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Failed installation: RuntimeError: Failure building small C++ program for obtaining unsigned sizes #33

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ahmedselim2017 opened this issue Dec 16, 2024 · 0 comments
Open

Failed installation: RuntimeError: Failure building small C++ program for obtaining unsigned sizes #33

ahmedselim2017 opened this issue Dec 16, 2024 · 0 comments

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@ahmedselim2017
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Hi, the installation command ./install_via_bootstrap.sh 12 fails with the error:

RuntimeError: Failure building small C++ program for obtaining unsigned sizes. Please inspect "config.log" for details:
  File "/home/ahmedselimuzum/tools/MolProbity/build/SConstruct", line 8:
    SConscript("boost_adaptbx/SConscript")
  File "/home/ahmedselimuzum/tools/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 660:
    return method(*args, **kw)
  File "/home/ahmedselimuzum/tools/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 597:
    return _SConscript(self.fs, *files, **subst_kw)
  File "/home/ahmedselimuzum/tools/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 285:
    exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals)
  File "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/boost_adaptbx/SConscript", line 770:
    write_type_id_eq_h()
  File "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/boost_adaptbx/SConscript", line 740:
    raise RuntimeError(see_message_above)

Full output:

++++++++++ creating build directories ...
Cloning into 'geostd'...
remote: Enumerating objects: 115651, done.
remote: Counting objects: 100% (115651/115651), done.
remote: Compressing objects: 100% (85696/85696), done.
remote: Total 115651 (delta 30257), reused 97547 (delta 29953), pack-reused 0 (from 0)
Receiving objects: 100% (115651/115651), 210.25 MiB | 5.23 MiB/s, done.
Resolving deltas: 100% (30257/30257), done.
Updating files: 100% (120079/120079), done.
Cloning into 'mon_lib'...
remote: Enumerating objects: 400, done.
remote: Counting objects: 100% (400/400), done.
remote: Compressing objects: 100% (213/213), done.
remote: Total 400 (delta 185), reused 394 (delta 184), pack-reused 0 (from 0)
Receiving objects: 100% (400/400), 604.41 KiB | 1.05 MiB/s, done.
Resolving deltas: 100% (185/185), done.
Cloning into 'rotarama_data'...
remote: Enumerating objects: 29, done.
remote: Counting objects: 100% (29/29), done.
remote: Compressing objects: 100% (29/29), done.
remote: Total 29 (delta 0), reused 29 (delta 0), pack-reused 0 (from 0)
Receiving objects: 100% (29/29), 7.60 MiB | 2.01 MiB/s, done.
Cloning into 'cablam_data'...
remote: Enumerating objects: 19, done.
remote: Counting objects: 100% (19/19), done.
remote: Compressing objects: 100% (19/19), done.
remote: Total 19 (delta 0), reused 19 (delta 0), pack-reused 0 (from 0)
Receiving objects: 100% (19/19), 59.99 MiB | 4.90 MiB/s, done.
HTTP response 302  [https://github.com/rlabduke/reference_data/raw/master/Top8000/rama_z/top8000_rama_z_dict.pkl]
Adding URL: https://raw.githubusercontent.com/rlabduke/reference_data/master/Top8000/rama_z/top8000_rama_z_dict.pkl
Saving 'rama_z/top8000_rama_z_dict.pkl'
HTTP response 200  [https://raw.githubusercontent.com/rlabduke/reference_data/master/Top8000/rama_z/top8000_rama_z_dict.pkl]
rama_z/top8000_rama_ 100% [===========================================================================================================================================================================================================================>]    1.06M    --.-KB/s
                          [Files: 1  Bytes: 1.06M [734.46KB/s] Redirects: 1  Todo: 0  Errors: 0                                                                                                                                                        ]
HTTP response 302  [https://github.com/cctbx/cctbx_project/raw/master/libtbx/auto_build/bootstrap.py]
Adding URL: https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py
Saving 'bootstrap.py'
HTTP response 200  [https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py]
bootstrap.py         100% [===========================================================================================================================================================================================================================>]   26.16K    --.-KB/s
                          [Files: 1  Bytes: 26.16K [19.15KB/s] Redirects: 1  Todo: 0  Errors: 0                                                                                                                                                        ]
Performing actions: hot update base build
Installing base packages using:
  /usr/bin/python modules/cctbx_project/libtbx/auto_build/install_conda.py --builder=molprobity --install_conda --python=37
===== Running in modules: git clone --recursive https://github.com/dials/cbflib.git cbflib --progress --verbose
Cloning into 'cbflib'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (gzip 2702 to 1328 bytes)
remote: Enumerating objects: 8637, done.
remote: Counting objects: 100% (925/925), done.
remote: Compressing objects: 100% (256/256), done.
remote: Total 8637 (delta 713), reused 867 (delta 668), pack-reused 7712 (from 1)
Receiving objects: 100% (8637/8637), 27.91 MiB | 4.35 MiB/s, done.
Resolving deltas: 100% (6320/6320), done.
  setting branch main to rebase
===== Running in modules/cbflib: git rev-parse HEAD
e10582128a632307d66a59066571a82773f70d8c
===== Running in modules: git clone --recursive https://github.com/cctbx/cctbx_project.git cctbx_project --progress --verbose
Cloning into 'cctbx_project'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (gzip 16102 to 8214 bytes)
remote: Enumerating objects: 308552, done.
remote: Counting objects: 100% (3950/3950), done.
remote: Compressing objects: 100% (1601/1601), done.
remote: Total 308552 (delta 2491), reused 3705 (delta 2331), pack-reused 304602 (from 1)
Receiving objects: 100% (308552/308552), 127.03 MiB | 4.94 MiB/s, done.
Resolving deltas: 100% (243055/243055), done.
Updating files: 100% (6895/6895), done.
Submodule 'xfel/euxfel/definitions' (https://github.com/nexusformat/definitions) registered for path 'xfel/euxfel/definitions'
Cloning into '/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/xfel/euxfel/definitions'...
remote: Enumerating objects: 39934, done.
remote: Counting objects: 100% (8098/8098), done.
remote: Compressing objects: 100% (639/639), done.
remote: Total 39934 (delta 7718), reused 7477 (delta 7458), pack-reused 31836 (from 1)
Receiving objects: 100% (39934/39934), 217.33 MiB | 6.29 MiB/s, done.
Resolving deltas: 100% (29567/29567), done.
Submodule path 'xfel/euxfel/definitions': checked out '6971682e65da020dcb5dc6e3cab3a29e554c3222'
  setting branch master to rebase
===== Running in modules/cctbx_project: git rev-parse HEAD
c312cdb76521cd6ece7361221aa496ac2485a522
===== Running in modules/cctbx_project: /usr/bin/python libtbx/version.py
Writing files containing version information for cctbx_project
===============================================================================
Wrote /home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/libtbx/../../cctbx_project/cctbx_version.txt
Wrote /home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/libtbx/../../cctbx_project/cctbx_version.h
Wrote /home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/libtbx/../../cctbx_project/setup.py
===============================================================================
===== Running in modules: git clone --recursive https://github.com/cctbx/ccp4io.git ccp4io --progress --verbose
Cloning into 'ccp4io'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (452 bytes)
remote: Enumerating objects: 1585, done.
remote: Counting objects: 100% (23/23), done.
remote: Compressing objects: 100% (11/11), done.
remote: Total 1585 (delta 12), reused 18 (delta 12), pack-reused 1562 (from 1)
Receiving objects: 100% (1585/1585), 2.53 MiB | 1.41 MiB/s, done.
Resolving deltas: 100% (977/977), done.
  setting branch master to rebase
===== Running in modules/ccp4io: git rev-parse HEAD
b58c4fb68902e4e6a58f4a585d0722e542516076
===== Running in modules: git clone --recursive https://github.com/cctbx/ccp4io_adaptbx.git ccp4io_adaptbx --progress --verbose
Cloning into 'ccp4io_adaptbx'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (302 bytes)
remote: Enumerating objects: 508, done.
remote: Counting objects: 100% (122/122), done.
remote: Compressing objects: 100% (9/9), done.
remote: Total 508 (delta 118), reused 114 (delta 113), pack-reused 386 (from 1)
Receiving objects: 100% (508/508), 271.25 KiB | 1.18 MiB/s, done.
Resolving deltas: 100% (297/297), done.
  setting branch master to rebase
===== Running in modules/ccp4io_adaptbx: git rev-parse HEAD
3d9dc50bfe9dd3c6bc59ba242f5c7e07b6ed25ba
===== Running in modules: git clone --recursive https://github.com/cctbx/annlib.git annlib --progress --verbose
Cloning into 'annlib'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (252 bytes)
remote: Enumerating objects: 84, done.
remote: Counting objects: 100% (10/10), done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 84 (delta 2), reused 1 (delta 0), pack-reused 74 (from 1)
Receiving objects: 100% (84/84), 537.83 KiB | 1.24 MiB/s, done.
Resolving deltas: 100% (17/17), done.
  setting branch master to rebase
===== Running in modules/annlib: git rev-parse HEAD
e23a7c1be859508878fe07ed49d5f82b836b5fe7
===== Running in modules: git clone --recursive https://github.com/cctbx/annlib_adaptbx.git annlib_adaptbx --progress --verbose
Cloning into 'annlib_adaptbx'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (gzip 1202 to 338 bytes)
remote: Enumerating objects: 190, done.
remote: Counting objects: 100% (15/15), done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 190 (delta 5), reused 15 (delta 5), pack-reused 175 (from 1)
Receiving objects: 100% (190/190), 166.87 KiB | 659.00 KiB/s, done.
Resolving deltas: 100% (82/82), done.
  setting branch master to rebase
===== Running in modules/annlib_adaptbx: git rev-parse HEAD
fb1097bc37fa304eb9aba68fdc709ec08cf4a61a
===== Running in modules: git clone --recursive https://github.com/cctbx/tntbx.git tntbx --progress --verbose
Cloning into 'tntbx'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (252 bytes)
remote: Enumerating objects: 232, done.
remote: Total 232 (delta 0), reused 0 (delta 0), pack-reused 232 (from 1)
Receiving objects: 100% (232/232), 75.93 KiB | 740.00 KiB/s, done.
Resolving deltas: 100% (137/137), done.
  setting branch master to rebase
===== Running in modules/tntbx: git rev-parse HEAD
1aefe762bb9633dda7e98cc32e469d688ad5aa59
===== Running in .: git clone --recursive https://github.com/rlabduke/MolProbity.git molprobity --progress --verbose
Cloning into 'molprobity'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (gzip 1902 to 955 bytes)
remote: Enumerating objects: 9129, done.
remote: Counting objects: 100% (321/321), done.
remote: Compressing objects: 100% (188/188), done.
remote: Total 9129 (delta 183), reused 211 (delta 133), pack-reused 8808 (from 1)
Receiving objects: 100% (9129/9129), 123.64 MiB | 5.30 MiB/s, done.
Resolving deltas: 100% (5808/5808), done.
Updating files: 100% (384/384), done.
  setting branch master to rebase
===== Running in ./molprobity: git rev-parse HEAD
daee5253054c978010b782c840bd3e3ec24b1b4d
Existing non-git directory -- don't know what to do. skipping: chem_data
===== Running in modules/chem_data/geostd: git pull --rebase
Already up to date.
===== Running in modules: git clone --recursive https://github.com/rlabduke/reduce.git reduce --progress --verbose
Cloning into 'reduce'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (gzip 1702 to 878 bytes)
remote: Enumerating objects: 2984, done.
remote: Counting objects: 100% (446/446), done.
remote: Compressing objects: 100% (173/173), done.
remote: Total 2984 (delta 293), reused 402 (delta 272), pack-reused 2538 (from 1)
Receiving objects: 100% (2984/2984), 39.71 MiB | 4.13 MiB/s, done.
Resolving deltas: 100% (2138/2138), done.
  setting branch master to rebase
===== Running in modules/reduce: git rev-parse HEAD
7ed9f01d856d67fd934d40905b762cf1b8693ebc
===== Running in modules: git clone --recursive https://github.com/rlabduke/probe.git probe --progress --verbose
Cloning into 'probe'...
POST git-upload-pack (175 bytes)
POST git-upload-pack (1002 bytes)
remote: Enumerating objects: 410, done.
remote: Counting objects: 100% (141/141), done.
remote: Compressing objects: 100% (17/17), done.
remote: Total 410 (delta 129), reused 128 (delta 124), pack-reused 269 (from 1)
Receiving objects: 100% (410/410), 412.21 KiB | 921.00 KiB/s, done.
Resolving deltas: 100% (257/257), done.
  setting branch master to rebase
===== Running in modules/probe: git rev-parse HEAD
d561a5aabe16e90420d6c6c470e9db0da7d68550

  removing .pyc files in /home/ahmedselimuzum/tools/MolProbity/modules, walk? True
  removed 0 files
===== Running in .: base
Base conda installation:
  /usr
Installing molprobity environment with:
  /home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/libtbx/auto_build/conda_envs/cctbx_py37_linux-64.txt
Retrieving notices: ...working... done

Downloading and Extracting Packages:


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: /
done
Completed installation into:
  /home/ahmedselimuzum/tools/MolProbity/conda_base
===== Running in build: run configure.py
Python: 3.7.16 "/home/ahmedselimuzum/tools/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: /home/ahmedselimuzum/tools/MolProbity/build
Top-down list of all modules involved:
  mmtbx           "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/mmtbx"
  probe           "/home/ahmedselimuzum/tools/MolProbity/modules/probe"
  reduce          "/home/ahmedselimuzum/tools/MolProbity/modules/reduce"
  iotbx           "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/iotbx"
  cbflib+adaptbx  "/home/ahmedselimuzum/tools/MolProbity/modules/cbflib"
                  "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/cbflib_adaptbx"
  ccp4io+adaptbx  "/home/ahmedselimuzum/tools/MolProbity/modules/ccp4io"
                  "/home/ahmedselimuzum/tools/MolProbity/modules/ccp4io_adaptbx"
  smtbx           "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/smtbx"
  ucif            "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/ucif"
  cctbx           "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/cctbx"
  scitbx          "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/scitbx"
  fable           "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/fable"
  cma_es          "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/cma_es"
  omptbx          "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/omptbx"
  boost+adaptbx   "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/boost"
                  "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/boost_adaptbx"
  tbxx            "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/tbxx"
  chiltbx         "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/chiltbx"
  libtbx          "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/libtbx"
Creating files in build directory: "/home/ahmedselimuzum/tools/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: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/libtbx/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/boost_adaptbx/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/fable/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/scitbx/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/cctbx/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/smtbx/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/cbflib_adaptbx/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/iotbx/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/reduce/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/probe/command_line"
  Ignored: [Errno 2] No such file or directory: '/home/ahmedselimuzum/tools/MolProbity/build/probe/exe/probe'
  Ignored: [Errno 2] No such file or directory: '/home/ahmedselimuzum/tools/MolProbity/build/probe/exe/probe'
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/mmtbx/command_line"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/libtbx/libtbx_refresh.py"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py"
  Generating C++ header files in:
    "/home/ahmedselimuzum/tools/MolProbity/build/include/scitbx/array_family"
  Generating C++ files in:
    "/home/ahmedselimuzum/tools/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: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py"
  Generating C++ files in:
    "/home/ahmedselimuzum/tools/MolProbity/build/cctbx/eltbx"
  Generating C++ files in:
    "/home/ahmedselimuzum/tools/MolProbity/build/include/cctbx/boost_python"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py"
  Generating C++ files in:
    "/home/ahmedselimuzum/tools/MolProbity/build/include/smtbx/boost_python"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/cbflib_adaptbx/libtbx_refresh.py"
  Copying to lib: "/home/ahmedselimuzum/tools/MolProbity/modules/cbflib/pycbf/pycbf.py"
Processing: "/home/ahmedselimuzum/tools/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: "/home/ahmedselimuzum/tools/MolProbity/modules/reduce/libtbx_refresh.py"
Processing: "/home/ahmedselimuzum/tools/MolProbity/modules/probe/libtbx_refresh.py"
Processing: "/home/ahmedselimuzum/tools/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.
Error while loading conda entry point: conda-libmamba-solver (/home/ahmedselimuzum/tools/MolProbity/build/../conda_base/lib/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /usr/lib64/python3.12/site-packages/libmambapy/bindings.cpython-312-x86_64-linux-gnu.so))
Base conda installation:
  /usr
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 ...
libtbx.scons: OpenMP is disabled.
BOOST_VERSION: 107400
RuntimeError: Failure building small C++ program for obtaining unsigned sizes. Please inspect "config.log" for details:
  File "/home/ahmedselimuzum/tools/MolProbity/build/SConstruct", line 8:
    SConscript("boost_adaptbx/SConscript")
  File "/home/ahmedselimuzum/tools/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 660:
    return method(*args, **kw)
  File "/home/ahmedselimuzum/tools/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 597:
    return _SConscript(self.fs, *files, **subst_kw)
  File "/home/ahmedselimuzum/tools/MolProbity/conda_base/lib/python3.7/site-packages/SCons/Script/SConscript.py", line 285:
    exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals)
  File "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/boost_adaptbx/SConscript", line 770:
    write_type_id_eq_h()
  File "/home/ahmedselimuzum/tools/MolProbity/modules/cctbx_project/boost_adaptbx/SConscript", line 740:
    raise RuntimeError(see_message_above)
usr+sys time: 0.30 seconds
wall clock time: 1.77 seconds
Process failed with return code 2
++++++++++ MolProbity configure.sh finished.
++++++++++ Run molprobity/setup.sh to complete installation.
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