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esheldon
cfitsio build failure
On a Linux Ubuntu system (33~22.04.1-Ubuntu) in Python 3.11, I am encountering an error with, 'pip install fitsio', which is trying to install fitsio 1.2.0. The error is below.
Collecting fitsio
Using cached fitsio-1.2.0.tar.gz (4.6 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in ./venv/test-lincc-release/lib/python3.11/site-packages (from fitsio) (1.26.0)
Building wheels for collected packages: fitsio
Building wheel for fitsio (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for fitsio (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [191 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-311
creating build/lib.linux-x86_64-cpython-311/fitsio
copying fitsio/__init__.py -> build/lib.linux-x86_64-cpython-311/fitsio
copying fitsio/util.py -> build/lib.linux-x86_64-cpython-311/fitsio
copying fitsio/fitslib.py -> build/lib.linux-x86_64-cpython-311/fitsio
copying fitsio/header.py -> build/lib.linux-x86_64-cpython-311/fitsio
creating build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/makedata.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/__init__.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/test_warnings.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/test_table.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/test_header_junk.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/test_image_compression.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/test_lib.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/checks.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/test_header.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
copying fitsio/tests/test_image.py -> build/lib.linux-x86_64-cpython-311/fitsio/tests
creating build/lib.linux-x86_64-cpython-311/fitsio/hdu
copying fitsio/hdu/__init__.py -> build/lib.linux-x86_64-cpython-311/fitsio/hdu
copying fitsio/hdu/table.py -> build/lib.linux-x86_64-cpython-311/fitsio/hdu
copying fitsio/hdu/base.py -> build/lib.linux-x86_64-cpython-311/fitsio/hdu
copying fitsio/hdu/image.py -> build/lib.linux-x86_64-cpython-311/fitsio/hdu
running egg_info
writing fitsio.egg-info/PKG-INFO
writing dependency_links to fitsio.egg-info/dependency_links.txt
writing requirements to fitsio.egg-info/requires.txt
writing top-level names to fitsio.egg-info/top_level.txt
reading manifest file 'fitsio.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'fitsio.egg-info/SOURCES.txt'
/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'fitsio.test_images' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'fitsio.test_images' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'fitsio.test_images' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'fitsio.test_images' to be distributed and are
already explicitly excluding 'fitsio.test_images' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
copying fitsio/fitsio_pywrap.c -> build/lib.linux-x86_64-cpython-311/fitsio
creating build/lib.linux-x86_64-cpython-311/fitsio/test_images
copying fitsio/test_images/test_gzip_compressed_image.fits.fz -> build/lib.linux-x86_64-cpython-311/fitsio/test_images
running build_ext
checking file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/fitscore.c
patching file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/fitscore.c
checking file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/putcols.c
patching file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/putcols.c
checking file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/fitsio.h
patching file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/fitsio.h
checking file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/configure.in
patching file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/configure.in
checking file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/Makefile.in
patching file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/Makefile.in
checking file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/configure
patching file build/temp.linux-x86_64-cpython-311/cfitsio-4.2.0/configure
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for main in -lbz2... yes
checking for bzlib.h... yes
checking for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
checking for gfortran... gfortran
checking whether we are using GNU Fortran...
yes
cfitsio: == Adding wrapper support for GNU Fortran...
done
checking for ar... ar
checking for ranlib... ranlib
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for math.h... yes
checking for limits.h... yes
cfitsio: == Using gcc version 11
checking for curl-config... curl-config
checking for inflateEnd in -lz... no
configure: error: Unable to locate zlib compression library
Traceback (most recent call last):
File "/home/blanton/venv/test-lincc-release/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/blanton/venv/test-lincc-release/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/blanton/venv/test-lincc-release/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 434, in build_wheel
return self._build_with_temp_dir(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 419, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 507, in run_setup
super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in run_setup
exec(code, locals())
File "<string>", line 313, in <module>
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 103, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 989, in run_command
super().run_command(command)
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 364, in run
self.run_command("build")
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 989, in run_command
super().run_command(command)
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 131, in run
self.run_command(cmd_name)
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 989, in run_command
super().run_command(command)
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "<string>", line 106, in run
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/command/build_ext.py", line 88, in run
_build_ext.run(self)
File "/tmp/pip-build-env-scg3c2db/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
self.build_extensions()
File "<string>", line 130, in build_extensions
File "<string>", line 266, in configure_cfitsio
ValueError: could not configure cfitsio 4.2.0
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for fitsio
Failed to build fitsio
ERROR: Could not build wheels for fitsio, which is required to install pyproject.toml-based projects
Looks like the build cannot find zlib. What kinds of variables that effect include and linking are in your environment?
Like LD_LIBRARY_PATH or C_INCLUDE_PATH? Nothing like that (I think!). My env is reproduced below ...
SYSTEMD_EXEC_PID=2044
MODULEPATH=/home/blanton/modulefiles:/usr/modulefiles/Linux:/usr/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
VENDOR=unknown
SESSION_MANAGER=local/snow:@/tmp/.ICE-unix/2000,unix/snow:/tmp/.ICE-unix/2000
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/d491ca30_07bc_4e5a_b46c_b6e8407f7112
XDG_CURRENT_DESKTOP=ubuntu:GNOME
LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod
WAYLAND_DISPLAY=wayland-0
TARG_TITLE_BAR_PAREN=
LMOD_DIR=/usr/share/lmod/lmod/libexec
LMOD_SETTARG_CMD=:
SSH_AUTH_SOCK=/tmp/ssh-XXXXXXRusQuP/agent.94762
COLORTERM=truecolor
QT_IM_MODULE=ibus
USER=blanton
DESKTOP_SESSION=ubuntu
XDG_MENU_PREFIX=gnome-
HOME=/home/blanton
BASH_ENV=/usr/share/lmod/lmod/init/bash
MODULESHOME=/usr/share/lmod/lmod
LMOD_COLORIZE=yes
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
MANPATH=/usr/share/lmod/lmod/share/man::
MODULEPATH_ROOT=/usr/modulefiles
LMOD_sys=Linux
SSH_AGENT_LAUNCHER=gnome-keyring
GTK_MODULES=gail:atk-bridge
XDG_DATA_DIRS=/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
OSTYPE=linux
XDG_SESSION_DESKTOP=ubuntu
MACHTYPE=x86_64
QT_ACCESSIBILITY=1
LMOD_PKG=/usr/share/lmod/lmod
LMOD_PREPEND_BLOCK=normal
GNOME_SETUP_DISPLAY=:1
LANG=en_US.UTF-8
LOGNAME=blanton
GNOME_TERMINAL_SERVICE=:1.124
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
HOST=snow
GNOME_SHELL_SESSION_MODE=ubuntu
LMOD_FULL_SETTARG_SUPPORT=no
PATH=/home/blanton/venv/test-lincc-release/bin:/opt/cisco/anyconnect/bin:/home/blanton/anaconda3/bin:/usr/local/bin:/home/blanton/.local/bin:/home/blanton/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin
XDG_RUNTIME_DIR=/run/user/1000
XDG_SESSION_TYPE=wayland
LMOD_arch=x86_64
HOSTTYPE=x86_64-linux
LMOD_VERSION=6.6
SHELL=/bin/tcsh
VTE_VERSION=6800
USERNAME=blanton
XMODIFIERS=@im=ibus
XAUTHORITY=/run/user/1000/.mutter-Xwaylandauth.VN8OB2
PWD=/home/blanton
GROUP=blanton
XDG_SESSION_CLASS=user
TERM=wsvt25m
GDMSESSION=ubuntu
DISPLAY=:0
SHLVL=1
PAGER=less
EDITOR=vi
RSYNC_RSH=ssh
PERLLIB=/home/blanton/Dropbox/unixenv/perl
CONDA_EXE=/home/blanton/anaconda3/bin/conda
_CONDA_ROOT=/home/blanton/anaconda3
_CONDA_EXE=/home/blanton/anaconda3/bin/conda
CONDA_PYTHON_EXE=/home/blanton/anaconda3/bin/python
CONDA_SHLVL=0
BROWSER=/snap/bin/firefox
SSH_AGENT_PID=94763
VIRTUAL_ENV=/home/blanton/venv/test-lincc-release
VIRTUAL_ENV_PROMPT=(test-lincc-release)
"apt install zlib1g" claims it is already installed, yes. Presumably wherever Ubuntu normally puts it. I am not 100% sure what it calls itself, but there is this:
/usr/lib/x86_64-linux-gnu/libz.so.1
A bit surprised configure can't find that, but I haven't really used configure in anger in a very long time!
Ok. It looks like you have a conda env going? You can use conda install fitsio maybe?
For using fitsio myself yes that does work. And in pretty much every context I work we have miniconda or conda distributions.
My test was of installing the dependencies of a different product (kcorrect) in a generic Python distribution on Ubuntu (in this case a venv). That failed, and I would prefer it not fail, so I removed the fitsio dependency in favor of astropy.io.fits (the dependency on FITS I/O is really only in two lines in the code).
But it might still be considered a problem if 'pip install fitsio==1.2.0' fails on non-Anaconda Python distributions ... I will leave it up to you to decide that!
Mike, can you please post a minimal example of using the ubuntu python to create a venv and install fitsio?
