp4io+adaptbx "/usr/local/MolProbity/modules/ccp4io" "/usr/local/MolProbity/modules/ccp4io_adaptbx" smtbx "/usr/local/MolProbity/modules/cctbx_project/smtbx" ucif "/usr/local/MolProbity/modules/cctbx_project/ucif" cctbx "/usr/local/MolProbity/modules/cctbx_project/cctbx" scitbx "/usr/local/MolProbity/modules/cctbx_project/scitbx" fable "/usr/local/MolProbity/modules/cctbx_project/fable" cma_es "/usr/local/MolProbity/modules/cctbx_project/cma_es" omptbx "/usr/local/MolProbity/modules/cctbx_project/omptbx" boost+adaptbx "/usr/local/MolProbity/modules/cctbx_project/boost" "/usr/local/MolProbity/modules/cctbx_project/boost_adaptbx" tbxx "/usr/local/MolProbity/modules/cctbx_project/tbxx" chiltbx "/usr/local/MolProbity/modules/cctbx_project/chiltbx" libtbx "/usr/local/MolProbity/modules/cctbx_project/libtbx" Creating files in build directory: "/usr/local/MolProbity/build" dispatcher_include_template.sh dispatcher_head.sh setpaths.sh setpaths.csh setpaths_all.sh setpaths_all.csh setpaths_debug.sh unsetpaths.sh setpaths_debug.csh unsetpaths.csh SConstruct Makefile run_tests.csh Processing: "/usr/local/MolProbity/modules/cctbx_project/libtbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/fable/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/scitbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/cctbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/smtbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/cbflib_adaptbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/iotbx/command_line" Processing: "/usr/local/MolProbity/modules/reduce/command_line" Processing: "/usr/local/MolProbity/modules/probe/command_line" Ignored: [Errno 2] No such file or directory: '/usr/local/MolProbity/build/probe/exe/probe' Ignored: [Errno 2] No such file or directory: '/usr/local/MolProbity/build/probe/exe/probe' Processing: "/usr/local/MolProbity/modules/cctbx_project/mmtbx/command_line" Processing: "/usr/local/MolProbity/modules/cctbx_project/libtbx/libtbx_refresh.py" Processing: "/usr/local/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" Processing: "/usr/local/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" Generating C++ header files in: "/usr/local/MolProbity/build/include/scitbx/array_family" Generating C++ files in: "/usr/local/MolProbity/build/include/scitbx/array_family/boost_python" Using fable to convert scitbx/lbfgs.f Updating entry points for scitbx 1 entries for entry point pytest_randomly.random_seeder Processing: "/usr/local/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" Generating C++ files in: "/usr/local/MolProbity/build/cctbx/eltbx" Generating C++ files in: "/usr/local/MolProbity/build/include/cctbx/boost_python" Processing: "/usr/local/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" Generating C++ files in: "/usr/local/MolProbity/build/include/smtbx/boost_python" Processing: "/usr/local/MolProbity/modules/cctbx_project/cbflib_adaptbx/libtbx_refresh.py" Copying to lib: "/usr/local/MolProbity/modules/cbflib/pycbf/pycbf.py" Processing: "/usr/local/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" Using fable to convert iotbx/pdb/hybrid_36_f.f Writing: iotbx/pdb/hybrid_36_fem.cpp Processing: "/usr/local/MolProbity/modules/reduce/libtbx_refresh.py" Processing: "/usr/local/MolProbity/modules/probe/libtbx_refresh.py" Processing: "/usr/local/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" Done. ===== Running in build: save configure command ===== Running in build: permit execution of config_modules.sh ===== Running in build: Writing additional setup scripts for conda. Base conda installation: /usr/local/MolProbity/mc3 conda_setpaths.sh has been written successfully. conda_unsetpaths.sh has been written successfully. conda_setpaths.csh has been written successfully. conda_unsetpaths.csh has been written successfully. ===== Running in build: libtbx.scons scons: Reading SConscript files ... TypeError: '>=' not supported between instances of 'NoneType' and 'int': File "/usr/local/MolProbity/build/SConstruct", line 6: SConscript("libtbx/SConscript") File "/usr/local/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 660: return method(*args, *kw) File "/usr/local/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 597: return _SConscript(self.fs, files, **subst_kw) File "/usr/local/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 285: exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals) File "/usr/local/MolProbity/modules/cctbx_project/libtbx/SConscript", line 644: if (env_etc.gcc_version >= 40400 and determine_cpp0x_flag()): usr+sys time: 0.08 seconds wall clock time: 0.10 seconds Process failed with return code 2 ++++++++++ MolProbity configure.sh finished. ++++++++++ Run molprobity/setup.sh to complete installation.
Any hint?