Problems with pip install numpy - RuntimeError: Broken toolchain: cannot link a simple C program

Question

I'm trying to install numpy (and scipy and matplotlib) into a virturalenv.

I keep getting these errors though:

RuntimeError: Broken toolchain: cannot link a simple C program

----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1

I have the command line tools for xcode installed

$ which gcc
/usr/bin/gcc
$ which cc
/usr/bin/cc

I'm on Mac OSX 10.9 Using a brew installed python

Edit
Yes, trying to install with pip.
The whole traceback is huge (>400 lines)

Here is a section of it:

C compiler: cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe



compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c'

cc: _configtest.c

clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]

clang: note: this will be a hard error (cannot be downgraded to a warning) in the future

clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]

clang: note: this will be a hard error (cannot be downgraded to a warning) in the future

failure.

removing: _configtest.c _configtest.o

Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/Users/bdhammel/Documents/research_programming/julia_env/build/numpy/setup.py", line 192, in <module>

    setup_package()

  File "/Users/bdhammel/Documents/research_programming/julia_env/build/numpy/setup.py", line 185, in setup_package

    configuration=configuration )

  File "/Users/bdhammel/Documents/research_programming/julia_env/build/numpy/numpy/distutils/core.py", line 169, in setup

    return old_setup(**new_attr)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 152, in setup

    dist.run_commands()

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands

    self.run_command(cmd)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "/Users/bdhammel/Documents/research_programming/julia_env/build/numpy/numpy/distutils/command/egg_info.py", line 10, in run

    self.run_command("build_src")

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command

    self.distribution.run_command(command)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "/Users/bdhammel/Documents/research_programming/julia_env/build/numpy/numpy/distutils/command/build_src.py", line 153, in run

    self.build_sources()

  File "/Users/bdhammel/Documents/research_programming/julia_env/build/numpy/numpy/distutils/command/build_src.py", line 164, in build_sources

    self.build_library_sources(*libname_info)

  File "/Users/bdhammel/Documents/research_programming/julia_env/build/numpy/numpy/distutils/command/build_src.py", line 299, in build_library_sources

    sources = self.generate_sources(sources, (lib_name, build_info))

  File "/Users/bdhammel/Documents/research_programming/julia_env/build/numpy/numpy/distutils/command/build_src.py", line 386, in generate_sources

    source = func(extension, build_dir)

  File "numpy/core/setup.py", line 674, in get_mathlib_info

    raise RuntimeError("Broken toolchain: cannot link a simple C program")

RuntimeError: Broken toolchain: cannot link a simple C program

please show several of the lines above the `RuntimeError` line, so we can see which commands are failing. Also, are you installing via `pip` or by building the source directly? — MattDMo, Mar 13 '14 at 19:20

score 132 · Answer 1 · edited Jun 14 '19 at 10:35

132

For Docker (Alpine) and Python 3.x this worked for me:

RUN apk update
RUN apk add make automake gcc g++ subversion python3-dev

edited Jun 14 '19 at 10:35

Mousam Singh

578
2
7
24

answered Jan 19 '18 at 20:36

Willem Bressers

1,791
1
9
3

29

For anyone using docker python3 alpine image, this is the solution. – xssChauhan Dec 11 '18 at 09:11
5

I needed an `apk update` first, otherwise I got a `ERROR: unsatisfiable constraints` message. – yair Jan 21 '19 at 20:49
Thank you so much! – Amorphous Feb 12 '19 at 19:25
This is also the solution for the docker python2 alpine image. – Eduard May 14 '19 at 15:49
9

I was able to do this on alpine with only `gcc g++ make python3-dev` for numpy/nmslib. The cause of this particular issue seems to be the missing c++ compiler `g++` (it looks by the error that `gcc` and `make` are already installed). The other important parts of `numpy` build is the python3 headers which come with `python3-dev`. – ThisGuyCantEven Oct 02 '19 at 16:06
Not sure, if `subversion` is necessary. The official Python docker base on `buildpack-deps` where subversion is not listed. – phi Feb 18 '21 at 11:10
Thank you! This works for python3 + Alpine – May 20 '21 at 17:04

score 81 · Accepted Answer · edited May 23 '17 at 12:02

81

While it's ugly, it appears to work

sudo ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future pip install --upgrade numpy

Note that if you are getting this error for a package other than numpy, (such as lxml) specify that package name instead of numpy at the end of the commnd.

I saw a similar issue someone was having with installing a gem

Ruby Gem install Json fails on Mavericks and Xcode 5.1 - unknown argument: '-multiply_definedsuppress'

This is only a temporary fix, at some point the compiler options will have to be fixed

edited May 23 '17 at 12:02

Community

1
1

answered Mar 14 '14 at 17:14

Derrick Shoemake

936
7
6

1

@Ben: FWIW, I have the same issue (not using brew). It appeared after updating Xcode to 5.1. However ugly, this does appear to be the answer (for now). – orome Mar 24 '14 at 17:16
2

There is an explanation in the [XCode 5.1 release notes](https://developer.apple.com/library/ios/releasenotes/developertools/rn-xcode/xc5_release_notes/xc5_release_notes.html#//apple_ref/doc/uid/TP40001051-CH2-SW12). – badzil Apr 10 '14 at 17:33
Is `unused-command-line-argument-hard-error-in-future` still needed with the latest Xcode under Yosemite? Things seem to work (at least for the packages I've tired) without it. – orome Oct 23 '14 at 15:07
1

Anyone have a windows solution? – Zack Plauché Oct 18 '20 at 05:47

score 17 · Answer 3 · answered Nov 05 '14 at 18:37

17

The problem is that you are unable to compile.

First, make sure that you have accepted the new Terms and Conditions with Xcode. To do this, just open up xCode and accept.

Then, try installing gcc with

brew install gcc

Finally, try to install Numpy with

pip install numpy

Hope this helps.

answered Nov 05 '14 at 18:37

Desmond

181
1
4

this worked for me. Problem was I didn't open up xcode and accept terms and conditions. – Stephens Apr 02 '16 at 04:41
For those running **Big Sur Beta**: (1) download and install [Command Line Tools for Xcode 12.2 beta 3](https://developer.apple.com/download/more/) (2) on terminal type `sudo xcode-select --switch /Library/Developer/CommandLineTools` (3) `brew install gcc` (4) `pip install numpy` – Felipe Oct 18 '20 at 17:51

score 9 · Answer 4 · answered Mar 31 '14 at 17:07

9

If you don't want to use sudo (so permissions and things like that are preserved when using venv), you can add the ARCHFLAGS declaration to your .bash_profile, and run as normal. This worked for me with Mavericks and Xcode 5.1 using with venv:

In ~/.bash_profile:

export ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future

Then, just run the command:

pip install --upgrade numpy

answered Mar 31 '14 at 17:07

Brian

91
1

4

the `sudo` above is for system-wide installation, can run without in a virtualenv – Eren Güven Apr 06 '14 at 17:55

score 6 · Answer 5 · answered Nov 02 '16 at 18:46

If you are running a linux distribution, you may need a C compiler, especially if you see telltale log lines like sh: gcc: command not found. You can follow the instructions here, which I've summarized below:

Fedora, Red Hat, CentOS, or Scientific Linux

# yum groupinstall 'Development Tools'
Debian or Ubuntu Linux

$ sudo apt-get update $ sudo apt-get install build-essential manpages-dev

Then you can try rerunning:

sudo pip install numpy

score 5 · Answer 6 · answered Dec 29 '14 at 15:29

5

I simply had to open XCode and accept the agreement and let it install the tools. I then went back to PyCharm and installed numpy again with no issues.

answered Dec 29 '14 at 15:29

user3589327

51
1
1

score 5 · Answer 7 · answered Dec 16 '16 at 14:11

5

On Fedora 22 this was resolved by updating pip itself: sudo pip install --upgrade pip

answered Dec 16 '16 at 14:11

zenperttu

754
1
7
13

The same solution worked for a problem with MacOS on Big Sur – Jack L. Sep 24 '21 at 23:29

score 4 · Answer 8 · answered May 10 '16 at 17:46

For fedora users that are having a similar problem try installing these packeges:

(if not using python3 use python-devel and pip instead of pip3)

sudo dnf install python3-devel
sudo dnf install make automake gcc gcc-c++ gcc-gfortran
sudo dnf install redhat-rpm-config
sudo dnf install subversion

then try

sudo pip3 install numpy

score 4 · Answer 9 · answered Oct 12 '20 at 13:14

4

In my case this happened during a docker build. The problem was that the base image wasn't fixed to a specific python version and numpy couldn't compile with the new one.

FROM python:3-slim  # BAD

After I changed it to the following it worked:

FROM python:3.8-slim  # GOOD

Remember to fix your versions! :-)

answered Oct 12 '20 at 13:14

MoRe

1,438
11
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Same thing cropped up for me today. Looks like they removed the c compiler + associated make utilities in 3.9.0. – PF1 Oct 19 '20 at 19:42

score 3 · Answer 10 · answered Sep 21 '15 at 23:01

In some cases after OS X upgrades XCode, XCode will require the user (with administrative privileges) to accept a new license. Until the license is accepted, clang and gcc will issue an error when attempting to compile and link code. Or at least python packages.

If you launch XCode and accept the license, the errors no longer appear.

At least, this was the case for me.

score 1 · Answer 11 · answered Dec 25 '15 at 08:49

1

This means it can't find your C compiler. Try installing the gcc compiler if linking other compiler fails.

answered Dec 25 '15 at 08:49

Inc33

1,564
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score 0 · Answer 12 · answered Aug 22 '14 at 20:36

0

The above worked for me only after installing python3-dev.

answered Aug 22 '14 at 20:36

Iliyan Bobev

2,900
2
19
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score 0 · Answer 13 · answered Apr 20 '21 at 08:28

0

I solved this by using Conda instead of pip in my Dockerfile: FROM continuumio/miniconda3:latest

answered Apr 20 '21 at 08:28

mnalavadi

1

score 0 · Answer 14 · answered May 12 '21 at 14:19

0

Old thread, by my problem was that I didn't have Xcode installed. The following solved it.

xcode-select --install

answered May 12 '21 at 14:19

mbryanne

1

Problems with pip install numpy - RuntimeError: Broken toolchain: cannot link a simple C program

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