How to install twisted 10.2.0 with pypy 1.4.1? - python

I can't install twisted 10.2.0 to my ubuntu box. After download twisted source I issue the command: pypy setup.py install. After that I receive the error:
building 'twisted.runner.portmap' extension
creating build/temp.linux-x86_64-2.5
creating build/temp.linux-x86_64-2.5/twisted
creating build/temp.linux-x86_64-2.5/twisted/runner
cc -I/builds/pypy-1.4.1-linux64/include -c twisted/runner/portmap.c -o build/temp.linux-x86_64-2.5/twisted/runner/portmap.o
cc -shared build/temp.linux-x86_64-2.5/twisted/runner/portmap.o -o build/lib.linux-x86_64-2.5/twisted/runner/portmap.pypy-14.so
/usr/bin/ld.bfd.real: build/temp.linux-x86_64-2.5/twisted/runner/portmap.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
build/temp.linux-x86_64-2.5/twisted/runner/portmap.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
error: command 'cc' failed with exit status 1
So, how can I fix it? Thanks.

That's a "bug" in twisted build. It might be or might not be a bug - twisted does not consider it's C extensions optional, although they're far from necessary for the most part. Twisted would still work if you just point PYTHONPATH to where it is situated, but without those C extensions.

You may be able to skip building extensions by commenting off the following line in setup.py (73):
conditionalExtensions = getExtensions(),
This should avoid collecting and trying to build extensions scattered in the directory tree.

As for now Twisted trunk could be compiled OK with PyPy (I used 1.6.1-dev0).
However in order to install Twisted you'd need to apply a patch to zipfile.py that I have submitted to stdlib.
zipfile.py 2.7.1+ leaks file descriptors because of CPython-oriented programming style used in zipfile.py
Therefore installation fails under PyPy that uses other GC model than CPython does.

Related

How to install C++ dependencies "from source" for a Python package on Mac OS?

There is a Github repo containing Python "bindings" for a C++ library that I am interested in playing with. The README has abundant information about how to install the C++ library on Linux like machines, but no information about how to do so with a mac OS.
I have also opened up an issue requesting the README installation instructions include mac OS-specific installs in addition to linux. There hasn't been any activity on that issue.
Here are the two repos:
(Python) https://github.com/asiffer/python3-libspot
(C++) https://github.com/asiffer/libspot
Since the C++ package isn't available for installing via Brew/pip/anaconda, I'm not sure how to get going.
What I've Tried:
I have tried ./configure, and make. There is no ./configure file.
To address the lack of ./configure, read about a tool called autoconf which supposedly generates ./configure for you. I installed it with brew, but am not sure what arguments to pass it. These docs were pretty hard to understand: https://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Making-configure-Scripts.html
Just using make results in the error clang: error: unsupported option '-fopenmp'That sent me down a whole different rabbit hole which had me adding lines to the Makefile:
CPP = /usr/local/opt/llvm/bin/clang
CPPFLAGS = -I/usr/local/opt/llvm/include -fopenmp
LDFLAGS = -L/usr/local/opt/llvm/lib
omp_hello: omp_hello.c
$(CPP) $(CPPFLAGS) $^ -o $# $(LDFLAGS)
That felt dangerous because I have no idea what any of that stuff means. Plus it resulted in a new error: *** missing separator. Stop.
So then I read that's probably due to using "soft" tabs instead of "hard" tabs which can be identified using cat -e -t -v makefile_name. I found the one line where a "hard" tab was missing (the indented line above) and inserted it. This resulted in a new error:
make: *** No rule to make target `omp_hello.c', needed by `omp_hello'. Stop.
Next, following the advice of Yang Yushi and his follow on comments, I changed lines 39 and 40 according to his answer, plus added the locations of some additional files to the CXXFLAGS variable:
-I//opt/homebrew/Cellar/libomp/11.0.1/include
-L/opt/homebrew/Cellar/libomp/11.0.1/lib
And this got me a little further. Next, OSX didn't like where this script was trying to install, as explained by this answer. So I changed these two lines in the makefile which seemed to dictate install location:
INSTALL_HEAD_DIR = $(DESTDIR)/usr/include/libspot
INSTALL_LIB_DIR = $(DESTDIR)/usr/lib
to
INSTALL_HEAD_DIR = $(DESTDIR)/usr/local/include/libspot
INSTALL_LIB_DIR = $(DESTDIR)/usr/local/lib
And that indeed got me a little farther. Next I ran into an error complaining about the flat -t at these lines in the makefile:
#install -t $(INSTALL_LIB_DIR) $(LIB_DIR)/*.so
#install -t $(INSTALL_HEAD_DIR) $(INC_DIR)/*.h
So I deleted those flags, which then resulted in this error:
Checking the headers installation directory (/usr/local/include/libspot)
Checking the library installation directory (/usr/local/lib)
Installing the shared library (libspot.so)
install: /usr/local/lib: Inappropriate file type or format
For which I can find no reading material and have no clue how to fix. Any further assistance appreciated.
Here's a list of SO and other resources I've perused trying to answer this question:
Enable OpenMP support in clang in Mac OS X (sierra & Mojave)
makefile error: make: *** No rule to make target `omp.h' ; with OpenMP
makefile:4: *** missing separator. Stop
http://www.idryman.org/blog/2016/03/10/autoconf-tutorial-1/
https://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Making-configure-Scripts.html
https://developer.gnome.org/anjuta-build-tutorial/stable/create-autotools.html.en
My Question
How do I proceed.
If you know how to do this, could you also include a brief explanation of the concepts behind each step? I'd be happy to learn a little instead of just copying and pasting commands in the right order.
Compile the C++ source code with Apple Clang
I downloaded the prjoect (libspot) and successfully compiled it on my Mac. I change two lines (39 and 40) in the Makefile to make it work. (Following this answer)
CC = clang++ # change from g++ to default Apple clang
CXXFLAGS = -std=c++11 -Wall -pedantic -Xpreprocessor -fopenmp -lomp # additional flags
You should get the binary file by just type make with a "correct" Makefile.
(If you see something like "cant find omp.h", add -I/usr/local/opt/libomp/include to the CXXFLAGS.)
For the Question
The error message in the updated question description
make: *** No rule to make target omp_hello.c', needed by omp_hello'. Stop.
is telling us that the file omp_hello.c is missing. The Makefile is written to compile the source code omp_hello.c to an executable binary file omp_hello. If I have the C source file (omp_hello.c), the Makefile will allow me to compile by just typing
make
instead of
/usr/local/opt/llvm/bin/clang \
-I/usr/local/opt/llvm/include -fopenmp \
-L/usr/local/opt/llvm/lib \
omp_hello.c -o omp_hello
This is just a normal compile process, it has nothing to do with Python. The error message is saying the source code to be compiled (omp_hello.c) is missing.
It looks like this is a small project with custom Makefile. Normally you compile the code with just make. The error you got seems to suggest the lack of llvm. You may want to try install llvm following this answer.
Usually it comes to running brew install <your C++ package> or downloading the source code to some directory and running a set of commands:
./configure
make
make install
While usually it works, some packages can not be installed on Mac since their maintainers did not prepare configuration for Mac.

Which version of `gcc` supports the `--no-undefined` switch?

I am trying to compile pynifti package from source (long story involving Anaconda Python distribution).
After running make, I receive the following error:
gcc: error: unrecognized command line option ‘--Wl,--no-undefined’
Indeed, the manual (man gcc) contains no information about --no-undefined switch. My version of gcc is 4.8.5. Also, I can not find the no-undefined option in https://gcc.gnu.org/onlinedocs/gcc/Option-Index.html#Option-Index
However, from Force GCC to notify about undefined references in shared libraries I infer that it is a valid switch at least for some version of gcc.
This switch is a linker option for ld. It is not directly part of GCC but it is only encapsulated in a -Wl option to be passed to the linker (you seem to have --Wl which is wrong).
Edit:
Yugr deserves part of the credit as he pointed out the incorrect --Wl option!

compiling Cython with MinGW - undefined reference PyExc

I'm trying to compile a simple code snippet from the book "Cython - A guide for Python programmers", and when i compile, i get the following error:
H:\Cython>python setup.py build_ext -i --compiler=mingw32
running build_ext
building 'fib' extension
C:\MinGW\bin\gcc.exe -mdll -O -Wall -IC:\Anaconda3\include -IC:\Anaconda3\include -c fib.c -o build\temp.win32-3.4\Release\fib.o
writing build\temp.win32-3.4\Release\fib.def
C:\MinGW\bin\gcc.exe -shared -s build\temp.win32-3.4\Release\fib.o build\temp.win32-3.4\Release\fib.def -LC:\Anaconda3\libs -LC:\Ana
conda3\PCbuild -lpython34 -lmsvcr100 -o H:\Cython\fib.pyd
build\temp.win32-3.4\Release\fib.o:fib.c:(.text+0xb6): undefined reference to `_imp__PyExc_TypeError'
build\temp.win32-3.4\Release\fib.o:fib.c:(.text+0xf3): undefined reference to `_imp__PyExc_TypeError'
build\temp.win32-3.4\Release\fib.o:fib.c:(.text+0x3cc): undefined reference to `_imp___PyThreadState_Current'
build\temp.win32-3.4\Release\fib.o:fib.c:(.text+0x857): undefined reference to `_imp__PyExc_NameError'
build\temp.win32-3.4\Release\fib.o:fib.c:(.text+0xa55): undefined reference to `_imp__PyExc_ImportError'
c:/mingw/bin/../lib/gcc/mingw32/4.8.1/../../../../mingw32/bin/ld.exe: build\temp.win32-3.4\Release\fib.o: bad reloc address 0x0 in s
ection `.data'
collect2.exe: error: ld returned 1 exit status
error: command 'C:\\MinGW\\bin\\gcc.exe' failed with exit status 1
H:\Cython>
setup.py:
from distutils.core import setup
from Cython.Build import cythonize
setup(ext_modules=cythonize('fib.pyx'))
fib.pyx:
def fib(int n):
cdef int i
cdef double a=0.0, b=1.0
for i in range(n):
a, b = a + b, a
return a
When I google this problem, others who have had the error had a mix between 32 and 64 bit stuff, I'm not doing that.
I sat down and looked the errors over again today, and found the issue.
The problem is that I used Anaconda rather than compiling everything from scratch myself - that means that some Cython components were compiled with MSVC. As above you can see that I'm trying to use MinGW to compile the Cython test script. Why mixing compilers like that doesn't work is outside my scope of knowledge, but it doesn't. Compiling my Cython test scripts with MSVC works.
(use Visual Studio C++ 2008/2010 for python 2.x/3.x respectively)
As for the reason that I attempted to use MinGW (against standard recommendation) was that my msiserver service had somehow broken (I'm on an old laptop, so i don't recall the reason), and was hoping to find a quick way out, rather than fixing the msiserver service.
The fix for the msiserver service is pretty unrelated to this question, but it was rather hard to find, so i figured I'd link and mirror it here:
http://www.vistax64.com/vista-installation-setup/96680-repair-windows-installer-service-vista-all-versions.html
For all those unfortunate souls searching and Googling for how to
repair the Windows Installer Service, I have some info for you. A
couple days ago I tried to uninstall one of my apps and stalled on an
error "Windows Installer Service cannot be accessed". After many
trials and errors trying to fix this issue, I stumbled upon a new fix
for this issue that has worked in all these situations where the
Windows Installer Service will not manually start and in essense, not
allow install or uninstall tasks to complete.
Here's the easy steps:
1. Go to a Windows Vista (Any Version) computer that has the Windows
Installer service running correctly and run regedit(Start-Run-Regedit)
2. Go to the location
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\msiserver
3. Right click on this key and select "Export" and save the key to a Flash
Drive or other.
4. Run sfc /scannow on the damaged Vista computer - you won't need the
install disk as it goes to backup files on your HD. Do not reboot when
complete
5. Double click saved .reg file from working machine and import registry
settings into damaged Vista computer.
6. Now reboot and try to install/uninstall
If many of you have success with this method, please post this fix
around the WWW as I went through over 1000 links with users having the
same problem and not being able to solve it. Shame on Microsoft, very
sloppy. It would have been so nice if Microsoft released Windows
Installer 4.0 as a standalone installation with Vista's release so I
could have repaired it, most users have been doing fresh installs to
fix this. Get your act together Microsoft!!!!
The CAT
Thank you, the cat.

Linking against libgfortran and libstdc++ at the same time, in a python extension (.so)

I am having trouble building my own python extension. Building this code worked before (on Debian 7 Wheezy), but is now failing (on Ubuntu 15.04 Vivid).
The modules in question appear to link correctly, but I get an error on import. I have tried two linker lines, one with g++ (which gives me a missing symbol error for a fortran runtime function), and the other with gfortran (which gives me a missing symbol error for a runtime vtable.)
The module uses:
some polymorphic C++ code written by me,
a FORTRAN (90) routine from stripack, linked to C via a header file written by me using yolinux's guide,
a Cython file to expose some python entry points to the routines.
Thus, it needs to be linked with both the C++ standard libraries and the FORTRAN runtime, and be built into a monolithic shared object file.
I use a python build manager that I wrote myself to solve this problem: the currently published version generates the following linker line:
gfortran -fno-strict-aliasing -fPIC -pthread -shared \
-Wl,-O1 -Wl,-Bsymbolic-functions -lc -lstdc++ cpp1.o cpp2.o f90.o pyx.o -o \
module.so
(with some files omitted and paths shortened.)
This yields the following import error:
ImportError: module.so: undefined symbol: _ZTVN10__cxxabiv117__class_type_infoE
Which is apparently a reference to "vtable for __cxxabiv1::__class_type_info". This means, I think, that the -lstdc++ entry in the linker line is not doing its job correctly.
Similarly, I have tried to modify my build system to generate a g++ line linking against libgfortran like so:
c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -lgfortran cpp1.o cpp2.o \
f90.o pyx.o -o module.so
Again, this gives me a missing symbol error:
ImportError: module.so: undefined symbol: _gfortran_st_write_done
I have also experimented with static linking, which gives an error at link time itself (like "unable to move symbol"), and initially I thought that the runtimes may be split over separate files and tried -lfoo for many foo. However, I've checked the libgfortran.so file on the linker path with scanelf, and it does contain the relevant symbol.
This method of linking used to work (on Debian Wheezy, also tested on Mac OS X 10.7 a long time ago.) I am struggling to understand how it can have broken on the latest ubuntu (with a newer GCC, 4.9).
Any ideas, theories and tests to help debug/solve this would be much appreciated.
Thank you to #Marc Glisse for your comment: the order of the arguments is indeed wrong.
If the original gfortran line is modified so that the -lc and -lstdc++ terms are last, the ImportError goes away. Thank you!

python c++ extension: symbol not defined error

I have a working c++ code that I want to wrap into a python module on Windows XP and Python 2.7. I have never done this before, so I looked into swig and distutils.
I created an interface file and a setup.py and compiled using
python setup.py build_ext -c mingw32
The script creates a module_wrap.cpp from my module.i and module.cpp file, and then creates a module_wrap.o and a module.o. The creation of module.o creates a bunch of Warnings for unused variables and deprecated char*, but it seems to work. Because the C++-code is not mine, I don't really want to get into these right now.
The last step is executing
g++.exe -shared -s build\temp.win32-2.7\Release\module_wrap.o build\temp.win32-2.7\Release\module.o build\temp.win32-2.7\Release\_module.def -LC:\Programme\Python27\libs -LC:\Programme\Python27\PCbuild -lpython27 -o build\lib.win32-2.7\_module.pyd
I get
Cannot export init_module: symbol not defined
error: command 'g++' failed with exit status 1
I googled a lot to this now, and I just can not find a solution to this problem. The previously created _module.def seems to try to export this init since it contains
LIBRARY _module.pyd
EXPORTS
init_module
Obviously this doesn't work, but I have no idea why. Can anyone help me out here?
I figured it out. The problem was the (not posted) interface file module.i for swig. There I named the module %module usemodule, whereas in the setup.py i named the module name=module. This way swig created an init_function, that did not match the name the created module was expecting it. In the end: just a typo...
Thanks for your support nevertheless!

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