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PierrickRauby opened this issue Jun 1, 2018 · 8 comments
Closed

Pandas installation on arm - Beaglebone Black #21289

PierrickRauby opened this issue Jun 1, 2018 · 8 comments
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Build Library building on various platforms
Milestone
0.23.1

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@PierrickRauby
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Code Sample, a copy-pastable example if possible

No code since no install

Problem description

I am trying to install pandas on an Beaglebone Black ( Kernel: Linux 4.9.45-ti-r57 & Operating System: Debian GNU/Linux 9 (stretch)). I tried with python2.7 and python3.5.3 with the following install command:

  • pip install pandas (pip 9.0.1) or pip install pandas --no-build-isolation (pip 10.0.1) as suggested in Add pyproject.toml #20775 , but in both cases the result is :
Collecting pandas
  Downloading https://files.pythonhosted.org/packages/45/12/1e1ba99fb65df9f7f3724d3232feef35cc044d18604d57492d561e90219f/pandas-0.23.0.tar.gz (13.1MB)
    100% | 13.1MB 9.1kB/s
Requirement already satisfied: numpy>=1.9.0 in /usr/lib/python3/dist-packages (from pandas)
Collecting python-dateutil>=2.5.0 (from pandas)
  Downloading https://files.pythonhosted.org/packages/cf/f5/af2b09c957ace60dcfac112b669c45c8c97e32f94aa8b56da4c6d1682825/python_dateutil-2.7.3-py2.py3-none-any.whl (211kB)
    100% | 215kB 405kB/s
Collecting pytz>=2011k (from pandas)
  Downloading https://files.pythonhosted.org/packages/dc/83/15f7833b70d3e067ca91467ca245bae0f6fe56ddc7451aa0dc5606b120f2/pytz-2018.4-py2.py3-none-any.whl (510kB)
    100% | 512kB 214kB/s
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.5.0->pandas)
Building wheels for collected packages: pandas
  Running setup.py bdist_wheel for pandas ... |

But then it keeps running setup.py for hours (at least 16h), then I interrupted the process

  • apt-get install python3-pandas (for python 3) and the result is the following:
Reading package lists... Done
Building dependency tree      
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 python3-pandas : Depends: python3-pandas-lib (>= 0.19.2-5.1) but it is not installable
                  Recommends: python3-scipy but it is not going to be installed
                  Recommends: python3-matplotlib but it is not going to be installed
                  Recommends: python3-numexpr but it is not going to be installed
                  Recommends: python3-tables but it is not going to be installed
                  Recommends: python3-bs4 but it is not going to be installed
                  Recommends: python3-html5lib but it is not going to be installed
                  Recommends: python3-lxml but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

And I do not know how to install a "not installable" dependency

I know that it is doable thanks to this wiki buy Mark A. Yoder but I am not successful yet, can anyone help me on this?

Expected Output

cannot import module since I cannot install it

Thanks guys,
Pierrick
@chris-b1
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chris-b1 commented Jun 1, 2018

We don't test on ARM, but can you try pip install pandas -v (verbose) to see if it gives a hint where the build is stalling?

@PierrickRauby
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Thanks for your quick answer.

Yes sure, here is the result of pip install pandas -v :

  copying pandas/io/formats/templates/html.tpl -> build/lib.linux-armv7l-2.7/pandas/io/formats/templates
  UPDATING build/lib.linux-armv7l-2.7/pandas/_version.py
  set build/lib.linux-armv7l-2.7/pandas/_version.py to '0.23.0'
  running build_ext
  building 'pandas.io.sas._sas' extension
  creating build/temp.linux-armv7l-2.7
  creating build/temp.linux-armv7l-2.7/pandas
  creating build/temp.linux-armv7l-2.7/pandas/io
  creating build/temp.linux-armv7l-2.7/pandas/io/sas
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/io/sas/sas.c -o build/temp.linux-armv7l-2.7/pandas/io/sas/sas.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/io/sas/sas.c:566:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \
    ^~~~~~~
  pandas/io/sas/sas.c: In function ‘__pyx_f_6pandas_2io_3sas_4_sas_rdc_decompress’:
  pandas/io/sas/sas.c:4154:65: warning: ‘__pyx_v_ctrl_bits’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       __pyx_t_8 = (((__pyx_v_ctrl_bits & __pyx_v_ctrl_mask) == 0) != 0);
                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
  arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/pandas/io/sas/sas.o -o build/lib.linux-armv7l-2.7/pandas/io/sas/_sas.so
  building 'pandas._libs.testing' extension
  creating build/temp.linux-armv7l-2.7/pandas/_libs
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/testing.c -o build/temp.linux-armv7l-2.7/pandas/_libs/testing.o -Wno-unused-function
  pandas/_libs/testing.c: In function ‘inittesting’:
  pandas/_libs/testing.c:4967:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(((PyObject*)&PyBool_Type));
     ^~~~~~~~~~~~
  pandas/_libs/testing.c:4970:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
     ^~~~~~~~~~~~
  pandas/_libs/testing.c:4973:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(((PyObject *)(&PyFloat_Type)));
     ^~~~~~~~~~~~
  arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/pandas/_libs/testing.o -o build/lib.linux-armv7l-2.7/pandas/_libs/testing.so
  building 'pandas._libs.tslibs.ccalendar' extension
  creating build/temp.linux-armv7l-2.7/pandas/_libs/tslibs
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/tslibs/ccalendar.c -o build/temp.linux-armv7l-2.7/pandas/_libs/tslibs/ccalendar.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/_libs/tslibs/ccalendar.c:566:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \
    ^~~~~~~
  arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/pandas/_libs/tslibs/ccalendar.o -o build/lib.linux-armv7l-2.7/pandas/_libs/tslibs/ccalendar.so
  building 'pandas._libs.tslibs.resolution' extension
  creating build/temp.linux-armv7l-2.7/pandas/_libs/src
  creating build/temp.linux-armv7l-2.7/pandas/_libs/src/datetime
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/tslibs/resolution.c -o build/temp.linux-armv7l-2.7/pandas/_libs/tslibs/resolution.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/_libs/tslibs/resolution.c:566:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \
    ^~~~~~~
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/src/datetime/np_datetime.c -o build/temp.linux-armv7l-2.7/pandas/_libs/src/datetime/np_datetime.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/_libs/src/datetime/np_datetime.c:22:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \
    ^~~~~~~
  pandas/_libs/src/datetime/np_datetime.c: In function ‘pandas_datetimestruct_to_datetime’:
  pandas/_libs/src/datetime/np_datetime.c:518:5: warning: implicit declaration of function ‘convert_datetimestruct_to_datetime’ [-Wimplicit-function-declaration]
       convert_datetimestruct_to_datetime(fr, d, &result);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  pandas/_libs/src/datetime/np_datetime.c: In function ‘pandas_timedelta_to_timedeltastruct’:
  pandas/_libs/src/datetime/np_datetime.c:530:5: warning: implicit declaration of function ‘convert_timedelta_to_timedeltastruct’ [-Wimplicit-function-declaration]
       convert_timedelta_to_timedeltastruct(fr, val, result);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from pandas/_libs/src/datetime/np_datetime.c:20:0:
  At top level:
  /usr/include/python2.7/datetime.h:188:25: warning: ‘PyDateTimeAPI’ defined but not used [-Wunused-variable]
   static PyDateTime_CAPI *PyDateTimeAPI = NULL;
                           ^~~~~~~~~~~~~
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/src/datetime/np_datetime_strings.c -o build/temp.linux-armv7l-2.7/pandas/_libs/src/datetime/np_datetime_strings.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/_libs/src/datetime/np_datetime_strings.c:29:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \
    ^~~~~~~
  arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/pandas/_libs/tslibs/resolution.o build/temp.linux-armv7l-2.7/pandas/_libs/src/datetime/np_datetime.o build/temp.linux-armv7l-2.7/pandas/_libs/src/datetime/np_datetime_strings.o -o build/lib.linux-armv7l-2.7/pandas/_libs/tslibs/resolution.so
  building 'pandas._libs.internals' extension
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/internals.c -o build/temp.linux-armv7l-2.7/pandas/_libs/internals.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/_libs/internals.c:567:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \
    ^~~~~~~
  pandas/_libs/internals.c: In function ‘__pyx_gb_6pandas_5_libs_9internals_12generator’:
  pandas/_libs/internals.c:9335:36: warning: ‘__pyx_t_23’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           __pyx_cur_scope->__pyx_t_9 = __pyx_t_23;
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  pandas/_libs/internals.c:9332:36: warning: ‘__pyx_t_11’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           __pyx_cur_scope->__pyx_t_5 = __pyx_t_11;
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  pandas/_libs/internals.c:9329:36: warning: ‘__pyx_t_6’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           __pyx_cur_scope->__pyx_t_4 = __pyx_t_6;
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
  pandas/_libs/internals.c:9334:36: warning: ‘__pyx_t_15’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           __pyx_cur_scope->__pyx_t_8 = __pyx_t_15;
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  pandas/_libs/internals.c:9333:36: warning: ‘__pyx_t_12’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           __pyx_cur_scope->__pyx_t_7 = __pyx_t_12;
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/pandas/_libs/internals.o -o build/lib.linux-armv7l-2.7/pandas/_libs/internals.so
  building 'pandas._libs.tslibs.np_datetime' extension
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/tslibs/np_datetime.c -o build/temp.linux-armv7l-2.7/pandas/_libs/tslibs/np_datetime.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/_libs/tslibs/np_datetime.c:567:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \
    ^~~~~~~
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/src/datetime/np_datetime.c -o build/temp.linux-armv7l-2.7/pandas/_libs/src/datetime/np_datetime.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/_libs/src/datetime/np_datetime.c:22:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \
    ^~~~~~~
  pandas/_libs/src/datetime/np_datetime.c: In function ‘pandas_datetimestruct_to_datetime’:
  pandas/_libs/src/datetime/np_datetime.c:518:5: warning: implicit declaration of function ‘convert_datetimestruct_to_datetime’ [-Wimplicit-function-declaration]
       convert_datetimestruct_to_datetime(fr, d, &result);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  pandas/_libs/src/datetime/np_datetime.c: In function ‘pandas_timedelta_to_timedeltastruct’:
  pandas/_libs/src/datetime/np_datetime.c:530:5: warning: implicit declaration of function ‘convert_timedelta_to_timedeltastruct’ [-Wimplicit-function-declaration]
       convert_timedelta_to_timedeltastruct(fr, val, result);
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from pandas/_libs/src/datetime/np_datetime.c:20:0:
  At top level:
  /usr/include/python2.7/datetime.h:188:25: warning: ‘PyDateTimeAPI’ defined but not used [-Wunused-variable]
   static PyDateTime_CAPI *PyDateTimeAPI = NULL;
                           ^~~~~~~~~~~~~
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/src/datetime/np_datetime_strings.c -o build/temp.linux-armv7l-2.7/pandas/_libs/src/datetime/np_datetime_strings.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/_libs/src/datetime/np_datetime_strings.c:29:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \
    ^~~~~~~
  arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/pandas/_libs/tslibs/np_datetime.o build/temp.linux-armv7l-2.7/pandas/_libs/src/datetime/np_datetime.o build/temp.linux-armv7l-2.7/pandas/_libs/src/datetime/np_datetime_strings.o -o build/lib.linux-armv7l-2.7/pandas/_libs/tslibs/np_datetime.so
  building 'pandas._libs.algos' extension
  arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-sw1gMG/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Ipandas/_libs/src/klib -Ipandas/_libs/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c pandas/_libs/algos.c -o build/temp.linux-armv7l-2.7/pandas/_libs/algos.o -Wno-unused-function
  In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                   from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/_libs/algos.c:566:
  /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it by " \

I have not included the beginning of the process where pip is basically copying pandas ( copying pandas/... I'll include it if you want

@chris-b1
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chris-b1 commented Jun 1, 2018

Hmm, best guess would be that gcc ran out of memory since nothing obvious went wrong, but not sure.

@PierrickRauby
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Thanks,
Do you know how can I allocate more memory to GCC?

@gfyoung gfyoung added the Build Library building on various platforms label Jun 6, 2018
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gfyoung commented Jun 6, 2018

@PierrickRauby

Do you know how can I allocate more memory to GCC?

Try this: https://stackoverflow.com/questions/11289002/gcc-cc1-out-of-memory-allocating

And I do not know how to install a "not installable" dependency

Hmmm...yeah...this is an ugly problem indicating something really went wrong with package installation. You might want to start here:

https://askubuntu.com/questions/223237/unable-to-correct-problems-you-have-held-broken-packages

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gfyoung commented Jun 6, 2018 •
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Closing, as these issues are sounding like broader problems that are not limited to pandas.

@PierrickRauby : Feel free to re-post if the problems turn out to be pandas-related, and we can revisit!

@gfyoung gfyoung closed this as completed Jun 6, 2018
@gfyoung gfyoung added this to the 0.23.1 milestone Jun 6, 2018
@PierrickRauby
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I am reopenning this it to share a solution/work around that, even if not perfect, seems to work.

Using miniconda like explained in this post and then conda install pandas does the trick.

Unfortunately it only installs pandas 0.16.2, but it's enough for my purpose.
(BTW I am using Debian 9.3 2018-03-05 4GB SD IoT non graphic image)

Finally, I can confirm that it does not seems to be pandas related, I had the exact same issue with sklearn (again miniconda does the trick version 0.16.1). I'll try to understand what is the problem in the coming weeks/months

Thanks for your help !

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gfyoung commented Jun 8, 2018

@PierrickRauby : Interesting! Best of luck in the investigation!

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