I am currently using a mac version 11.6.1 with Big Sur on it. I have the latest version of python (3.9) on it, however I need to use 3.6 for a project at work. I attempted to use pyenv to install this version but ran into a number of issues with pyenv. So, I next went to https://www.python.org/downloads/release/python-3615/ and downloaded this version. In my terminal I ran the following commands.
$ cd Downloads
$ cd python-3.6.15
$ ./configure
$ make
Here I ran into this error.
./Modules/getpath.c:528:49: warning: incompatible pointer types passing 'unsigned long *' to parameter of type 'uint32_t *' (aka 'unsigned int *') [-Wincompatible-pointer-types]
else if(0 == _NSGetExecutablePath(execpath, &nsexeclength) && execpath[0] == SEP) {
^~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/mach-o/dyld.h:98:54: note: passing argument to parameter 'bufsize' here
extern int _NSGetExecutablePath(char* buf, uint32_t* bufsize) __OSX_AVAILABLE_STARTING(__MAC_10_2, __IPHONE_2_0);
^
1 warning generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Wstrict-prototypes -I. -I./Include -DPy_BUILD_CORE -c ./Modules/posixmodule.c -o Modules/posixmodule.o
./Modules/posixmodule.c:8210:15: error: implicit declaration of function 'sendfile' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
ret = sendfile(in, out, offset, &sbytes, &sf, flags);
^
./Modules/posixmodule.c:10432:5: warning: code will never be executed [-Wunreachable-code]
Py_FatalError("abort() called from Python code didn't abort!");
^~~~~~~~~~~~~
1 warning and 1 error generated.
make: *** [Modules/posixmodule.o] Error 1
I am banging my head against the wall here with the errors from pyenv and now this. My attempt here was to run a virtual environment with virtualenv and point it at the 3.6 version of python, however, as you can see I can't seem to install python correctly. Any assistance here would be appreciated.
Since I was asked about the error with pyenv I'll include that here too.
BUILD FAILED (OS X 11.6.1 using python-build 2.2.0-5-g54889eb8)
Inspect or clean up the working tree at /var/folders/77/93y4tp5x557ff0h_3f76bh5c0000gn/T/python-build.20211104075648.30324
Results logged to /var/folders/77/93y4tp5x557ff0h_3f76bh5c0000gn/T/python-build.20211104075648.30324.log
Last 10 log lines:
checking for --with-cxx-main=<compiler>... no
checking for clang++... no
configure:
By default, distutils will build C++ extension modules with "clang++".
If this is not intended, then set CXX on the configure command line.
checking for the platform triplet based on compiler characteristics... darwin
configure: error: internal configure error for the platform triplet, please file a bug report
make: *** No targets specified and no makefile found. Stop.
with penv try this:
# get latest pyenv version
brew unlink pyenv
brew install pyenv --HEAD
CFLAGS=-Wno-implicit-function-declaration pyenv install 3.6.15
Related
I built Python 3.6 from source and am trying to install lxml. Trying to install it from pip gives the following error:
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -Isrc -Isrc/lxml/includes -I/usr/local/include/python3.6m -c src/lxml/etree.c -o build/temp.linux-armv6l-3.6/src/lxml/etree.o -w
src/lxml/etree.c:91:20: fatal error: Python.h: No such file or directory
compilation terminated.
Compile failed: command 'gcc' failed with exit status 1
cc -I/usr/include/libxml2 -I/usr/include/libxml2 -c /tmp/xmlXPathInitln68cjsn.c -o tmp/xmlXPathInitln68cjsn.o
cc tmp/xmlXPathInitln68cjsn.o -L/usr/lib -lxml2 -o a.out
error: command 'gcc' failed with exit status 1
The same error is raised if I try to install Cython to compile lxml from source. I installed libxml2-dev and libxslt1-dev, but python3.6-dev, which is apparently also required, is not found in Raspbian repository. I added the following line to /etc/apt/sources.list:
deb http://ftp.de.debian.org/debian sid main
But when trying to install it afterwards, I receive the following error:
The following packages have unmet dependencies:
libdbus-1-3 : Breaks: dbus (< 1.9.16-1~) but 1.6.8-1+deb7u1 is to be installed
E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.
In fact, this error is raised on any package that is found in Debian repository that is not in Raspbian one. What can I do about this?
Since you installed Python from source, you should have the header files already. Should also use header files for the version that you built as opposed to the version in the package manager.
Either
Add the source code directory to includes used by GCC (gcc -I<dir>) or
Install the from source package in a system directory that is automatically included like /usr/include or /usr/local/include
The second option is probably easiest and should be possible from the standard configure/make scripts.
I am trying to install PyCrypto on OS X 10.11.3 (El Capitan). I am using Python 3.5.1. I downloaded the gzip file from https://pypi.python.org/pypi/pycrypto and decompressed it. Then I ran python setup.py build like the instructions said and it appeared to do something, then it produced this output:
/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -fwrapv -Wall -Wstrict-prototypes -std=c99 -O3 -fomit-frame-pointer -Isrc/ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/MD2.c -o build/temp.macosx-10.6-intel-2.7/src/MD2.o
src/MD2.c:30:10: fatal error: 'string.h' file not found
#include <string.h>
^
1 error generated.
error: command '/usr/bin/clang' failed with exit status 1
I tried python3 setup.py build and got some very similar output:
/usr/bin/clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -fno-common -dynamic -fwrapv -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -std=c99 -O3 -fomit-frame-pointer -Isrc/ -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/MD2.c -o build/temp.macosx-10.6-intel-3.5/src/MD2.o
src/MD2.c:30:10: fatal error: 'string.h' file not found
#include <string.h>
^
1 error generated.
error: command '/usr/bin/clang' failed with exit status 1
I tried Googling to figure out what to do, but I couldn't find anything useful. How can I install PyCrypto?
EDIT: I also tried several other things like pip install pycrypto and sudo pip3 install pycrypto and they didn't work. #l'L'l helped me get it to work by doing several strange, complex things that I never would have though have myself. They are summarized in the answer below.
Overview:
The manual build you're trying looks like it might be failing because it's referencing the OS X 10.6 SDK, which you likely don't have, and is outdated for the most part. Also, SDKs are now stored in a completely different location than when the 10.6 SDK was in it's prime.
New SDKs location:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/
Old SDKs location:
/Developer/SDKs/
Non-existent / outdated SDK:
Since it appears that when trying to build PyCrypto it's referencing the MacOSX10.6.sdk there are several things to consider:
Why does it reference an outdated SDK
Where is the SDK it's referencing set
What should be done to correct the issue
Unless we audit the source code carefully we might not know exactly where the incorrect flags are set, but we can do our best to work with the information we have. From the error we can see that there are several instances where the 10.6 SDK's name pops up:
/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -fwrapv -Wall -Wstrict-prototypes -std=c99 -O3 -fomit-frame-pointer -Isrc/ -I/Library
Building from source:
/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/MD2.c -o build/temp.macosx-10.6-intel-2.7/src/MD2.o
src/MD2.c:30:10: fatal error: 'string.h' file not found
#include <string.h>
^
1 error generated.
error: command '/usr/bin/clang' failed with exit status 1
Analyzing this we can see that the PyCrypto's MD2.c file is trying to be built using the flag -isysroot /Developer/SDKs/MacOSX10.6.sdk. It might be worth trying pip instead:
Installing with pip:
...
fatal error: 'string.h' file not found #include <string.h>
...
Same error; we should probably find out if the <string.h> header even exists on the system — Let's make a quick test C application to find out:
Testing the C headers:
$ echo "#include <string.h>
#include <stdio.h>
int main() { printf(\"TEST\n\"); return 0; }" > t.c
$ clang t.c -o t
$ ./t
TEST
It's apparent the header does exist because the test worked fine. This tells us that the problem is more likely related directly to the 10.6 SDK (which doesn't seem to exist on the system).
Symlinking (non-existing) 10.6 SDK to 10.11 SDK:
Since we haven't determined where the SDK is actually getting set we'll go ahead and try to create symlinks so that any reference of the old 10.6 SDK links to the latest SDK (10.11 at this time):
$ cd /Developer/SDKs
$ sudo ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk MacOSX10.6.sdk
We can verify the symlink by issuing the following command:
$ ls -lat
total 8
drwxr-xr-x 3 root wheel 102 Feb 21 15:54 .
lrwxr-xr-x 1 root wheel 99 Feb 21 15:54 MacOSX10.6.sdk -> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
drwxr-xr-x 3 root wheel 102 Feb 21 15:52 ..
Now that we've successfully created the symlink let's try installing PyCrypto with pip once more:
$ sudo pip install pycrypto
Collecting pycrypto
Downloading pycrypto-2.6.1.tar.gz (446kB)
100% |████████████████████████████████| 446kB 1.2GB/s
Installing collected packages: pycrypto
Running setup.py install for pycrypto ... done
Successfully installed pycrypto-2.6.1
No errors! It looks like our problem is solved! Well, almost...
We still need to figure out what is responsible for setting the wrong (10.6) SDK during builds. Let's use the xcrun tool to see what the defaults are set at:
$ xcrun --show-sdk-version
10.11
The system default SDK is set to 10.11, so it must be get set incorrectly to 10.6 by Python, PyCrypto, or some other anomaly we might not have considered.
UPDATE:
After doing some recon it was discovered that Python 3 appears to be built with the OS X 10.6 SDK. In addition it's also setting the SDK to 10.6 and setting the (outdated) path in numerous places throughout the Python_Framework. There are so many references I won't bother listing them all, although here's an example:
Python_Framework Folder/Versions/3.5/lib/python3.5/config-3.5m/Makefile:79:CONFIGURE_CFLAGS= -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk
I can only assume the developers were trying to be as backward compatible as possible, however, it's unfortunately breaking forward compatibility in the process.
Notes:
Installing Python packages with pip can make life much easier in a lot of ways (package management, updating, uninstalling, etc.). For example installing PyCrypto should just be a matter of issuing the command:
$ sudo pip install pycrypto
If you have multiple Python's you can use the version number to install for that Python accordingly:
$ sudo pip3.5 install pycrypto
↳ https://pip.pypa.io/en/stable/installing/
I had what might be a related issue on OSX El Capitan when I would run pip install pycrypto. I was seeing RuntimeError: autoconf error. All I had to do was run sudo xcodebuild -license and type agree after reviewing the licence agreement. Afterward I was able to use pip to install pycrypto.
When I execute the install script, I get the following:
creating build/temp.macosx-10.6-intel-3.3/extensions/data
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -arch x86_64 -Ilibastro-3.7.5 -I/Library/Frameworks/Python.framework/Versions/3.3/include/python3.3m -c extensions/_libastro.c -o build/temp.macosx-10.6-intel-3.3/extensions/_libastro.o
In file included from extensions/_libastro.c:3:
/Library/Frameworks/Python.framework/Versions/3.3/include/python3.3m/Python.h:25:10: fatal error:
'stdio.h' file not found
#include <stdio.h>
^
1 error generated.
error: command '/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang' failed with exit status 1
Any clues? Thanks
Rather than try to debug your reported error, it is probably easier to just to use:
sudo pip install pyephem
If you don't have pip installed, you should get it using easy_install, but you could also just install it with the other command recommended in the INSTALL instructions:
sudo easy_install ephem
That .h file is a fundamental C standard library file, so its absence indicates that your problem may be that you are missing the full install of your system's C compiler. Try installing the Xcode command line tools that I think you can find here:
https://developer.apple.com/xcode/
A similar Stack Overflow questioner found that they were also necessary to build Python itself from source:
fatal error 'stdio.h' Python 2.7.3 on Mac OS X 10.7.5
Update: the following command might also help, so here it is just in case:
http://www.bitemyapp.com/post/os-x-fsevent-fatal-error-stdio-h-file-not-found/
I've tried using pip install matplotlib and git clone then python setup.py install as described in the installation faq for Mac OS 10.7. But I get the same error:
[...]
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -I. -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/freetype2 -I./freetype2 -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/ft2font.cpp -o build/temp.macosx-10.7-intel-2.7/src/ft2font.o
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
In file included from src/ft2font.cpp:3:
src/ft2font.h:16:22: error: ft2build.h: No such file or directory
src/ft2font.h:17:10: error: #include expects "FILENAME" or <FILENAME>
src/ft2font.h:18:10: error: #include expects "FILENAME" or <FILENAME>
src/ft2font.h:19:10: error: #include expects "FILENAME" or <FILENAME>
src/ft2font.h:20:10: error: #include expects "FILENAME" or <FILENAME>
src/ft2font.h:21:10: error: #include expects "FILENAME" or <FILENAME>
In file included from src/ft2font.cpp:3:
src/ft2font.h:34: error: ‘FT_Bitmap’ has not been declared
src/ft2font.h:34: error: ‘FT_Int’ has not been declared
src/ft2font.h:34: error: ‘FT_Int’ has not been declared
src/ft2font.h:86: error: expected ‘,’ or ‘...’ before ‘&’ token
[...]
It seems like I'm missing some package installed in my system? Or there any other better way to install matplotlib?
Thanks!
UPDATE: by googling and search on SO I've found that I might lack the package freetype2, however, if I try to install it by homebrew I get a warning message:
[me # my mac]$ brew search freetype
Apple distributes freetype with OS X, you can find it in /usr/X11/lib.
However not all build scripts look here, so you may need to call ENV.x11
in your formula's install function.
I had this issue on Ubuntu server 12.04.
I had to install libfreetype6-dev and libpng-dev from the repositories. I was using a virtualenv and installing matplotlib using pip when I ran into this issue.
Hints that I needed to do this came from the warning messages that popup early in the matplotlib installation so keep an eye out for those messages which indicate a dependency is found, but not the headers.
Same error, the install worked on one of my Lion machines but not the other. Tracked it down to a missing pkg-config
$ brew install pkg-config
$ pip install -U 'http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.1.0/matplotlib-1.1.0.tar.gz/download'
(see also https://jholewinski.org/blog/installing-matplotlib-on-os-x-10-7-with-homebrew/ )
Thanks for the link above. I was able to get matplotlib working with some minor changes. I am documenting the specific error message I ran into, for future reference.
Env:
Mac OS X 10.7.4 (Lion) running stock python 2.7.1 (found in /usr/bin)
I started out trying to get matplotlib working against the default install. setup.py hinted at some problems specifically:
freetype2: found, but unknown version (no pkg-config)
* WARNING: Could not find 'freetype2' headers in any
* of '.', './freetype2'.
and
OPTIONAL BACKEND DEPENDENCIES
libpng: found, but unknown version (no pkg-config)
* Could not find 'libpng' headers in any of '.'
the setup step would fail with the following error message:
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__multiarray_api.h:1187: warning: ‘int _import_array()’ defined but not used
lipo: can't open input file: /var/tmp//ccG28dDI.out (No such file or directory)
Googling for this file did not help with anything. I dug around a bit and decided it was not worth my time to go down the virtualenv route.
I ended up following the steps outlined in the jholewinski link above. Installed a new python 2.7.4 in /usr/local/ and followed the instructions there. (I re-installed pkg-config).
I was able to pull the latest version of matplotlib from git and it worked just fine.
Both the libpng (1.5.4) and freetype2 (13.2.7) libraries were present this time.
I'm not a windows user typically, but I need to build exe's from my python code so I'd like to use py2exe to do this. I have an XP system where I installed python 2.6.6. I downloaded the py2exe-0.6.9 source, but when I attempted to install (via "python setup.py install"), I got the error "Unable to find vcvarsall.bat". I googled and came across this post where a respondent suggested installing a customized version of the MinGW GCC binaries available here. I did so, and now when I attempt to install py2exe I get a new error. Here is the output:
C:\Documents and Settings\Administrator\Desktop\py2exe-0.6.9>python setup.py install
C:\Documents and Settings\Administrator\Desktop\py2exe-0.6.9\py2exe\build_exe.py:16: DeprecationWarning: the sets module is deprecated
import sets
running install
running build
running build_py
running build_ext
building '_memimporter' extension
creating build\temp.win32-2.6
creating build\temp.win32-2.6\Release
creating build\temp.win32-2.6\Release\source
c:\mingw\bin\gcc.exe -mno-cygwin -mdll -O -Wall -DPYTHONDLL=\"PYTHON26.DLL\" -DPYTHONCOM=\"pythoncom26.dll\" -IC:\Python26\include -IC:\Python26\PC -c source/MemoryModule.c -o build\temp.win32-2.6\Release\source\memorymodule.o
source/MemoryModule.c:30: warning: ignoring #pragma warning
source/MemoryModule.c: In function 'BuildImportTable':
source/MemoryModule.c:364: warning: pointer targets in passing argument 1 of 'MyLoadLibrary' differ in signedness
source/MemoryModule.c: In function 'GetNameTable':
source/MemoryModule.c:610: warning: passing argument 4 of 'qsort' from incompatible pointer type
source/MemoryModule.c: In function 'MemoryGetProcAddress':
source/MemoryModule.c:637: warning: passing argument 5 of 'bsearch' from incompatible pointer type
c:\mingw\bin\gcc.exe -mno-cygwin -mdll -O -Wall -DPYTHONDLL=\"PYTHON26.DLL\" -DPYTHONCOM=\"pythoncom26.dll\" -IC:\Python26\include -IC:\Python26\PC -c source/_memimporter_module.c -o build\temp.win32-2.6\Release\source\_memimporter_module.o
In file included from source/_memimporter.c:8,
from source/_memimporter_module.c:2:
source/Python-version.h:13: error: redefinition of typedef 'Py_ssize_t'
C:\Python26\include/pyport.h:115: error: previous declaration of 'Py_ssize_t' was here
error: command 'gcc' failed with exit status 1
http://bugs.python.org/issue1485576 might be a bug you may want to re-open, providing your testcase to support it.