Installing 0.13.0 failed while building 'pandas.msgpack' extension.

[bicycle1885]

Hi all,

I've tried to install pandas 0.13.0 through pip install pandas, but failed to install it.
The last few lines of the error says:

fatal error: too many errors emitted, stopping now [-ferror-limit=]

1 warning and 20 errors generated.

error: command 'clang' failed with exit status 1

, and more detailed massages from clang suggests that the issue occurred while building the msgpack extension:

building 'pandas.msgpack' extension

clang -fno-strict-aliasing -fno-common -dynamic -I/usr/local/include -I/usr/local/opt/sqlite/include -I/usr/local/opt/tcl-tk/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D__LITTLE_ENDIAN__=1 -Ipandas/src/klib -Ipandas/src -I/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -I/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pandas/msgpack.cpp -o build/temp.macosx-10.7-x86_64-2.7/pandas/msgpack.o

In file included from pandas/msgpack.cpp:316:

In file included from /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:

In file included from /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:

In file included from /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:

/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "          "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

#warning "Using deprecated NumPy API, disable it by " \

 ^

pandas/msgpack.cpp:835:3: error: unknown type name 'template_context'

  template_context ctx;

  ^

pandas/msgpack.cpp:854:70: error: C++ requires a type specifier for all declarations

  PyObject *(*_unpack)(struct __pyx_obj_6pandas_7msgpack_Unpacker *, execute_fn, PyObject *, struct __pyx_opt_args_6pandas_7msgpack_8Unpacker__unpack *__pyx_optional_args);

                                                                     ^~~~~~~~~~

pandas/msgpack.cpp:1355:66: error: unknown type name 'template_context'

static CYTHON_INLINE PyObject *__pyx_f_6pandas_7msgpack_init_ctx(template_context *, PyObject *, PyObject *, PyObject *, int, char *, char *); /*proto*/

                                                                 ^

pandas/msgpack.cpp:1854:20: error: no member named 'buf' in 'msgpack_packer'

  __pyx_v_self->pk.buf = ((char *)malloc(__pyx_v_buf_size));

  ~~~~~~~~~~~~~~~~ ^

pandas/msgpack.cpp:1863:34: error: no member named 'buf' in 'msgpack_packer'

  __pyx_t_1 = ((__pyx_v_self->pk.buf == NULL) != 0);

                ~~~~~~~~~~~~~~~~ ^

pandas/msgpack.cpp:1889:20: error: no member named 'buf_size' in 'msgpack_packer'

  __pyx_v_self->pk.buf_size = __pyx_v_buf_size;

  ~~~~~~~~~~~~~~~~ ^

pandas/msgpack.cpp:1898:20: error: no member named 'length' in 'msgpack_packer'

  __pyx_v_self->pk.length = 0;

  ~~~~~~~~~~~~~~~~ ^

(continue)

Note that this is a part of the whole error message.

The pip.log file is also available from https://dl.dropboxusercontent.com/u/25281592/pip-pandas.log

My environment is:

• Mac OS X Mavericks 10.9.1
• Python 2.7.6 (installed through homebrew)
• pip 1.4.1
• clang
  • Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
  • Target: x86_64-apple-darwin13.0.0
  • Thread model: posix

The previous version (pandas 0.12.0) can be successfully installed in this environment.
Does anyone have any suggestions, or am I doing something wrong?

[jreback]

cc @TomAugspurger

iirc u build in Mac

can u comment

[jreback]

#5396, #5997 relevant?

[TomAugspurger]

Yeah, I'm trying now in a fresh env. @bicycle1885 did you install numpy though pip? What version?

[TomAugspurger]

I was able to build successfully on a fresh virtualenv.

[ghost]

@TomAugspurger , what's your clang version?

[TomAugspurger]

Same as @bicycle1885 I believe.

(tst) ~/E/t/l/p/s/pandas clang -v
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin13.0.0
Thread model: posix
(tst) ~/E/t/l/p/s/pandas 

And my versions:

(tst) ~/E/t/l/p/s/pandas python util/print_versions.py

INSTALLED VERSIONS
------------------
Python: 2.7.6.final.0
OS: Darwin
Release: 13.0.0
Processor: i386
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8

cannot import name StringIO
pandas: Not installed
Cython: Not installed
Numpy: 1.8.0
Scipy: Not installed
statsmodels: Not installed
    patsy: Not installed
scikits.timeseries: Not installed
dateutil: 2.2
pytz: Not installed
bottleneck: Not installed
PyTables: Not Installed
    numexpr: Not Installed
matplotlib: Not installed
openpyxl: Not installed
xlrd: Not installed
xlwt: Not installed
xlsxwriter: Not installed
sqlalchemy: Not installed
lxml: Not installed
bs4: Not installed
html5lib: Not installed
bigquery: Not installed
apiclient: Not installed

Looks like there may be something wrong with the printout. I installed nose and all the tests pass.

Before I started using virtualenvs I had trouble with python picking up the version of numpy that Apple ships. That doesn't seem to be the case here though.

[ghost]

Will leave open for now, but bumping to 0.14 since you can't repro. Thanks @TomAugspurger

[bicycle1885]

@TomAugspurger Yes, I installed numpy through pip, and its version is 1.8.0. I installed numpy before failing to install pandas.

Surprisingly, I've successfully installed pandas 0.13 in a fresh virtualenv environment.
So, this may be caused by some unique state in my machine.

[ghost]

Sold.