libtbx build failing on Ubuntu 24.04.2 LTS

[dagewa]

python3 bootstrap.py --libtbx is failing with an error for me on Ubuntu 24.02.2 LTS. It looks like the critical bit is here:

/tmp/conda_base/bin/x86_64-conda-linux-gnu-c++ -o boost/libs/timer/src/cpu_timer.o -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tmp/conda_base/include -std=c++14 -I/tmp/modules/boost -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /tmp/conda_base/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /tmp/conda_base/include -DBOOST_SYSTEM_NO_DEPRECATED=1 -DBOOST_TIMER_DYN_LINK=1 -I/tmp/modules -I/tmp/modules/cctbx_project -I/tmp/build/annlib_adaptbx/include -I/tmp/conda_base/include /tmp/modules/boost/libs/timer/src/cpu_timer.cpp
In file included from /tmp/conda_base/include/python3.12/Python.h:44,
                 from /tmp/modules/boost/boost/python/detail/wrap_python.hpp:178,
                 from /tmp/modules/boost/boost/python/detail/prefix.hpp:13,
                 from /tmp/modules/boost/boost/python/object/life_support.hpp:7,
                 from /tmp/modules/boost/libs/python/src/object/life_support.cpp:5:
/tmp/modules/boost/libs/python/src/object/life_support.cpp: In function 'PyObject* boost::python::objects::make_nurse_and_patient(PyObject*, PyObject*)':
/tmp/conda_base/include/python3.12/object.h:223:30: error: lvalue required as left operand of assignment
  223 | #  define Py_TYPE(ob) Py_TYPE(_PyObject_CAST(ob))
      |                       ~~~~~~~^~~~~~~~~~~~~~~~~~~~

Full stderr: error.txt

[ndevenish]

Do you know what version of python it has pulled in?

[dagewa]

Yeah, looks like 3.12.10, but I did try with --python=3.10 too, but I think then I get a different error

/tmp/modules/boost/libs/python/src/exec.cpp:109:14: error: '_Py_fopen' was not declared in this scope; did you mean '_Py_wfopen'?
  109 |   FILE *fs = _Py_fopen(f, "r");

[dwpaley]

I failed to reproduce your build error with the following script:

FROM ubuntu:24.04
SHELL ["/bin/bash", "-c"]o


RUN apt-get update && \
  apt-get install -y build-essential git wget

RUN mkdir -p ~/miniconda3 && \
  wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh && \
  bash ~/miniconda3/miniconda.sh -b -u -p /usr/share/miniconda && \
  rm ~/miniconda3/miniconda.sh

RUN mkdir /app && \
  cd /app && \
  wget https://raw.githubusercontent.com/dials/dials/main/installer/bootstrap.py

RUN source /usr/share/miniconda/etc/profile.d/conda.sh && \
  conda activate base && \
  cd /app && \
  python bootstrap.py --libtbx

[including a typo on line 2 which was apparently inconsequential.]

It also seems to be building successfully in CI on ubuntu-latest. Any ideas for how to reproduce? (I realize answering this is pretty much equivalent to fixing the bug...)

[dwpaley]

Same result on Ubuntu 24.04.2 Server in Parallels with the same procedure, this also built with no complaints.

[dagewa]

Thanks for trying it out. I rebooted the computer and in a fresh terminal

wget https://raw.githubusercontent.com/dials/dials/main/installer/bootstrap.py
python3 bootstrap.py --libtbx

ran successfully to completion 🤦. I can only assume the environment was messed up in some way previously. Sorry for the noise.