pyenv install fails to build 2.7.14 with ImportError: No module named pyexpat

[justinjdickow]

pyenv version: 1.2.0
MacOS 10.13.2
python-build version: 20160602

I've run

brew install readline xz and xcode-select --install

I'm sourcing flags using the following

export CFLAGS="-I$(xcrun --show-sdk-path)/usr/include"
export CFLAGS="-I$(brew --prefix readline)/include $CFLAGS"
export LDFLAGS="-L$(brew --prefix readline)/lib $LDFLAGS"
export CFLAGS="-I$(brew --prefix openssl)/include $CFLAGS"
export LDFLAGS="-L$(brew --prefix openssl)/lib $LDFLAGS"
export PKG_CONFIG_PATH="$(brew --prefix openssl)/lib/pkgconfig"

When I run pyenv install 2.7.14 I get the following error

Traceback (most recent call last):
  File "get-pip.py", line 20061, in <module>
    main()
  File "get-pip.py", line 194, in main
    bootstrap(tmpdir=tmpdir)
  File "get-pip.py", line 82, in bootstrap
    import pip
  File "/var/folders/t5/4dd3lpyj50j05f9xn49hzj8n8mjnmf/T/tmpXrOLYp/pip.zip/pip/__init__.py", line 26, in <module>
  File "/var/folders/t5/4dd3lpyj50j05f9xn49hzj8n8mjnmf/T/tmpXrOLYp/pip.zip/pip/utils/__init__.py", line 27, in <module>
  File "/var/folders/t5/4dd3lpyj50j05f9xn49hzj8n8mjnmf/T/tmpXrOLYp/pip.zip/pip/_vendor/pkg_resources/__init__.py", line 1027, in <module>
  File "/var/folders/t5/4dd3lpyj50j05f9xn49hzj8n8mjnmf/T/tmpXrOLYp/pip.zip/pip/_vendor/pkg_resources/__init__.py", line 1030, in Environment
  File "/var/folders/t5/4dd3lpyj50j05f9xn49hzj8n8mjnmf/T/tmpXrOLYp/pip.zip/pip/_vendor/pkg_resources/__init__.py", line 272, in get_supported_platform
  File "/var/folders/t5/4dd3lpyj50j05f9xn49hzj8n8mjnmf/T/tmpXrOLYp/pip.zip/pip/_vendor/pkg_resources/__init__.py", line 444, in _macosx_vers
  File "/usr/local/opt/pyenv/versions/2.7.14/lib/python2.7/platform.py", line 764, in mac_ver
    info = _mac_ver_xml()
  File "/usr/local/opt/pyenv/versions/2.7.14/lib/python2.7/platform.py", line 741, in _mac_ver_xml
    pl = plistlib.readPlist(fn)
  File "/usr/local/opt/pyenv/versions/2.7.14/lib/python2.7/plistlib.py", line 78, in readPlist
    rootObject = p.parse(pathOrFile)
  File "/usr/local/opt/pyenv/versions/2.7.14/lib/python2.7/plistlib.py", line 401, in parse
    from xml.parsers.expat import ParserCreate
  File "/usr/local/opt/pyenv/versions/2.7.14/lib/python2.7/xml/parsers/expat.py", line 4, in <module>
    from pyexpat import *
ImportError: No module named pyexpat

[webknjaz]

Hi, I'm getting exactly same issue, when trying to pyenv install 3.6.4 in CircleCI.

Here's the build log:
https://circleci.com/gh/cherrypy/cheroot/291

[webknjaz]

@yyuu @joshfriend any ideas regarding this failure?

[webknjaz]

Here's the full log of python-build: https://gist.github.com/webknjaz/91d479ef19fcda866b44dacd7d3fedcc

[natecox]

Have you updated brew and installed the updated pyenv? The current pyenv version is 1.2.1, and it looks like you're running 1.2.0.

The newest version is working flawlessly for me on 10.13.2.

Edit: it looks like your CircleCI config is explicitly set to avoid updates, which may also be the problem there.

[webknjaz]

@natecox yeah, it takes some time to to upgrade, so I've disabled it, but this problem existed before that. I just wanted to speed-up testing.

Should I install pyenv via brew as well?

[justinjdickow]

Same error with pyenv 1.2.1 and macOS 10.13.2

[webknjaz]

1.2.1 + 10.13.5 doesn't work either: https://circleci.com/gh/cherrypy/cheroot/298

[webknjaz]

So it basically fails to build pyexpat module:

clang -bundle -undefined dynamic_lookup -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -L/Users/distiller/.pyenv/versions/3.6.4/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -L/Users/distiller/.pyenv/versions/3.6.4/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -L/Users/distiller/.pyenv/versions/3.6.4/lib -L/usr/local/opt/openssl/lib -I/usr/local/opt/openssl/include -I/Applications/Xcode-9.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include -I/usr/local/opt/readline/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/Users/distiller/.pyenv/versions/3.6.4/include build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/_decimal.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/basearith.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/constants.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/context.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/convolute.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/crt.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/difradix2.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/fnt.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/fourstep.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/io.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/memory.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/mpdecimal.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/numbertheory.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/sixstep.o build/temp.macosx-10.12-x86_64-3.6/private/var/folders/ms/xg67k5sn16xc7sdr_w3q45840000gn/T/python-build.20180115145538.1345/Python-3.6.4/Modules/_decimal/libmpdec/transpose.o -L/usr/local/opt/readline/lib -L/Users/distiller/.pyenv/versions/3.6.4/lib -L/usr/local/opt/openssl/lib -L/usr/local/lib -o build/lib.macosx-10.12-x86_64-3.6/_decimal.cpython-36m-darwin.so
*** WARNING: renaming "pyexpat" since importing it failed: dlopen(build/lib.macosx-10.12-x86_64-3.6/pyexpat.cpython-36m-darwin.so, 2): Symbol not found: _XML_ErrorString
  Referenced from: build/lib.macosx-10.12-x86_64-3.6/pyexpat.cpython-36m-darwin.so
  Expected in: flat namespace
 in build/lib.macosx-10.12-x86_64-3.6/pyexpat.cpython-36m-darwin.so
*** WARNING: renaming "_elementtree" since importing it failed: PyCapsule_Import could not import module "pyexpat"

Python build finished successfully!
The necessary bits to build these optional modules were not found:
ossaudiodev           spwd                                     
To find the necessary bits, look in setup.py in detect_modules() for the module's name.

The following modules found by detect_modules() in setup.py, have been
built by the Makefile instead, as configured by the Setup files:
atexit                pwd                   time               

Failed to build these modules:
readline                                                       


Following modules built successfully but were removed because they could not be imported:
_elementtree          pyexpat                                  

and then pip run fails to import it.

but installing expat doesn't fix the problem..

[justinjdickow]

@webknjaz It makes sense that installing expat doesn't fix the problem. pyenv is creating a whole new installation of python that is independent and it's trying to install pyexpat there.

[natecox]

The expat issue is the same I was having pre 1.2.1, but updating did fix the issue because they patched the builder. Aside from that, I'm not sure why it wouldn't be working

[webknjaz]

I don't see anything in log noticing installation of expat: AFAIU it just builds pyexpat module during the python build process. I thought it should be linked against some external libexpat

[justinjdickow]

I guess maybe I don't understand it :P I could see that as well

[webknjaz]

It looks just like #1073, except for different dependency failing

[natecox]

I just went back and installed a new version to make sure that this was indeed still working.

•100% ➜ pyenv install 3.6.4
python-build: use openssl from homebrew
python-build: use readline from homebrew
Downloading Python-3.6.4.tar.xz...
-> https://www.python.org/ftp/python/3.6.4/Python-3.6.4.tar.xz
Installing Python-3.6.4...
python-build: use readline from homebrew
Installed Python-3.6.4 to /Users/nate/.pyenv/versions/3.6.4

My brew info for pyenv

~
•100% ➜ brew info pyenv
pyenv: stable 1.2.1 (bottled), HEAD
Python version management
https://github.com/pyenv/pyenv
/usr/local/Cellar/pyenv/1.1.5 (594 files, 2.3MB)
  Poured from bottle on 2017-11-30 at 12:43:09
/usr/local/Cellar/pyenv/HEAD-6f27c91 (584 files, 2.3MB) *
  Built from source on 2018-01-13 at 11:39:57
/usr/local/Cellar/pyenv/HEAD-85a66a9 (579 files, 2.2MB)
  Built from source on 2017-12-04 at 13:34:03
/usr/local/Cellar/pyenv/HEAD-e71ac9e (580 files, 2.3MB)
  Built from source on 2017-12-14 at 15:55:34
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/pyenv.rb
==> Dependencies
Recommended: autoconf ✔, pkg-config ✔, openssl ✔, readline ✔
==> Options
--without-autoconf
    Build without autoconf support
--without-openssl
    Build without openssl support
--without-pkg-config
    Build without pkg-config support
--without-readline
    Build without readline support
--HEAD
    Install HEAD version
==> Caveats
Bash completion has been installed to:
  /usr/local/etc/bash_completion.d

zsh functions have been installed to:
  /usr/local/share/zsh/site-functions

Pyenv version

~
•100% ➜ pyenv --version
pyenv 1.2.1

Hopefully this helps shine a light on the issue for you.

[webknjaz]

Turns out that adding

export CFLAGS="-I$(xcrun --show-sdk-path)/usr/include $CFLAGS"

breaks the build.

[webknjaz]

It lead me to wrong guesses at the beginning when I combined installation of several versions asynchronously. And then adding CFLAGS caused build error with pyexpat.
After I removed CFLAGS I realised that most of builds are successful, except for pypy2.7-5.10.0, which is failing for different reason.

Here's what works for me (except pypy2.7-5.10.0):

# No additional env vars
brew install pyenv readline xz
pyenv install {{version}}

https://circleci.com/gh/cherrypy/cheroot/323

[jklemm]

Thanks @webknjaz!

I have this error on Mac OS High Sierra v 10.13.4 when trying to install python 2.7.12

Unset the variable saves the day!

unset CFLAGS
brew install pyenv readline xz
pyenv install {{version}}

[danwiesenthal]

I'm seeing this issue again with macOS 10.14.5 and pyenv 1.2.12. I was able to install python 3.6.7, but can't install anything on the 3.7.x branch, for lack of pyexpat. Here's the output:

pyenv install 3.7.3                                                                                                                               ▸▸▸▸▸▸▸▸▸▸
python-build: use openssl from homebrew
python-build: use readline from homebrew
Downloading Python-3.7.3.tar.xz...
-> https://www.python.org/ftp/python/3.7.3/Python-3.7.3.tar.xz
Installing Python-3.7.3...
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 10.14.5 using python-build 20180424)

Inspect or clean up the working tree at /var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/python-build.20190613152307.55015
Results logged to /var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/python-build.20190613152307.55015.log

Last 10 log lines:
  File "/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/tmphic5qgk5/pip-19.0.3-py2.py3-none-any.whl/pip/_internal/cli/cmdoptions.py", line 22, in <module>
  File "/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/tmphic5qgk5/pip-19.0.3-py2.py3-none-any.whl/pip/_internal/utils/hashes.py", line 10, in <module>
  File "/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/tmphic5qgk5/pip-19.0.3-py2.py3-none-any.whl/pip/_internal/utils/misc.py", line 21, in <module>
  File "/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/tmphic5qgk5/pip-19.0.3-py2.py3-none-any.whl/pip/_vendor/pkg_resources/__init__.py", line 35, in <module>
  File "/private/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/python-build.20190613152307.55015/Python-3.7.3/Lib/plistlib.py", line 65, in <module>
    from xml.parsers.expat import ParserCreate
  File "/private/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/python-build.20190613152307.55015/Python-3.7.3/Lib/xml/parsers/expat.py", line 4, in <module>
    from pyexpat import *
ModuleNotFoundError: No module named 'pyexpat'
make: *** [install] Error 1

[iamlordaubrey]

@danwiesenthal I had this same issue just yesterday. Fixed it by downloading and reinstalling command line tools. Also downloaded and reinstalled Xcode itself (not sure this helped)
https://developer.apple.com/download/more/?=command%20line%20tools

[danwiesenthal]

Ah, alas. I tried to start fresh: I uninstalled Xcode and Command Line Tools (including deleting their directories, etc, per googling instructions on how to remove them). I uninstalled everything brew had installed. I reinstalled both Xcode and the Command Line tools. I brew installed openssl, and set the compiler flags to find openssl per brew's suggestion. I ran the command to link to the command line tool headers. I brew installed pyenv. And yet... back where I started.

pyenv install 3.7.2                                                                                                                                                     
python-build: use openssl from homebrew
python-build: use readline from homebrew
Downloading Python-3.7.2.tar.xz...
-> https://www.python.org/ftp/python/3.7.2/Python-3.7.2.tar.xz
Installing Python-3.7.2...
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 10.14.5 using python-build 20180424)

Inspect or clean up the working tree at /var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/python-build.20190614151842.24131
Results logged to /var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/python-build.20190614151842.24131.log

Last 10 log lines:
  File "/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/tmpvv82ceeh/pip-18.1-py2.py3-none-any.whl/pip/_internal/cli/cmdoptions.py", line 20, in <module>
  File "/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/tmpvv82ceeh/pip-18.1-py2.py3-none-any.whl/pip/_internal/utils/hashes.py", line 10, in <module>
  File "/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/tmpvv82ceeh/pip-18.1-py2.py3-none-any.whl/pip/_internal/utils/misc.py", line 21, in <module>
  File "/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/tmpvv82ceeh/pip-18.1-py2.py3-none-any.whl/pip/_vendor/pkg_resources/__init__.py", line 35, in <module>
  File "/private/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/python-build.20190614151842.24131/Python-3.7.2/Lib/plistlib.py", line 65, in <module>
    from xml.parsers.expat import ParserCreate
  File "/private/var/folders/z3/g070g97n7qv88q0qjcldl9h00000gn/T/python-build.20190614151842.24131/Python-3.7.2/Lib/xml/parsers/expat.py", line 4, in <module>
    from pyexpat import *
ModuleNotFoundError: No module named 'pyexpat'
make: *** [install] Error 1

[lgw4]

@danwiesenthal I fixed this by installing the Command_Line_Tools_for_Xcode_11_Beta.dmg package from the site linked to by @iamlordaubrey above. You can verify which version you have installed by running pkgutil --pkg-info=com.apple.pkg.CLTools_Executables. You should see output similar to this:

package-id: com.apple.pkg.CLTools_Executables
version: 11.0.0.0.1.1559496560
volume: /
location: /
install-time: 1560561423
groups: com.apple.FindSystemFiles.pkg-group

[neverfox]

I reinstalled the tools which are still at v10.x and can now install 3.7.3:

❯ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 10.2.1.0.1.1554506761
volume: /
location: /
install-time: 1560789554
groups: com.apple.FindSystemFiles.pkg-group

[danwiesenthal]

THRILLED to say that I've got a working system now. Thank you all for your help! :)

For whatever reason, the previous stable build of CLT (for macOS 10.14, Xcode 10.2.1) did NOT work for me (even though I'm not running anything else beta; no Catalina, no Xcode 11; running vanilla macOS 10.14.5), regardless of compiler flags, header re-linking, etc.

What DID work for me was installing the Xcode CLT 11 Beta 1. With that, and these compiler flags:

• $CFLAGS="-I/usr/local/Cellar/openssl/1.0.2s/include"
• $LDFLAGS="-L/usr/local/Cellar/openssl/1.0.2s/lib"

I was successfully able to install pyenv and install arbitrary Python versions successfully without the pyexpat error. Hooray!

For the curious, here's the output from pkgutil for the working configuration (in conjunction with aforementioned flags):

pkgutil --pkg-info=com.apple.pkg.CLTools_Executables

package-id: com.apple.pkg.CLTools_Executables
version: 11.0.0.0.1.1559496560
volume: /
location: /
install-time: 1560795402
groups: com.apple.FindSystemFiles.pkg-group

[sophiebits-humu]

It appears that the zlib fix last week (4157973301f7f064e8dd0a90c4a21e04da3f58bf; cc @mikeroll @joshfriend) exacerbates this problem. In particular, it causes pyexpat to fail to link when installing on a fresh Mojave system with the 10.14 Command Line Tools and SDK headers (/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg) installed.

Here, a log from my coworker's machine when installing Python 3.7.3 using pyenv 1.2.12:

clang -bundle -undefined dynamic_lookup -L/Users/brianh/usr/local/opt/readline/lib -L/Users/brianh/usr/local/opt/readline/lib -L/Users/brianh/.pyenv/versions/3.7.3/lib -L/Users/brianh/usr/local/opt/readline/lib -L/Users/brianh/usr/local/opt/readline/lib -L/Users/brianh/.pyenv/versions/3.7.3/lib -L/Users/brianh/usr/local/opt/readline/lib -L/Users/brianh/usr/local/opt/readline/lib -L/Users/brianh/.pyenv/versions/3.7.3/lib -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Users/brianh/usr/local/opt/readline/include -I/Users/brianh/usr/local/opt/readline/include -I/Users/brianh/.pyenv/versions/3.7.3/include build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/_ctypes.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/callbacks.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/callproc.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/stgdict.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/cfield.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/malloc_closure.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/darwin/dlfcn_simple.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/libffi_osx/ffi.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/libffi_osx/x86/darwin64.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/libffi_osx/x86/x86-darwin.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/libffi_osx/x86/x86-ffi_darwin.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/libffi_osx/x86/x86-ffi64.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/libffi_osx/powerpc/ppc-darwin.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/libffi_osx/powerpc/ppc-darwin_closure.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/libffi_osx/powerpc/ppc-ffi_darwin.o build/temp.macosx-10.14-x86_64-3.7/private/var/folders/lz/81t0dgy54kg4jmlyn21vz6bh0000gn/T/python-build.20190614142435.36559/Python-3.7.3/Modules/_ctypes/libffi_osx/powerpc/ppc64-darwin_closure.o -L/Users/brianh/usr/local/opt/readline/lib -L/Users/brianh/.pyenv/versions/3.7.3/lib -L/usr/local/lib -o build/lib.macosx-10.14-x86_64-3.7/_ctypes.cpython-37m-darwin.so
ld: warning: could not create compact unwind for _ffi_call_unix64: does not use RBP or RSP based frame
*** WARNING: renaming "pyexpat" since importing it failed: dlopen(build/lib.macosx-10.14-x86_64-3.7/pyexpat.cpython-37m-darwin.so, 2): Symbol not found: _XML_ErrorString
  Referenced from: build/lib.macosx-10.14-x86_64-3.7/pyexpat.cpython-37m-darwin.so
  Expected in: flat namespace
 in build/lib.macosx-10.14-x86_64-3.7/pyexpat.cpython-37m-darwin.so
*** WARNING: renaming "_elementtree" since importing it failed: PyCapsule_Import could not import module "pyexpat"

Most people who have run into this problem in the past recommend unsetting CFLAGS in the global environment to work around the problem. However, the aforementioned commit means that the use_xcode_sdk_zlib branch is taken on any machine where xcrun --show-sdk-path returns successfully, causing CFLAGS to be set to include -I${xc_sdk_path}/usr/include. As far as I can tell, there is no way to override this behavior using command line flags or environment variables.

We opted to downgrade to pyenv 1.2.11 and were able to successfully build on that version (using a copy of zlib from Homebrew).

I think one possible fix would be to swap the order of the checks (that is, use_homebrew_zlib || use_xcode_sdk_zlib instead of use_xcode_sdk_zlib || use_homebrew_zlib). Then you would either need to (a) install zlib using brew, as was required before or (b) upgrade to the beta Command Line Tools (as mentioned above). Whereas right now the latter appears to be the only option using pyenv 1.2.12.

[cicorias]

same boat as @sophiebits-humu -- rolling / downgrading Pyenv back to 1.2.11 fixes this for me.

[amyccaldwell]

Like @neverfox, reinstalling the command line tools (still at 10.2.1.0.1.1554506761) resolved the pyexpat errors for me.

[phazel]

@iamlordaubrey Thankyou for figuring out the solution! I guess xcode-select --install still installs the old xcode command line tools because the new one for Mojave is still in beta.

[hrdchz]

I my case installing Command Line Tools for Xcode 10.2.1, using the dmg installer which makes you agree to the license, seems to have been the solution. I never use Xcode so I at least ran it once out of superstition.

Additionally I did brew reinstall pyenv readline xv after the CLI tools install and included and exports in my startup files (.zshrc / .bash_profile): brew info openssl / brew info readline

EDIT appears to be same solution as @amyccaldwell @neverfox etc

[henriquebastos]

I had the same problem with version 3.7.3.

The solution I found on the web is:

SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14 pyenv install 3.7.3

[anilsg]

I've worked through almost all of the offered solutions comprehensively.
To potentially save others some time I summarise:

As per @cicorias and @sophiebits-humu I expect downgrading Pyenv back to 1.2.11 would fix (not tested). This may not be (easily) available through Homebrew if you don't have a previous local install.

As per @sophiebits-humu 8 days ago, upgrade to the beta Command Line Tools worked for me with pyenv 1.2.12. According to @sophiebits-humu this is the only available route with pyenv 1.2.12, and I believe her.

• I did not try Command_Line_Tools_for_Xcode_11_Beta.dmg.
• I downloaded Command_Line_Tools_for_Xcode_11_Beta_2.dmg from Apple Developer.
• I installed Beta 2 CLTools manually using the DMG and agreeing to the license.
• No Packages are provided in /Library/Developer/CommandLineTools/ for this version so there was no header package to install.
• pkgutil --pkg-info=com.apple.pkg.CLTools_Executables reports version: 11.0.0.0.1.1560537986.
• I then ran brew reinstall pyenv readline openssl.

Then pyenv install 2.7.16 and pyenv install 3.7.3 both succeeded.

As long as I had Command_Line_Tools_macOS_10.14_for_Xcode_10.2.1.dmg and pyenv 1.2.12 installed (pkgutil --pkg-info=com.apple.pkg.CLTools_Executables # version: 10.2.1.0.1.1554506761) the other options all failed.

As per @hrdchz @amyccaldwell @neverfox resolve from 6 days ago installing Command_Line_Tools_macOS_10.14_for_Xcode_10.2.1.dmg manually agreeing to license
and /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg manually agreeing to license pyenv install 3.7.3 still failed for me with ModuleNotFoundError: No module named 'pyexpat'

@hrdchz @amyccaldwell @neverfox route from 6 days ago also failed.

As per @amyccaldwell 7 days ago (apparently like @neverfox) reinstalling the same latest (not beta) command line tools still at 10.2.1.0.1.1554506761 even including the @hrdchz actlons to reinstall pyenv readline and all exports included still failed.

I didn't try @henriquebastos option using Xcode (SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14 pyenv install 3.7.3) since @markosamuli commented that for him Python 3.7.3 install still fails on Travis macOS 10.14

[j9ac9k]

FWIW the following let me install python 3.8-dev on macOS mojave:

SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14 pyenv install 3.8-dev

[tilgovi]

I was getting the pyexpat error. I fixed it by disabling SIP and manually uninstalling everything installed by macOS_SDK_headers_for_macOS_10.14.pkg. That's not fun and not easy and after telling a team of engineers to install that package for things to work before, I'm not going to try to tell them to uninstall it this way for things to work now.

Do we know why the beta command line tools works? Does it remove the old macOS_SDK_headers_for_macOS_10.14.pkg? If so, installing the beta, even if it's uninstalled and removed after, might be a great way to get around disabling SIP to uninstall the old headers.

[anilsg]

Randall, before I installed beta 2 CL Tools, I uninstalled the "old"
CLTools completely.

On Thu, 4 Jul. 2019, 03:03 Randall Leeds, [e-mail] wrote:

I was getting the pyexpat error. I fixed it by disabling SIP and manually
uninstalling everything installed by macOS_SDK_headers_for_macOS_10.14.pkg.
That's not fun and not easy and after telling a team of engineers to
install that package for things to work before, I'm not going to try to
tell them to uninstall it this way for things to work now.

Do we know why the beta command line tools works? Does it remove the old
macOS_SDK_headers_for_macOS_10.14.pkg? If so, installing the beta, even
if it's uninstalled and removed after, might be a great way to get around
disabling SIP to uninstall the old headers.

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[tilgovi]

I'm speaking specifically of the extra, optional headers package that installs common includes into /usr/include, outside the SDK directory.

[b-gale]

@j9ac9k 's solution worked for me for 3.5.7. system: pyenv 1.2.12, macOS 10.14.5, CL Tools Executables 10.2.1.0.1.1554506761. This is IMO the most elegant solution as it's one line and installs/uninstalls required.

SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14 pyenv install 3.5.7

[anilsg]

@b-gale , @j9ac9k 's solution includes the full install of Xcode, as does your quote of the solution. My statement of the requirement for Beta CLTools was based on not installing Xcode itself, as stated, because others identified it did not work in their case, and I didn't want Xcode. It seems installing Xcode works for some (e.g. you and j9), but not others (e.g. @markosamuli).

So there remains at least the posssibility of solutions by rolling back to earlier pyenv, installing full XCode, but otherwise you will need beta CLTools.

[bosconb]

same issue，when macOS is 14.3

$ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 10.1.0.0.1.1539992718
volume: /
location: /
install-time: 1550213543
groups: com.apple.FindSystemFiles.pkg-group

after upgrade my macos to 10.14.6 Beta, pyenv success to install python 3.7.3

$ pyenv install 3.7.3
python-build: use openssl from homebrew
python-build: use readline from homebrew
Downloading Python-3.7.3.tar.xz...
-> https://www.python.org/ftp/python/3.7.3/Python-3.7.3.tar.xz
Installing Python-3.7.3...
python-build: use readline from homebrew
python-build: use zlib from xcode sdk
Installed Python-3.7.3 to /Users/dazkarieh/.pyenv/versions/3.7.3

[michaelkarrer81]

pyenv install 2.7.16 worked for me after installing command line tools beta 2
But i am still stuck and can not use python because i can not pip install readline !

Error message:

    clang -fno-strict-aliasing -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_RL_CALLBACK -DHAVE_RL_CATCH_SIGNAL -DHAVE_RL_COMPLETION_APPEND_CHARACTER -DHAVE_RL_COMPLETION_DISPLAY_MATCHES_HOOK -DHAVE_RL_COMPLETION_MATCHES -DHAVE_RL_COMPLETION_SUPPRESS_APPEND -DHAVE_RL_PRE_INPUT_HOOK -I. -I/Users/michaelkarrer/.pyenv/versions/2.7.16/include/python2.7 -c Modules/2.x/readline.c -o build/temp.macosx-10.14-x86_64-2.7/Modules/2.x/readline.o -Wno-strict-prototypes
    creating build/lib.macosx-10.14-x86_64-2.7
    clang -bundle -undefined dynamic_lookup -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -L/Users/michaelkarrer/.pyenv/versions/2.7.16/lib build/temp.macosx-10.14-x86_64-2.7/Modules/2.x/readline.o readline/libreadline.a readline/libhistory.a -lncurses -o build/lib.macosx-10.14-x86_64-2.7/readline.so
    clang: error: no such file or directory: 'readline/libreadline.a'
    clang: error: no such file or directory: 'readline/libhistory.a'
    error: command 'clang' failed with exit status 1

I did a full install of XCode but it did not change anything?!?

Since -L/usr/local/opt/readline/lib is in the compiler flags and the two files are under /usr/local/opt/readline/lib i have no clue why clang can not find those files?!?

Any help or clue would be really appreciated!

[anilsg]

@michaelkarrer81 , I found I could not pip install readline either. The compilation fails and therefore the library files are not built. That's why the linker can't find them. I used brew install readline instead and created links to the libraries from that (brew link) but I haven't tested it yet ...

[michaelkarrer81]

After a lot more hours of testing if found a way that at least worked for me:

• Install complete Xcode (maybe not needed?)
• Install Command Line Tools via App (With License Dialogue Pop Up) I did use the non beta with success but maybe just because is had beta 2 installed at some point? I could not build python with pyenv before "Command Line Tools Beta 2" but after removing it and replacing it with the non beta version i still can do pyenv install 2.7.16 without a problem
• brew reinstall readline, xz, libxml2, libxmlsec1, python@2, pyenv, pyenv-virtualenv, ...
• Add Package Path for all custom brew applications in .bash_profile

# PYTHON PYENV PREREQUISITES
# ==========================
# ATTENTION: You need to set the PKG_CONFIG_PATH to make "pip install ..." use the right locations! Conmpiler Flags are not necessary.

# Xcode SDK Root (only needed if messed up) 
# export SDKROOT="/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14"

# openssl
# -------
export PATH="/usr/local/opt/openssl/bin:$PATH"
#export LDFLAGS="-L/usr/local/opt/openssl/lib $LDFLAGS"
#export CPPFLAGS="-I/usr/local/opt/openssl/include $CPPFLAGS"
export PKG_CONFIG_PATH="/usr/local/opt/openssl/lib/pkgconfig:$PKG_CONFIG_PATH"

# readline
# --------
#export LDFLAGS="-L/usr/local/opt/readline/lib $LDFLAGS"
#export CPPFLAGS="-I/usr/local/opt/readline/include $CPPFLAGS"
export PKG_CONFIG_PATH="/usr/local/opt/readline/lib/pkgconfig:$PKG_CONFIG_PATH"

# sqlite
# ------
export PATH="/usr/local/opt/sqlite/bin:$PATH"
#export LDFLAGS="-L/usr/local/opt/sqlite/lib $LDFLAGS"
#export CPPFLAGS="-I/usr/local/opt/sqlite/include $PKG_CONFIG_PATH"

# libxml2
# -------
export PATH="/usr/local/opt/libxml2/bin:$PATH"
#export LDFLAGS="-L/usr/local/opt/libxml2/lib"
#export CPPFLAGS="-I/usr/local/opt/libxml2/include"
export PKG_CONFIG_PATH="/usr/local/opt/libxml2/lib/pkgconfig:$PKG_CONFIG_PATH"

# libffi
# ------
#export LDFLAGS="-L/usr/local/opt/libffi/lib"
export PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig:$PKG_CONFIG_PATH"

# pyenv
if command -v pyenv 1>/dev/null 2>&1; then
 eval "$(pyenv init -)"
fi

# pyenv pyenv-virtualenv
if which pyenv-virtualenv-init > /dev/null; then eval "$(pyenv virtualenv-init -)"; fi

After all of this i can successfully build python and install readline in the venv via pip pip install readline

Pain in the a...

[pablopunk]

FWIW the following let me install python 3.8-dev on macOS mojave:

SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14 pyenv install 3.8-dev

I tried everything and this one was the only one that worked for me! 🎉

And I installed version 3.5.7 BTW

[anilsg]

@michaelkarrer81 , it seems more people are quoting success after installing Xcode itself. That might be the step that made the build possible for you.

[rgalanakis]

@pablopunk success with that (from a new shell window), thanks!!!

[markosamuli]

Definining MACOSX_DEPLOYMENT_TARGET and SDKROOT environment variables seems to fix my previously failing pyenv install on Travis builds. I've tested it with Xcode 10.2.1 and Xcode 11.0 images.

With Xcode 11.0 I'm setting SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk but looking at the output, MacOSX10.15.sdk seems to be just a symbolic link to MacOSX.sdk in the same directory.

Xcode 10 release notes would suggest I could also try SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk if using CLT.

[Rotonen]

The combination of the latest macOS point release (10.14.6), the latest XCode release (10.3) and the latest Command Line Tools has remedied this for me.

[subhashb]

I had the same experience as @Rotonen ☝️
Just upgrading to macOS 10.14.6 fixed the problem.

[RonaldZhao]

I had the same problem with version 3.7.3.

The solution I found on the web is:

SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14 pyenv install 3.7.3

thx. This is the only solution for me.

[NeilRoberts]

While setting up a spare MacBook from scratch (no data, so I can wipe and reinstall without much pain), I found that installing the macOS SDK headers results in the missing expat error when I try to install Python 3.x with pyenv (1.2.13, installed with homebrew). Starting over and skipping the header installation allows me to install a Python version.

My setup: fresh install of macOS 10.14.6, followed by the 10.14.6 supplemental update. Installed command line tools with xcode-select --install, install brew, pyenv, and pyenv-virtualenv. Neither SDKROOT nor CFLAGS are set. Xcode is not installed. /usr/include does not exist.

[elfotografo007]

The combination of the latest macOS point release (10.14.6), the latest XCode release (10.3) and the latest Command Line Tools has remedied this for me.

This was the clue to solve my problem. I was configuring a brand new Mac and also had the problem while installing 3.7.4. I had already installed the headers as other software required it. I had 10.14.6 and XCode 10.3. Downloading the latest Command Line Tools fixed the issue.

[tilgovi]

My previous comment aligns with what @NeilRoberts describes. Removing the headers package is not easy, but it does fix the problem. There is no longer any need to have the headers package installed for pyenv to build Python correctly.

I suspect / hope that perhaps the latest XCode uninstalls the headers, and that is why a number of folks here have reported that this fixes things. After all, Apple only published the headers package as a transitional package for software that depends on headers in the standard /usr/include location.

Can anyone who installed the SDK headers package and subsequently installed XCode 10.3 check whether or not they have a /usr/include directory?

[NeilRoberts]

I verified that I did not have a /usr/include directory, then installed the macOS SDK headers. After installation, /usr/include exists and is populated. pyenv install 3.6.9 fails with

ModuleNotFoundError: No module named 'pyexpat'

After installing Xcode 10.3 (from the App Store), launching it, and allowing it to install components, the /usr/include directory still exists and is populated and pyenv install 3.6.9 fails with the same error.

However, this worked after installing Xcode 10.3 (I did not try it after installing the headers, but before Xcode):

SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/ pyenv install 3.6.9

Misc other observations:

• xcode-select -p returns /Applications/Xcode.app/Contents/Developer
• After "reset to the default command line tools path", the previous command returns the same thing (I don't know what this was before installing Xcode).

[tilgovi]

Thanks, @NeilRoberts! Since some folks also seem to be reporting success with the XCode 11 Beta and you seem to have a spare machine to test these clean installs on, can you try installing XCode 11 Beta and see if that either fixes the problem, removes /usr/include, or both?

If we can conclude that things should Just Work going into the future, there may be nothing to do for this issue anymore.

[NeilRoberts]

~I've started the download and will update this post tonight after I get the beta installed.~

I've downloaded and installed Xcode 11.0 beta 5 (11M382q) and let it install its components. The /usr/include dir exists and is populated. pyenv install 3.5.4 again fails because it's unable to find pyexpat:

➜  ~ pyenv install 3.5.4
python-build: use [email protected] from homebrew
python-build: use readline from homebrew
Downloading Python-3.5.4.tar.xz...
-> https://www.python.org/ftp/python/3.5.4/Python-3.5.4.tar.xz
Installing Python-3.5.4...
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 10.14.6 using python-build 20180424)

Inspect or clean up the working tree at /var/folders/qn/lhhj_r5j2256_kynk30w3f1r0000gn/T/python-build.20190814204029.11806
Results logged to /var/folders/qn/lhhj_r5j2256_kynk30w3f1r0000gn/T/python-build.20190814204029.11806.log

Last 10 log lines:
    import pip
  File "/var/folders/qn/lhhj_r5j2256_kynk30w3f1r0000gn/T/tmp9l40c4tv/pip-9.0.1-py2.py3-none-any.whl/pip/__init__.py", line 26, in <module>
  File "/var/folders/qn/lhhj_r5j2256_kynk30w3f1r0000gn/T/tmp9l40c4tv/pip-9.0.1-py2.py3-none-any.whl/pip/utils/__init__.py", line 27, in <module>
  File "/var/folders/qn/lhhj_r5j2256_kynk30w3f1r0000gn/T/tmp9l40c4tv/pip-9.0.1-py2.py3-none-any.whl/pip/_vendor/pkg_resources/__init__.py", line 35, in <module>
  File "/private/var/folders/qn/lhhj_r5j2256_kynk30w3f1r0000gn/T/python-build.20190814204029.11806/Python-3.5.4/Lib/plistlib.py", line 65, in <module>
    from xml.parsers.expat import ParserCreate
  File "/private/var/folders/qn/lhhj_r5j2256_kynk30w3f1r0000gn/T/python-build.20190814204029.11806/Python-3.5.4/Lib/xml/parsers/expat.py", line 4, in <module>
    from pyexpat import *
ImportError: No module named 'pyexpat'
make: *** [install] Error 1

I've noticed a subtle change in the error, though I don't know if it's meaningful. The original error that I saw was:

ModuleNotFoundError: No module named 'pyexpat'

But the error that I've seen most recently is:

ImportError: No module named 'pyexpat'

Other things:

I tried changing the path for the active developer directory with sudo xcode-select -s /Applications/Xcode-beta.app/Contents/Developer, which yields the same error:

I thought it was odd that python-build is using lib from the Xcode SDK, so I checked my brew install and it has zlib, with this note:

For compilers to find zlib you may need to set:
  export LDFLAGS="-L/usr/local/opt/zlib/lib"
  export CPPFLAGS="-I/usr/local/opt/zlib/include"

I tried those exports and installing Python 3.5.4 (at this point I'm just picking different versions to avoid uninstalling a previous one), but I received the ImportError again. Does anyone know how to determine which version of lib is installed/active?

@tilgovi you are correct: I can burn this system to the ground to try anything new - just make a suggestion.

[khyox]

@danwiesenthal I had this same issue just yesterday. Fixed it by downloading and reinstalling command line tools. Also downloaded and reinstalled Xcode itself (not sure this helped)
https://developer.apple.com/download/more/?=command%20line%20tools

For me, in macOS Mojave 10.14.6 using MacPorts 2.5.4 (and fish shell, to make the environment more exotic), the way to overcome the ImportError was just to install the CLT for XCode 11 Beta 6.

 > pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 11.0.0.0.1.1565314599
volume: /
location: /
install-time: 1566678646
groups: com.apple.FindSystemFiles.pkg-group 

 > pyenv doctor
Cloning /Users/u/.pyenv/plugins/pyenv-doctor/bin/.....
Installing python-pyenv-doctor...
python-build: use zlib from xcode sdk
Installed python-pyenv-doctor to /tmp/pyenv-doctor.20190824133239.69236/prefix

Congratulations! You are ready to build pythons!



md5-624b540628bea467cc9e14ce773c2bb7



 > pyenv install 3.7.4
/Users/u/.pyenv/plugins/python-build/bin/python-build: line 1538: brew: command not found
/Users/u/.pyenv/plugins/python-build/bin/python-build: line 1538: brew: command not found
Downloading openssl-1.1.0j.tar.gz...
-> https://www.openssl.org/source/openssl-1.1.0j.tar.gz
Installing openssl-1.1.0j...
Installed openssl-1.1.0j to /Users/u/.pyenv/versions/3.7.4

Downloading readline-8.0.tar.gz...
-> https://ftpmirror.gnu.org/readline/readline-8.0.tar.gz
Installing readline-8.0...
Installed readline-8.0 to /Users/u/.pyenv/versions/3.7.4

Downloading Python-3.7.4.tar.xz...
-> https://www.python.org/ftp/python/3.7.4/Python-3.7.4.tar.xz
Installing Python-3.7.4...
python-build: use zlib from xcode sdk
Installed Python-3.7.4 to /Users/u/.pyenv/versions/3.7.4

[gitsteveno]

SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/ pyenv install 3.6.9

This worked for me. On 10.14.6 Mojave with Xcode 10.3. Pyenv version 1.2.13. Fresh system - all freshly installed.

[yebo29]

I had the same problem with version 3.7.3.

The solution I found on the web is:

SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14 pyenv install 3.7.3

This too worked for me. Mojave version 10.14.6, after a fresh install of Xcode. I thought I had it installed previously. Did not have to reinstall Command Line Tools which was already installed by homebrew. Did not have to install a beta version of Xcode; version 10.3 installed. Pyenv 1.2.13 installed via homebrew.

[alexhermida]

FYI.

• macOS Mojave 10.14.6 fresh system
• No xcode but already installed command line tools

• pyenv 1.2.13 installed with homebrew

  It works for me just downloading and installing https://download.developer.apple.com/Developer_Tools/Command_Line_Tools_macOS_10.14_for_Xcode_10.3/Command_Line_Tools_macOS_10.14_for_Xcode_10.3.dmg

[minhoryang]

Why don't we just change the order between use_homebrew_zlib and use_xcode_sdk_zlib.

https://github.com/pyenv/pyenv/blob/4157973301f7f064e8dd0a90c4a21e04da3f58bf/plugins/python-build/bin/python-build#L763-L764
to

use_homebrew_zlib || use_xcode_sdk_zlib || true 

And change Common Build Problem wiki page to install all the requirements by homebrew.

brew install readline xz openssl zlib

[scottschreckengaust]

Fresh Mojave 10.14.6 installation:
Downloading command line tools 11 GM seed fixed this pyexpat issue:

pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 11.0.0.0.1.1567737322
volume: /
location: /
install-time: 1568296328
groups: com.apple.FindSystemFiles.pkg-group 

FYI: tried lots of proposed solutions...

[Proletariat99]

I have a totally borked 10.14.6 Mojave install with the same error here. Fixed it by running the following from the top of this blog post

sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /

and running this to add the .sdk +path to my .zshrc environment variable.

echo "export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk" >> ~/.zshrc

Then I was able to pyenv install 3.7.4

[palmerc]

Python includes its own copy of expat.h and expat_external.h. The issue is a conflict with the headers on the system for these two files, which ultimately renames a bunch of symbols in the python included pyexpatns.h.

I created a diff that renames the two files and everything works again. This happens on 2.7 and 3.x python builds when running Mojave with the Command-Line Tools and system headers installed (no longer the default by-the-way). After installing the Command-Line Tools you must go into /Library/Developer/CommandLineTools and install an additional .pkg to get the headers.

The diff I made for 3.7.4 is available as a gist

So without spending too much more time on this, the issue seems to be how pyenv handles include paths, because running configure && make with the same tarball just works. It only fails when using pyenv.

[trinitronx]

Confirming on fresh macOS Mojave 10.14.6 install that the following fixes the issue:

sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target / 
SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/ pyenv install  3.7.4


python-build: use [email protected] from homebrew
python-build: use readline from homebrew
Downloading Python-3.7.4.tar.xz...
-> https://www.python.org/ftp/python/3.7.4/Python-3.7.4.tar.xz
Installing Python-3.7.4...
python-build: use readline from homebrew
python-build: use zlib from xcode sdk
Installed Python-3.7.4 to ~/.pyenv/versions/3.7.4

CLT + Headers package versions:

$ pkgutil  --pkg-info com.apple.pkg.macOS_SDK_headers_for_macOS_10.14
package-id: com.apple.pkg.macOS_SDK_headers_for_macOS_10.14
version: 10.3.0.1.1.1562985497
volume: /
location: /
install-time: 1568682016
groups: com.apple.FindSystemFiles.pkg-group

$ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 10.3.0.0.1.1562985497
volume: /
location: /
install-time: 1568681976
groups: com.apple.FindSystemFiles.pkg-group

Homebrew package versions:

brew info pyenv readline xz
pyenv: stable 1.2.13 (bottled), HEAD
Python version management
https://github.com/pyenv/pyenv
/usr/local/Cellar/pyenv/1.2.13_1 (650 files, 2.4MB) *
  Poured from bottle on 2019-09-30 at 11:43:36
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/pyenv.rb
==> Dependencies
Required: autoconf ✔, [email protected] ✔, pkg-config ✔, readline ✔
==> Options
--HEAD
    Install HEAD version
==> Analytics
install: 47,365 (30 days), 129,532 (90 days), 481,291 (365 days)
install_on_request: 42,965 (30 days), 118,058 (90 days), 429,115 (365 days)
build_error: 0 (30 days)

readline: stable 8.0.1 (bottled) [keg-only]
Library for command-line editing
https://tiswww.case.edu/php/chet/readline/rltop.html
/usr/local/Cellar/readline/8.0.1 (48 files, 1.5MB)
  Poured from bottle on 2019-09-17 at 02:24:22
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/readline.rb
==> Caveats
readline is keg-only, which means it was not symlinked into /usr/local,
because macOS provides the BSD libedit library, which shadows libreadline.
In order to prevent conflicts when programs look for libreadline we are
defaulting this GNU Readline installation to keg-only.

For compilers to find readline you may need to set:
  export LDFLAGS="-L/usr/local/opt/readline/lib"
  export CPPFLAGS="-I/usr/local/opt/readline/include"

For pkg-config to find readline you may need to set:
  export PKG_CONFIG_PATH="/usr/local/opt/readline/lib/pkgconfig"

==> Analytics
install: 571,428 (30 days), 1,285,454 (90 days), 4,899,656 (365 days)
install_on_request: 65,137 (30 days), 126,111 (90 days), 493,577 (365 days)
build_error: 0 (30 days)

xz: stable 5.2.4 (bottled)
General-purpose data compression with high compression ratio
https://tukaani.org/xz/
/usr/local/Cellar/xz/5.2.4 (92 files, 1MB) *
  Poured from bottle on 2019-09-16 at 09:52:51
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/xz.rb
==> Analytics
install: 213,115 (30 days), 652,959 (90 days), 2,671,873 (365 days)
install_on_request: 4,261 (30 days), 14,542 (90 days), 70,085 (365 days)
build_error: 0 (30 days)

[MikeBosw]

FWIW the following let me install python 3.8-dev on macOS mojave:

SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14 pyenv install 3.8-dev

I tried everything and this one was the only one that worked for me! 🎉

And I installed version 3.5.7 BTW

This worked for me with 3.5.2. I also did unset CFLAGS, but that by itself hadn't done the trick.

I did not reinstall Xcode or upgrade to the latest version of OS X.

[tilgovi]

I recently installed XCode 11. I now have a 10.15 SDK in the XCode bundle and the macOS_SDK_headers_for_macOS_10.14.pkg seems to be superseded with a stub file, maybe marking that it's obsolete.

I did not have macOS_SDK_headers_for_macOS_10.14.pkg installed before I upgraded XCode. I wonder if, for those who have installed it, if upgrading replaces its contents (erasing everything from /usr/include) and replaces it with the same stub / bookkeeping files.

> ls /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform
/DeveloperEntitlements.plist Library            SDKSettings.json   SDKSettings.plist  System             usr

> pkgutil --files com.apple.pkg.macOS_SDK_headers_for_macOS_10.14
private
private/tmp
private/tmp/.BBE72B41371180178E084EEAF106AED4F350939DB95D3516864A1CC62E7AE82F

[trinitronx]

I recently installed XCode 11. I now have a 10.15 SDK in the XCode bundle and the macOS_SDK_headers_for_macOS_10.14.pkg seems to be superseded with a stub file, maybe marking that it's obsolete.

Oh no! This would totally break compiling a lot of things, using tools such as rvm, Homebrew, pyenv, etc... For reference, the proper macOS_SDK_headers_for_macOS_10.14 package contains all these files.

Let's hope Apple gets their act together maintaining these header files, and hopefully providing an easily scriptable way to install them. It's an enormous pain to try and provision a macOS system without these! It's especially difficult to automate given that the XCode .dmg / .xip file is behind a web login, they have an interactive license accept process, and now even going through all this doesn't even get us what we need: Command Line Tools + Header files!

🤦‍♂

[tilgovi]

Oh no! This would totally break compiling a lot of things, using tools such as rvm, Homebrew, pyenv, etc... For reference, the proper macOS_SDK_headers_for_macOS_10.14 package contains all these files.

I'm afraid this is by design. Apple _is_ getting their act together by providing a way to support multiple SDKs installed in parallel. They released the macOS_SDK_headers_for_macOS_10.14 as a transitional package while the community gets _its_ act together. This issue is the pyenv community doing that. Python builds without issue through pyenv since it was updated to look for the SDK in its new location, rather than assuming it's installed at /usr/include.

[strokirk]

We've encountered this error as well. We've debugged it by running pyenv install -kv 2.7.13, and after pyexpat fails to compile going to ~/.pyenv/sources/2.7.13/Python-2.7.13 to manually recompile the failing pyexpat module to get better error output.

It seems that the issue is that issue is that clang inserts /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include before ~/.pyenv/sources/2.7.13/Python-2.7.13/./Modules/expat, which causes the compilation to fail.

On my older machine, recompilation works fine, and it seems that clang automatically inserts a -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk statement there. If we manually append isysroot on the failing computer, the compilation succeeds.

Anyone know how and why the -isysroot option is added automatically on certain machines?

I'm including the verbose logs below from our failing and working machines.

Logs from newer, failing OSX machine

clang -fno-strict-aliasing -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_EXPAT_CONFIG_H=1 -DXML_POOR_ENTROPY=1 -DUSE_PYEXPAT_CAPI -I.  -I./Include -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13 -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13/./Modules/expat -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Include -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/sqlite/include -I/usr/local/opt/zlib/include -IInclude -c $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.c -o build/temp.macosx-10.14-x86_64-2.7$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.o -v
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
 "/Library/Developer/CommandLineTools/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.14.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -disable-free -disable-llvm-verifier -discard-value-names -main-file-name pyexpat.c -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -relaxed-aliasing -fno-strict-return -masm-verbose -munwind-tables -target-cpu penryn -dwarf-column-info -debug-info-kind=standalone -dwarf-version=4 -debugger-tuning=lldb -target-linker-version 450.3 -v -coverage-notes-file $HOME/code/$HOME/build/temp.macosx-10.14-x86_64-2.7$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.gcno -resource-dir /Library/Developer/CommandLineTools/usr/lib/clang/10.0.1 -I /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -D NDEBUG -D HAVE_EXPAT_CONFIG_H=1 -D XML_POOR_ENTROPY=1 -D USE_PYEXPAT_CAPI -I . -I ./Include -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13 -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13/./Modules/expat -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Include -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include -I /usr/local/include -I /usr/local/opt/openssl/include -I /usr/local/opt/readline/include -I /usr/local/opt/sqlite/include -I /usr/local/opt/zlib/include -I Include -O3 -Wall -Wstrict-prototypes -Wno-atomic-implicit-seq-cst -Wno-framework-include-private-from-public -Wno-atimport-in-framework-header -Wno-quoted-include-in-framework-header -fdebug-compilation-dir $HOME/code/$HOME -ferror-limit 19 -fmessage-length 211 -fwrapv -stack-protector 1 -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fobjc-runtime=macosx-10.14.0 -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -vectorize-loops -vectorize-slp -o build/temp.macosx-10.14-x86_64-2.7$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.o -x c $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.c
clang -cc1 version 10.0.1 (clang-1001.0.46.4) default target x86_64-apple-darwin18.7.0
ignoring nonexistent directory "$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include"
ignoring nonexistent directory "$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include"
ignoring nonexistent directory "/usr/local/opt/openssl/include"
ignoring nonexistent directory "/usr/local/opt/zlib/include"
ignoring duplicate directory "./Include"
ignoring duplicate directory "/usr/local/include"
  as it is a non-system directory that duplicates a system directory
#include "..." search starts here:
#include <...> search starts here:
 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
 .
 ./Include
 $HOME/.pyenv/sources/2.7.13/Python-2.7.13
 $HOME/.pyenv/sources/2.7.13/Python-2.7.13/./Modules/expat
 $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Include
 /usr/local/opt/readline/include
 /usr/local/opt/sqlite/include
 /usr/local/include
 /Library/Developer/CommandLineTools/usr/lib/clang/10.0.1/include
 /Library/Developer/CommandLineTools/usr/include
 /usr/include
 /System/Library/Frameworks (framework directory)
 /Library/Frameworks (framework directory)
End of search list.
In file included from $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.c:1:
In file included from $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Include/Python.h:33:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:64:

Logs from working, older OSX machine

clang -fno-strict-aliasing -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_EXPAT_CONFIG_H=1 -DXML_POOR_ENTROPY=1 -DUSE_PYEXPAT_CAPI -I.  -I./Include -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13 -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13/./Modules/expat -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Include -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include -I$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -I/usr/local/opt/sqlite/include -I/usr/local/opt/zlib/include -IInclude -c $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.c -o build/temp.macosx-10.14-x86_64-2.7$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.o -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -v
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
 "/Library/Developer/CommandLineTools/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.14.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -disable-free -disable-llvm-verifier -discard-value-names -main-file-name pyexpat.c -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -relaxed-aliasing -fno-strict-return -masm-verbose -munwind-tables -target-sdk-version=10.14 -target-cpu penryn -dwarf-column-info -debug-info-kind=standalone -dwarf-version=4 -debugger-tuning=lldb -target-linker-version 450.3 -v -coverage-notes-file $HOME/code/kundo/build/temp.macosx-10.14-x86_64-2.7$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.gcno -resource-dir /Library/Developer/CommandLineTools/usr/lib/clang/10.0.1 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -D NDEBUG -D HAVE_EXPAT_CONFIG_H=1 -D XML_POOR_ENTROPY=1 -D USE_PYEXPAT_CAPI -I . -I ./Include -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13 -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13/./Modules/expat -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Include -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include -I $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include -I /usr/local/include -I /usr/local/opt/openssl/include -I /usr/local/opt/readline/include -I /usr/local/opt/sqlite/include -I /usr/local/opt/zlib/include -I Include -O3 -Wall -Wstrict-prototypes -Wno-atomic-implicit-seq-cst -Wno-framework-include-private-from-public -Wno-atimport-in-framework-header -Wno-quoted-include-in-framework-header -fdebug-compilation-dir $HOME/code/kundo -ferror-limit 19 -fmessage-length 211 -fwrapv -stack-protector 1 -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fobjc-runtime=macosx-10.14.0 -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -vectorize-loops -vectorize-slp -o build/temp.macosx-10.14-x86_64-2.7$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.o -x c $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Modules/pyexpat.c
clang -cc1 version 10.0.1 (clang-1001.0.46.4) default target x86_64-apple-darwin18.7.0
ignoring nonexistent directory "$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include"
ignoring nonexistent directory "$HOME/.pyenv/sources/2.7.13/Python-2.7.13/Mac/Include"
ignoring nonexistent directory "/usr/local/opt/openssl/include"
ignoring nonexistent directory "/usr/local/opt/zlib/include"
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/local/include"
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/Library/Frameworks"
ignoring duplicate directory "./Include"
ignoring duplicate directory "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
  as it is a non-system directory that duplicates a system directory
#include "..." search starts here:
#include <...> search starts here:
 .
 ./Include
 $HOME/.pyenv/sources/2.7.13/Python-2.7.13
 $HOME/.pyenv/sources/2.7.13/Python-2.7.13/./Modules/expat
 $HOME/.pyenv/sources/2.7.13/Python-2.7.13/Include
 /usr/local/include
 /usr/local/opt/readline/include
 /usr/local/opt/sqlite/include
 /Library/Developer/CommandLineTools/usr/lib/clang/10.0.1/include
 /Library/Developer/CommandLineTools/usr/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks (framework directory)
End of search list.

[byoung562]

Reinstalling the CLI tools resolved this issue for me.

# This location may be different defendant on how the CLI tools were installed.
$ sudo rm -rf /Library/Developer/CommandLineTools

$ xcode-select --install

$ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 10.3.0.0.1.1562985497
volume: /
location: /
install-time: 1570155487
groups: com.apple.FindSystemFiles.pkg-group

[takashyx]

Reinstalling the CLI tools resolved this issue for me.

This worked for me. Thank you for the info.

[defiantgoat]

@byoung562 That worked for me as well.

[tilgovi]

I think this can probably be closed. Enough people have posted with workarounds for various OS versions and Xcode versions and it seems to be resolved with the latest.

[exequiel09]

Reinstalling the CLI tools resolved this issue for me.

Worked for me as well.

[david-ninox]

I reinstalled the tools which are still at v10.x and can now install 3.7.3:

❯ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 10.2.1.0.1.1554506761
volume: /
location: /
install-time: 1560789554
groups: com.apple.FindSystemFiles.pkg-group

I was having trouble installing 3.6.0 with pyenv and followed these steps to resolve the issue. I have developer tools 10.3.0.0.1.1562985497 on OSX 10.14.6. I just removed it and reinstalled it, then my pyenv installations worked fine.

[oasis44]

Recently ran into this issue. Upgrading my OS to Catalina (10.15.4) and then installing the latest command line tools fixed it for me

[bryanmobrien]

Failing to install python versions on 10.15.4 (Catalina).
I uninstalled and reinstalled Xcode CLT using @byoung562 excellent instructions above.

ProductName:    Mac OS X
ProductVersion: 10.15.4
BuildVersion:   19E287
HOMEBREW_VERSION: 2.2.15-31-g29abc81
yenv 1.2.18-12-g098227f2
Xcode 11.4.1

From the log file generated,

*** WARNING: renaming "pyexpat" since importing it failed: dlopen(build/lib.macosx-10.15-x86_64-3.8/pyexpat.cpython-38-darwin.so, 2): Symbol not found: _XML_ErrorString
  Referenced from: build/lib.macosx-10.15-x86_64-3.8/pyexpat.cpython-38-darwin.so
  Expected in: flat namespace
 in build/lib.macosx-10.15-x86_64-3.8/pyexpat.cpython-38-darwin.so
*** WARNING: renaming "_elementtree" since importing it failed: PyCapsule_Import could not import module "pyexpat"

Python build finished successfully!
The necessary bits to build these optional modules were not found:
ossaudiodev           spwd                                     
To find the necessary bits, look in setup.py in detect_modules() for the module's name.


The following modules found by detect_modules() in setup.py, have been
built by the Makefile instead, as configured by the Setup files:
_abc                  atexit                pwd                
time                                                           


Failed to build these modules:
_tkinter              readline                                 


Following modules built successfully but were removed because they could not be imported:
_elementtree          pyexpat  

... and the last 10 lines of the log file:

Last 10 log lines:
  File "/var/folders/8f/qkn0rcp16tn_9298l7np3_qc0000gn/T/tmpxwts05da/pip-19.2.3-py2.py3-none-any.whl/pip/_internal/cli/cmdoptions.py", line 24, in <module>
  File "/var/folders/8f/qkn0rcp16tn_9298l7np3_qc0000gn/T/tmpxwts05da/pip-19.2.3-py2.py3-none-any.whl/pip/_internal/models/search_scope.py", line 11, in <module>
  File "/var/folders/8f/qkn0rcp16tn_9298l7np3_qc0000gn/T/tmpxwts05da/pip-19.2.3-py2.py3-none-any.whl/pip/_internal/utils/misc.py", line 21, in <module>
  File "/var/folders/8f/qkn0rcp16tn_9298l7np3_qc0000gn/T/tmpxwts05da/pip-19.2.3-py2.py3-none-any.whl/pip/_vendor/pkg_resources/__init__.py", line 35, in <module>
  File "/private/var/folders/8f/qkn0rcp16tn_9298l7np3_qc0000gn/T/python-build.20200507224208.5472/Python-3.7.7/Lib/plistlib.py", line 65, in <module>
    from xml.parsers.expat import ParserCreate
  File "/private/var/folders/8f/qkn0rcp16tn_9298l7np3_qc0000gn/T/python-build.20200507224208.5472/Python-3.7.7/Lib/xml/parsers/expat.py", line 4, in <module>
    from pyexpat import *
ModuleNotFoundError: No module named 'pyexpat'
make: *** [install] Error 1

So, I've uninstalled and reinstalled Xcode CLT, but still cannot run
pyenv install 3.8.2
or
pyenv install 3.7.7
or any other version I try...

Found the answer for my setup here.

Using the SDK for MacOSX10.14 and a DEPLOYMENT_TARGET or 10.14, I was successfully able to install (via pyenv) both python 2.7.18 and python 3.8.2

SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk MACOSX_DEPOLOYMENT_TARGET=10.14 pyenv install 2.7.18

SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk MACOSX_DEPOLOYMENT_TARGET=10.14 pyenv install 3.8.2

It appears to be an issue with the SDK version of CommandLineTools. I ran the pyenv install command again, specifically pointing to the 10.15 versions of the SDK and set a DEPLOYMENT_TARGET of 10.15.

SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk MACOSX_DEPOLOYMENT_TARGET=10.15 pyenv install 3.8.1

Then, scratching my head - and stepping away for a bit - I realized I had mistyped MACOSX_DEPOLOYMENT_TARGET (not DEPLOYMENT). My poor spelling skills might be paying off. setting MACOSX_DEPLOYMENT_TARGET (or DEPOLOYMENT) is irrelevant, but setting SDKROOT is critical. pyenv install was working when specifying an SDKROOT environment variable and failing with not specifying an SDKROOT variable.

I unset SDKROOT and tried again, this time with pyenv install 3.8.0. The install failed with the dreaded:

```from pyexpat import *
ModuleNotFoundError: No module named 'pyexpat'
make: * [install] Error 1

BUILD FAILED (OS X 10.15.4 using python-build 1.2.18-12-g098227f2)
```
So, I searched for SDKROOT in the error log during a build failure. No occurrences found. Definitely confused, but pyenv is working.

pyenv install works when I set SDKROOT, and fails when I do not.
I was able to get pyenv to work when I set SDKROOT to any of the following:

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk

Sorry for the long-winded post, but hoping this can be added to the FAQ - specifically for Mac users. Thank you, for pyenv!

tl;dr - I got pyenv install working on macOS Catalina and Xcode 11.4.1 command line utilities by setting SDKROOT.

[lgzajac]

Mojave 10.14.6 + Xcode 11.3.1 + reinstalled CLT 10.3.0.0.1.1562985497 (earlier) + unset CFLAGS didn't worked, setting SDKROOT did
SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk MACOSX_DEPLOYMENT_TARGET=10.14 pyenv install 3.8.2

Thanks guys!