Cannot pip install GDAL from environment.yml

[astrojuanlu]

I was trying to create an environment like this:

name: r35_test
channels:
- conda-forge
- defaults
dependencies:
- python=3.5
- libgdal=1.11
- pip:
  - gdal>=1.10,<2

But it fails when installing gdal:

Installing collected packages: gdal
  Running setup.py install for gdal ... error
    Complete output from command /home/juanlu/.miniconda36/envs/r35_test/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-3hvcy74h/gdal/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-np6n0pqf-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.5
    copying gdal.py -> build/lib.linux-x86_64-3.5
    copying ogr.py -> build/lib.linux-x86_64-3.5
    copying osr.py -> build/lib.linux-x86_64-3.5
    copying gdalconst.py -> build/lib.linux-x86_64-3.5
    creating build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/osr.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/gdal_array.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/ogr.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/gdalconst.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/gdalnumeric.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/__init__.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/gdal.py -> build/lib.linux-x86_64-3.5/osgeo
    Fixing build/lib.linux-x86_64-3.5/gdal.py build/lib.linux-x86_64-3.5/ogr.py build/lib.linux-x86_64-3.5/osr.py build/lib.linux-x86_64-3.5/gdalconst.py build/lib.linux-x86_64-3.5/osgeo/osr.py build/lib.linux-x86_64-3.5/osgeo/gdal_array.py build/lib.linux-x86_64-3.5/osgeo/ogr.py build/lib.linux-x86_64-3.5/osgeo/gdalconst.py build/lib.linux-x86_64-3.5/osgeo/gdalnumeric.py build/lib.linux-x86_64-3.5/osgeo/__init__.py build/lib.linux-x86_64-3.5/osgeo/gdal.py
    Skipping optional fixer: ws_comma
    Fixing build/lib.linux-x86_64-3.5/gdal.py build/lib.linux-x86_64-3.5/ogr.py build/lib.linux-x86_64-3.5/osr.py build/lib.linux-x86_64-3.5/gdalconst.py build/lib.linux-x86_64-3.5/osgeo/osr.py build/lib.linux-x86_64-3.5/osgeo/gdal_array.py build/lib.linux-x86_64-3.5/osgeo/ogr.py build/lib.linux-x86_64-3.5/osgeo/gdalconst.py build/lib.linux-x86_64-3.5/osgeo/gdalnumeric.py build/lib.linux-x86_64-3.5/osgeo/__init__.py build/lib.linux-x86_64-3.5/osgeo/gdal.py
    Skipping optional fixer: ws_comma
    running build_ext
    building 'osgeo._gdal' extension
    creating build/temp.linux-x86_64-3.5
    creating build/temp.linux-x86_64-3.5/extensions
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I/home/juanlu/.miniconda36/envs/r35_test/include/python3.5m -I. -I/usr/include -c extensions/gdal_wrap.cpp -o build/temp.linux-x86_64-3.5/extensions/gdal_wrap.o
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    extensions/gdal_wrap.cpp: In function ‘void SWIG_Python_SetModule(swig_module_info*)’:
    extensions/gdal_wrap.cpp:2535:22: warning: unused variable ‘swig_empty_runtime_method_table’ [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    extensions/gdal_wrap.cpp: In function ‘CPLErr GDALRasterBandShadow_GetHistogram(GDALRasterBandShadow*, double, double, int, int*, int, int, GDALProgressFunc, void*)’:
    extensions/gdal_wrap.cpp:4597:66: warning: ‘CPLErr GDALGetRasterHistogram(GDALRasterBandH, double, double, int, int*, int, int, GDALProgressFunc, void*)’ is deprecated [-Wdeprecated-declarations]
                                              callback, callback_data );
                                                                      ^
    In file included from extensions/gdal_wrap.cpp:2860:0:
    /usr/include/gdal.h:757:28: note: declared here
     CPLErr CPL_DLL CPL_STDCALL GDALGetRasterHistogram( GDALRasterBandH hBand,
                                ^~~~~~~~~~~~~~~~~~~~~~
    extensions/gdal_wrap.cpp: In function ‘CPLErr GDALRasterBandShadow_GetDefaultHistogram(GDALRasterBandShadow*, double*, double*, int*, int**, int, GDALProgressFunc, void*)’:
    extensions/gdal_wrap.cpp:4603:61: warning: ‘CPLErr GDALGetDefaultHistogram(GDALRasterBandH, double*, double*, int*, int**, int, GDALProgressFunc, void*)’ is deprecated [-Wdeprecated-declarations]
                                         callback, callback_data );
                                                                 ^
    In file included from extensions/gdal_wrap.cpp:2860:0:
    /usr/include/gdal.h:769:28: note: declared here
     CPLErr CPL_DLL CPL_STDCALL GDALGetDefaultHistogram( GDALRasterBandH hBand,
                                ^~~~~~~~~~~~~~~~~~~~~~~
    extensions/gdal_wrap.cpp: In function ‘CPLErr GDALRasterBandShadow_SetDefaultHistogram(GDALRasterBandShadow*, double, double, int, int*)’:
    extensions/gdal_wrap.cpp:4607:44: warning: ‘CPLErr GDALSetDefaultHistogram(GDALRasterBandH, double, double, int, int*)’ is deprecated [-Wdeprecated-declarations]
                    buckets_in, panHistogram_in );
                                                ^
    In file included from extensions/gdal_wrap.cpp:2860:0:
    /usr/include/gdal.h:781:28: note: declared here
     CPLErr CPL_DLL CPL_STDCALL GDALSetDefaultHistogram( GDALRasterBandH hBand,
                                ^~~~~~~~~~~~~~~~~~~~~~~
    extensions/gdal_wrap.cpp: In function ‘PyObject* _wrap_VirtualMem_GetAddr(PyObject*, PyObject*)’:
    extensions/gdal_wrap.cpp:11391:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "B";
                         ^~~
    extensions/gdal_wrap.cpp:11396:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "h";
                         ^~~
    extensions/gdal_wrap.cpp:11401:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "H";
                         ^~~
    extensions/gdal_wrap.cpp:11406:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "i";
                         ^~~
    extensions/gdal_wrap.cpp:11411:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "I";
                         ^~~
    extensions/gdal_wrap.cpp:11416:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "f";
                         ^~~
    extensions/gdal_wrap.cpp:11421:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "F";
                         ^~~
    extensions/gdal_wrap.cpp:11426:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "B";
                         ^~~
    extensions/gdal_wrap.cpp: In function ‘PyObject* _wrap_Band_ComputeStatistics(PyObject*, PyObject*)’:
    extensions/gdal_wrap.cpp:15259:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
       CPLErr result;
              ^~~~~~
    extensions/gdal_wrap.cpp: At global scope:
    extensions/gdal_wrap.cpp:2535:22: warning: ‘swig_empty_runtime_method_table’ defined but not used [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    g++ -pthread -shared -L/home/juanlu/.miniconda36/envs/r35_test/lib -Wl,-rpath=/home/juanlu/.miniconda36/envs/r35_test/lib,--no-as-needed build/temp.linux-x86_64-3.5/extensions/gdal_wrap.o -L../../.libs -L../../ -L/home/juanlu/.miniconda36/envs/r35_test/lib -L/usr/lib -lpython3.5m -lgdal -o build/lib.linux-x86_64-3.5/osgeo/_gdal.cpython-35m-x86_64-linux-gnu.so
    building 'osgeo._gdalconst' extension
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I/home/juanlu/.miniconda36/envs/r35_test/include/python3.5m -I. -I/usr/include -c extensions/gdalconst_wrap.c -o build/temp.linux-x86_64-3.5/extensions/gdalconst_wrap.o
    extensions/gdalconst_wrap.c: In function ‘SWIG_Python_SetModule’:
    extensions/gdalconst_wrap.c:2511:22: warning: unused variable ‘swig_empty_runtime_method_table’ [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    At top level:
    extensions/gdalconst_wrap.c:2511:22: warning: ‘swig_empty_runtime_method_table’ defined but not used [-Wunused-variable]
    gcc -pthread -shared -L/home/juanlu/.miniconda36/envs/r35_test/lib -Wl,-rpath=/home/juanlu/.miniconda36/envs/r35_test/lib,--no-as-needed build/temp.linux-x86_64-3.5/extensions/gdalconst_wrap.o -L../../.libs -L../../ -L/home/juanlu/.miniconda36/envs/r35_test/lib -L/usr/lib -lpython3.5m -lgdal -o build/lib.linux-x86_64-3.5/osgeo/_gdalconst.cpython-35m-x86_64-linux-gnu.so
    building 'osgeo._osr' extension
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I/home/juanlu/.miniconda36/envs/r35_test/include/python3.5m -I. -I/usr/include -c extensions/osr_wrap.cpp -o build/temp.linux-x86_64-3.5/extensions/osr_wrap.o
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    extensions/osr_wrap.cpp: In function ‘void SWIG_Python_SetModule(swig_module_info*)’:
    extensions/osr_wrap.cpp:2535:22: warning: unused variable ‘swig_empty_runtime_method_table’ [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    extensions/osr_wrap.cpp: In function ‘OGRErr OSRSpatialReferenceShadow_ImportFromOzi(OSRSpatialReferenceShadow*, const char*, const char*, const char*)’:
    extensions/osr_wrap.cpp:3736:59: error: cannot convert ‘const char*’ to ‘const char* const*’ for argument ‘2’ to ‘OGRErr OSRImportFromOzi(OGRSpatialReferenceH, const char* const*)’
         return OSRImportFromOzi( self, datum, proj, projParms );
                                                               ^
    extensions/osr_wrap.cpp: At global scope:
    extensions/osr_wrap.cpp:3017:13: warning: ‘void GDALPythonFreeCStr(void*, int)’ defined but not used [-Wunused-function]
     static void GDALPythonFreeCStr(void* ptr, int bToFree)
                 ^~~~~~~~~~~~~~~~~~
    extensions/osr_wrap.cpp:2987:14: warning: ‘char* GDALPythonObjectToCStr(PyObject*, int*)’ defined but not used [-Wunused-function]
     static char* GDALPythonObjectToCStr(PyObject* pyObject, int* pbToFree)
                  ^~~~~~~~~~~~~~~~~~~~~~
    extensions/osr_wrap.cpp:2535:22: warning: ‘swig_empty_runtime_method_table’ defined but not used [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/home/juanlu/.miniconda36/envs/r35_test/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-3hvcy74h/gdal/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-np6n0pqf-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-3hvcy74h/gdal/                                                          
An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:

    https://github.com/conda/conda/issues

Current conda install:

               platform : linux-64
          conda version : 4.3.22
       conda is private : False
      conda-env version : 4.3.22
    conda-build version : not installed
         python version : 3.6.1.final.0
       requests version : 2.14.2
       root environment : /home/juanlu/.miniconda36  (writable)
    default environment : /home/juanlu/.miniconda36
       envs directories : /home/juanlu/.miniconda36/envs
                          /home/juanlu/.conda/envs
          package cache : /home/juanlu/.miniconda36/pkgs
                          /home/juanlu/.conda/pkgs
           channel URLs : https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
            config file : None
             netrc file : /home/juanlu/.netrc
           offline mode : False
             user-agent : conda/4.3.22 requests/2.14.2 CPython/3.6.1 Linux/4.11.6-3-ARCH arch/ glibc/2.25    
                UID:GID : 1000:100

However, if I create an environment without the gdal package in pip, things seem to work fine:

$ cat environment.yml
name: r35_test
channels:
- conda-forge
- defaults
dependencies:
- python=3.5
- libgdal=1.11
#- pip:
  #- gdal>=1.10,<2
$ conda env create -q
Fetching package metadata ...........
Solving package specifications: .
#
# To activate this environment, use:
# > source activate r35_test
#
# To deactivate an active environment, use:
# > source deactivate
#
$ source activate r35_test
(r35_test) $ pip install "gdal>=1.10,<2" --verbose --no-cache-dir --no-binary wheel
Collecting gdal<2,>=1.10
  1 location(s) to search for versions of gdal:
  * https://pypi.python.org/simple/gdal/
  Getting page https://pypi.python.org/simple/gdal/
  Starting new HTTPS connection (1): pypi.python.org
  "GET /simple/gdal/ HTTP/1.1" 200 3028
  Analyzing links from page https://pypi.python.org/simple/gdal/
    Skipping link https://pypi.python.org/packages/14/fd/cc5b8e4b1e32c852ef9fbb3c684c6b1d11a68155a7f12a57c48d5d88548f/GDAL-1.5.2.win32-py2.5.exe#md5=17db2b36b9417d767414373c3c87c780 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
    Skipping link https://pypi.python.org/packages/16/36/9a6bb42a2c484657c9324c1810d33e63e56039848fb4d072d3bb82b65a34/GDAL-1.5.2-py2.5-win32.egg#md5=bf618b4078409ecc6c843f4b75651841 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Skipping link https://pypi.python.org/packages/16/43/dac73405207378417422a9e2a9657d54ed312d8ad4d4557d370fc746118b/GDAL-1.5.0.win32-py2.5.exe#md5=bed0134d414c9787dfea64dbcf17ee7a (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
    Found link https://pypi.python.org/packages/29/03/e9a666aeeebcfcfa0c07b56c440a4e9fc45161cbf41fc23099427458f11c/GDAL-1.8.1.tar.gz#md5=cab9540923a71f448aeb0ef588e462ce (from https://pypi.python.org/simple/gdal/), version: 1.8.1
    Found link https://pypi.python.org/packages/2d/c7/e022017fea77611be7a68d2ca86ab17b82a67a35724f28b161c77b5224a5/GDAL-1.7.1.tar.gz#md5=38b838d528b309a28a3aa24d4fcef3cd (from https://pypi.python.org/simple/gdal/), version: 1.7.1
    Skipping link https://pypi.python.org/packages/30/42/edc77457b4a2f2027a9b60e08cb3c0708280032d01941149e7e7d0d592c9/GDAL-1.6.1-py2.6-win32.egg#md5=0d187c3a78279a79a12085ac6ed78711 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Skipping link https://pypi.python.org/packages/30/48/c239130bcf4eab3a858cf2347f477a54c9d669729a34091f68a756e40f66/GDAL-1.6.1-py2.5-win32.egg#md5=3aaff6dde620794dafc38e140e54d6aa (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Found link https://pypi.python.org/packages/36/d7/f89ac1347185db56939c156330efbfa2e3be560060b74e31f41e514ee627/GDAL-2.1.3.tar.gz#md5=519bff3c56b8af5dbf388f93947b1281 (from https://pypi.python.org/simple/gdal/), version: 2.1.3
    Skipping link https://pypi.python.org/packages/37/5b/e1fc1d540a71fd4a4e2469b62c92db3c6327ea45761df3de7ca2c5c7087d/GDAL-1.6.0.win32-py2.4.exe#md5=093f5025128bed17606206a2b8d3be01 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
    Skipping link https://pypi.python.org/packages/3c/3e/7a2ece4b7ae808e16bfed42cfed189ea3355180b697a17ae7157145e742c/GDAL-1.5.0-py2.5-macosx-10.5-i386.egg#md5=9783d84710086f91bd307c564de59ad7 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Skipping link https://pypi.python.org/packages/3e/64/9aea9ab17b29beea72d12cef586c709ed64d4873c06cfc5ac24c941d9707/GDAL-1.6.1.win32-py2.6.exe#md5=5e48c85a9ace1baad77dc26bb42ab4e1 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
    Found link https://pypi.python.org/packages/40/f9/8ad67763925b5c4f70a278ed725dc80dc774a4d30daf372a570a2faa9a8d/GDAL-2.2.0.tar.gz#md5=56dac195bcaaeffc1248e3f96cfb4e5a (from https://pypi.python.org/simple/gdal/), version: 2.2.0
    Found link https://pypi.python.org/packages/42/38/f2f0f57c2f3ebc5a9f0eb4ba9e130aa750e999a99de53cd5d96432fee258/GDAL-1.11.1.tar.gz#md5=1a6b51c8e2dd5990007a33e081b8a057 (from https://pypi.python.org/simple/gdal/), version: 1.11.1
    Found link https://pypi.python.org/packages/4b/6e/88fdda4f2c14c2d2cb13145383d9908fb8611ff047409140845b3ba1bf3c/GDAL-1.9.0.tar.gz#md5=415d043044e3c9616f80b69b95a8540d (from https://pypi.python.org/simple/gdal/), version: 1.9.0
    Skipping link https://pypi.python.org/packages/50/65/c90fcf4b9cd0091745b5bbc500d3200282bd74ddd9aedddcf1f0d15c8239/GDAL-1.6.1-py2.4-win32.egg#md5=e6d97e4571d11a996193714236d28506 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Skipping link https://pypi.python.org/packages/5c/fa/949485fc3f62bd7002605347c7b0fa5997850340334a2634c3c06be29815/GDAL-1.6.0.win32-py2.6.exe#md5=74d5643a1c00a2d40a7b2856cdb64325 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
    Skipping link https://pypi.python.org/packages/5e/44/a69ea99d81ef41753b904c864de3bff5419112c53c6701d5083340a8730f/GDAL-1.6.0-py2.4-win32.egg#md5=96c4fe637d22c7e211169a4d289c502f (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Skipping link https://pypi.python.org/packages/60/d3/83870329662e38efd4d7c6b1b622d0c8de8cca3d8b1d2d35df9efd8ed0de/GDAL-1.5.0-py2.4-win32.egg#md5=69e16e9b7e80f733f5bee96596d1824b (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Skipping link https://pypi.python.org/packages/6f/10/06dc4171cb26210c6d07920f497f5070134aa85fadbb17f311d2f6c1e33b/GDAL-1.6.0.win32-py2.5.exe#md5=1e0ff5c2da337a6ac9af3e5320aa3366 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
    Found link https://pypi.python.org/packages/76/41/8b41f24fb25fd0bfd69c98444b3cab79e519c88619c0ccef8891e096dbd9/GDAL-1.9.1.tar.gz#md5=60cb0e0b652dfb204e150bcb11190248 (from https://pypi.python.org/simple/gdal/), version: 1.9.1
    Found link https://pypi.python.org/packages/81/16/233ee7862013319c16dd282f0f443abf51593e6c3860187fb3d3cd8e3a18/GDAL-1.6.1.tar.gz#md5=e8671d4a77041cf0f7a027f3f3e8280c (from https://pypi.python.org/simple/gdal/), version: 1.6.1
    Found link https://pypi.python.org/packages/85/90/817ece7cbd212ed0475bddc3249c96c561ae8bd7326f59b98df0f64a8c91/GDAL-2.0.0.tar.gz#md5=03684d7aa3ef4527151c647b2330f0ac (from https://pypi.python.org/simple/gdal/), version: 2.0.0
    Found link https://pypi.python.org/packages/91/e2/643bb499663924b60a634549e64451881c8c73e2d88d33c6aa79d38f0775/GDAL-1.7.0.tar.gz#md5=3f737981ffe05c53af64a31172550b51 (from https://pypi.python.org/simple/gdal/), version: 1.7.0
    Found link https://pypi.python.org/packages/95/86/c60989985023f2ac560534fb2dc1f982e94a094433688981f8df95d8245f/GDAL-1.5.2.tar.gz#md5=6ae6f3c0ff4d29f5ef2ad312daed2c65 (from https://pypi.python.org/simple/gdal/), version: 1.5.2
    Skipping link https://pypi.python.org/packages/97/e2/037a293c10c7897c31b7c1043e22a2d36d7df850b6961989418e3d26a3f7/GDAL-1.6.0-py2.5-win32.egg#md5=f8291233c8688ea352d97875c2981139 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Skipping link https://pypi.python.org/packages/99/13/1976784a34220ff7cb4d6df6028f17940094f5b7cb32e37818c36044d39c/GDAL-1.5.0.win32-py2.4.exe#md5=5f7661e2dbf68d840a6b8327d6913dfa (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
    Skipping link https://pypi.python.org/packages/9e/cf/7bae2b43381303037dd383daeda8db8b92183f164bed2a7d6b74f922f8f6/GDAL-1.6.1.win32-py2.4.exe#md5=d48d82cbc1fd5061e1ad49d1845b3418 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
    Skipping link https://pypi.python.org/packages/9e/fa/6c71b1eaabe8ca81180acd14ad78ad6aa090318de44492b4c551c2302f49/GDAL-1.5.0-py2.5-win32.egg#md5=792b995a7b4cd4e93a184585b33025c1 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Found link https://pypi.python.org/packages/a1/9a/80903f2db295ea9f817fddb45ed90d92a8c9bd9c59140760d4aee317e887/GDAL-2.0.1.tar.gz#md5=df013c4417a3820b6d59c9b01d2c68c9 (from https://pypi.python.org/simple/gdal/), version: 2.0.1
    Skipping link https://pypi.python.org/packages/b9/ed/fc3747277cacb92cc71ab490e73552e4ed66e5a48d02df7c43fd8f0b93ab/GDAL-1.6.0-py2.6-win32.egg#md5=7db9547e5bcf26dafe9f612b4f0af1a9 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Found link https://pypi.python.org/packages/ba/9b/76aa2871642f774876461c8575f4bffc53a5dcc2eb1b9cff1a548372c806/GDAL-1.11.0.tar.gz#md5=505a9c1d1be06a73541dbb7bb6fca969 (from https://pypi.python.org/simple/gdal/), version: 1.11.0
    Found link https://pypi.python.org/packages/c7/02/91bdd33e763f0c97b58019fd6d328a9780fd4d153673fcfb6a835dbe8216/GDAL-1.11.2.tar.gz#md5=4351163daa608ef4aca7e9fc6ebb868a (from https://pypi.python.org/simple/gdal/), version: 1.11.2
    Skipping link https://pypi.python.org/packages/c7/36/32cc146a7881807d7f5ba19f798cb423b7ebb8e453c06a2cd75bf6c22e23/GDAL-1.5.2-py2.5-macosx-10.5-i386.egg#md5=1586f9ce07923e00c4190778de8df0b5 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Skipping link https://pypi.python.org/packages/cb/3a/056d4f86b8e402d1d3bbf92e8af29a3ad846a488fcf7ca89bb42c48fe5ed/GDAL-1.6.1.win32-py2.5.exe#md5=089ee8b47937f9abb104bbdc789925ff (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
    Skipping link https://pypi.python.org/packages/cc/ab/2c42c4e3164fe7f32df3ae687b48ff6c1411eb9041e33d1b01f284c8d6dd/GDAL-1.5.2-py2.4-win32.egg#md5=11fdc3adb0c2c78760dda6cbfa9520f8 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .egg
    Found link https://pypi.python.org/packages/d1/98/27fff31ad298f3ec50db19dc3adfd8387279e158b1c6331c531c5fc7d830/GDAL-2.1.0.tar.gz#md5=64084a5f114b4dffc53280e28d2ba4f3 (from https://pypi.python.org/simple/gdal/), version: 2.1.0
    Found link https://pypi.python.org/packages/e3/5c/aa4f71d88d66de95dab434135b1904f64a54e108aca60d7e10aa3575fc78/GDAL-1.6.0.tar.gz#md5=a38794c9ae1de8d1e34def65d0ee2152 (from https://pypi.python.org/simple/gdal/), version: 1.6.0
    Found link https://pypi.python.org/packages/e6/b5/346cbd96837f5ed525d0460090d24e8cfb31ad805c6d5297ee4998eb81b6/GDAL-1.10.0.tar.gz#md5=d908a070bec2bb86fde1f13d76a552c2 (from https://pypi.python.org/simple/gdal/), version: 1.10.0
    Found link https://pypi.python.org/packages/ed/42/9de3bfa170f94a60e096ff4559fa96e51ad3330a3fe1f7a5dde5e455808b/GDAL-1.5.0.tar.gz#md5=a7fcc5ec9c1719aa7b3aba1cd7c9c1e7 (from https://pypi.python.org/simple/gdal/), version: 1.5.0
    Skipping link https://pypi.python.org/packages/fc/13/e2b27c4ec0a6d1221e9fe90984087aeb35df49a7223a5e761aefb9885086/GDAL-1.5.2.win32-py2.4.exe#md5=2bea990ee7eebc1c3d93834613731056 (from https://pypi.python.org/simple/gdal/); unsupported archive format: .exe
  Using version 1.11.2 (newest of versions: 1.10.0, 1.11.0, 1.11.1, 1.11.2)
  "GET /packages/c7/02/91bdd33e763f0c97b58019fd6d328a9780fd4d153673fcfb6a835dbe8216/GDAL-1.11.2.tar.gz HTTP/1.1" 200 477922
  Downloading GDAL-1.11.2.tar.gz (477kB)
  Downloading from URL https://pypi.python.org/packages/c7/02/91bdd33e763f0c97b58019fd6d328a9780fd4d153673fcfb6a835dbe8216/GDAL-1.11.2.tar.gz#md5=4351163daa608ef4aca7e9fc6ebb868a (from https://pypi.python.org/simple/gdal/)
    100% |████████████████████████████████| 481kB 3.7MB/s 
  Running setup.py (path:/tmp/pip-build-2mhax_53/gdal/setup.py) egg_info for package gdal
    Running command python setup.py egg_info
    running egg_info
    creating pip-egg-info/GDAL.egg-info
    writing dependency_links to pip-egg-info/GDAL.egg-info/dependency_links.txt
    writing top-level names to pip-egg-info/GDAL.egg-info/top_level.txt
    writing pip-egg-info/GDAL.egg-info/PKG-INFO
    writing manifest file 'pip-egg-info/GDAL.egg-info/SOURCES.txt'
    reading manifest file 'pip-egg-info/GDAL.egg-info/SOURCES.txt'
    writing manifest file 'pip-egg-info/GDAL.egg-info/SOURCES.txt'
  Source in ./pip-build-2mhax_53/gdal has version 1.11.2, which satisfies requirement gdal<2,>=1.10 from https://pypi.python.org/packages/c7/02/91bdd33e763f0c97b58019fd6d328a9780fd4d153673fcfb6a835dbe8216/GDAL-1.11.2.tar.gz#md5=4351163daa608ef4aca7e9fc6ebb868a
Installing collected packages: gdal
  Running setup.py install for gdal ...     Running command /home/juanlu/.miniconda36/envs/r35_test/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-2mhax_53/gdal/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-s3n06txp-record/install-record.txt --single-version-externally-managed --compile
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.5
    copying gdal.py -> build/lib.linux-x86_64-3.5
    copying ogr.py -> build/lib.linux-x86_64-3.5
    copying osr.py -> build/lib.linux-x86_64-3.5
    copying gdalconst.py -> build/lib.linux-x86_64-3.5
    creating build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/osr.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/gdal_array.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/ogr.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/gdalconst.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/gdalnumeric.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/__init__.py -> build/lib.linux-x86_64-3.5/osgeo
    copying osgeo/gdal.py -> build/lib.linux-x86_64-3.5/osgeo
    Fixing build/lib.linux-x86_64-3.5/gdal.py build/lib.linux-x86_64-3.5/ogr.py build/lib.linux-x86_64-3.5/osr.py build/lib.linux-x86_64-3.5/gdalconst.py build/lib.linux-x86_64-3.5/osgeo/osr.py build/lib.linux-x86_64-3.5/osgeo/gdal_array.py build/lib.linux-x86_64-3.5/osgeo/ogr.py build/lib.linux-x86_64-3.5/osgeo/gdalconst.py build/lib.linux-x86_64-3.5/osgeo/gdalnumeric.py build/lib.linux-x86_64-3.5/osgeo/__init__.py build/lib.linux-x86_64-3.5/osgeo/gdal.py
    Skipping optional fixer: ws_comma
    Fixing build/lib.linux-x86_64-3.5/gdal.py build/lib.linux-x86_64-3.5/ogr.py build/lib.linux-x86_64-3.5/osr.py build/lib.linux-x86_64-3.5/gdalconst.py build/lib.linux-x86_64-3.5/osgeo/osr.py build/lib.linux-x86_64-3.5/osgeo/gdal_array.py build/lib.linux-x86_64-3.5/osgeo/ogr.py build/lib.linux-x86_64-3.5/osgeo/gdalconst.py build/lib.linux-x86_64-3.5/osgeo/gdalnumeric.py build/lib.linux-x86_64-3.5/osgeo/__init__.py build/lib.linux-x86_64-3.5/osgeo/gdal.py
    Skipping optional fixer: ws_comma
    running build_ext
    building 'osgeo._gdal' extension
    creating build/temp.linux-x86_64-3.5
    creating build/temp.linux-x86_64-3.5/extensions
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I/home/juanlu/.miniconda36/envs/r35_test/include/python3.5m -I. -I/home/juanlu/.miniconda36/envs/r35_test/include -c extensions/gdal_wrap.cpp -o build/temp.linux-x86_64-3.5/extensions/gdal_wrap.o
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    extensions/gdal_wrap.cpp: In function ‘void SWIG_Python_SetModule(swig_module_info*)’:
    extensions/gdal_wrap.cpp:2535:22: warning: unused variable ‘swig_empty_runtime_method_table’ [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    extensions/gdal_wrap.cpp: In function ‘PyObject* _wrap_VirtualMem_GetAddr(PyObject*, PyObject*)’:
    extensions/gdal_wrap.cpp:11391:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "B";
                         ^~~
    extensions/gdal_wrap.cpp:11396:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "h";
                         ^~~
    extensions/gdal_wrap.cpp:11401:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "H";
                         ^~~
    extensions/gdal_wrap.cpp:11406:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "i";
                         ^~~
    extensions/gdal_wrap.cpp:11411:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "I";
                         ^~~
    extensions/gdal_wrap.cpp:11416:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "f";
                         ^~~
    extensions/gdal_wrap.cpp:11421:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "F";
                         ^~~
    extensions/gdal_wrap.cpp:11426:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
           buf->format = "B";
                         ^~~
    extensions/gdal_wrap.cpp: In function ‘PyObject* _wrap_Band_ComputeStatistics(PyObject*, PyObject*)’:
    extensions/gdal_wrap.cpp:15259:10: warning: variable ‘result’ set but not used [-Wunused-but-set-variable]
       CPLErr result;
              ^~~~~~
    extensions/gdal_wrap.cpp: At global scope:
    extensions/gdal_wrap.cpp:2535:22: warning: ‘swig_empty_runtime_method_table’ defined but not used [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    g++ -pthread -shared -L/home/juanlu/.miniconda36/envs/r35_test/lib -Wl,-rpath=/home/juanlu/.miniconda36/envs/r35_test/lib,--no-as-needed build/temp.linux-x86_64-3.5/extensions/gdal_wrap.o -L../../.libs -L../../ -L/home/juanlu/.miniconda36/envs/r35_test/lib -L/home/juanlu/.miniconda36/envs/r35_test/lib -lpython3.5m -lgdal -o build/lib.linux-x86_64-3.5/osgeo/_gdal.cpython-35m-x86_64-linux-gnu.so
    building 'osgeo._gdalconst' extension
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I/home/juanlu/.miniconda36/envs/r35_test/include/python3.5m -I. -I/home/juanlu/.miniconda36/envs/r35_test/include -c extensions/gdalconst_wrap.c -o build/temp.linux-x86_64-3.5/extensions/gdalconst_wrap.o
    extensions/gdalconst_wrap.c: In function ‘SWIG_Python_SetModule’:
    extensions/gdalconst_wrap.c:2511:22: warning: unused variable ‘swig_empty_runtime_method_table’ [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    At top level:
    extensions/gdalconst_wrap.c:2511:22: warning: ‘swig_empty_runtime_method_table’ defined but not used [-Wunused-variable]
    gcc -pthread -shared -L/home/juanlu/.miniconda36/envs/r35_test/lib -Wl,-rpath=/home/juanlu/.miniconda36/envs/r35_test/lib,--no-as-needed build/temp.linux-x86_64-3.5/extensions/gdalconst_wrap.o -L../../.libs -L../../ -L/home/juanlu/.miniconda36/envs/r35_test/lib -L/home/juanlu/.miniconda36/envs/r35_test/lib -lpython3.5m -lgdal -o build/lib.linux-x86_64-3.5/osgeo/_gdalconst.cpython-35m-x86_64-linux-gnu.so
    building 'osgeo._osr' extension
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I/home/juanlu/.miniconda36/envs/r35_test/include/python3.5m -I. -I/home/juanlu/.miniconda36/envs/r35_test/include -c extensions/osr_wrap.cpp -o build/temp.linux-x86_64-3.5/extensions/osr_wrap.o
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    extensions/osr_wrap.cpp: In function ‘void SWIG_Python_SetModule(swig_module_info*)’:
    extensions/osr_wrap.cpp:2535:22: warning: unused variable ‘swig_empty_runtime_method_table’ [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    extensions/osr_wrap.cpp: At global scope:
    extensions/osr_wrap.cpp:3017:13: warning: ‘void GDALPythonFreeCStr(void*, int)’ defined but not used [-Wunused-function]
     static void GDALPythonFreeCStr(void* ptr, int bToFree)
                 ^~~~~~~~~~~~~~~~~~
    extensions/osr_wrap.cpp:2987:14: warning: ‘char* GDALPythonObjectToCStr(PyObject*, int*)’ defined but not used [-Wunused-function]
     static char* GDALPythonObjectToCStr(PyObject* pyObject, int* pbToFree)
                  ^~~~~~~~~~~~~~~~~~~~~~
    extensions/osr_wrap.cpp:2535:22: warning: ‘swig_empty_runtime_method_table’ defined but not used [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    g++ -pthread -shared -L/home/juanlu/.miniconda36/envs/r35_test/lib -Wl,-rpath=/home/juanlu/.miniconda36/envs/r35_test/lib,--no-as-needed build/temp.linux-x86_64-3.5/extensions/osr_wrap.o -L../../.libs -L../../ -L/home/juanlu/.miniconda36/envs/r35_test/lib -L/home/juanlu/.miniconda36/envs/r35_test/lib -lpython3.5m -lgdal -o build/lib.linux-x86_64-3.5/osgeo/_osr.cpython-35m-x86_64-linux-gnu.so
    building 'osgeo._ogr' extension
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I../../port -I../../gcore -I../../alg -I../../ogr/ -I/home/juanlu/.miniconda36/envs/r35_test/include/python3.5m -I. -I/home/juanlu/.miniconda36/envs/r35_test/include -c extensions/ogr_wrap.cpp -o build/temp.linux-x86_64-3.5/extensions/ogr_wrap.o
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
    extensions/ogr_wrap.cpp: In function ‘void SWIG_Python_SetModule(swig_module_info*)’:
    extensions/ogr_wrap.cpp:2535:22: warning: unused variable ‘swig_empty_runtime_method_table’ [-Wunused-variable]
       static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    extensions/ogr_wrap.cpp: At global scope:
    extensions/ogr_wrap.cpp:2535:22: warning: ‘swig_empty_runtime_method_table’ defined but not used [-Wunused-variable]
    g++ -pthread -shared -L/home/juanlu/.miniconda36/envs/r35_test/lib -Wl,-rpath=/home/juanlu/.miniconda36/envs/r35_test/lib,--no-as-needed build/temp.linux-x86_64-3.5/extensions/ogr_wrap.o -L../../.libs -L../../ -L/home/juanlu/.miniconda36/envs/r35_test/lib -L/home/juanlu/.miniconda36/envs/r35_test/lib -lpython3.5m -lgdal -o build/lib.linux-x86_64-3.5/osgeo/_ogr.cpython-35m-x86_64-linux-gnu.so
    running install_lib
    creating /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/_ogr.cpython-35m-x86_64-linux-gnu.so -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/_osr.cpython-35m-x86_64-linux-gnu.so -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/_gdalconst.cpython-35m-x86_64-linux-gnu.so -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/_gdal.cpython-35m-x86_64-linux-gnu.so -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/gdal.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/__init__.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/gdalnumeric.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/gdalconst.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/ogr.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/gdal_array.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/osgeo/osr.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo
    copying build/lib.linux-x86_64-3.5/gdalconst.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages
    copying build/lib.linux-x86_64-3.5/osr.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages
    copying build/lib.linux-x86_64-3.5/ogr.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages
    copying build/lib.linux-x86_64-3.5/gdal.py -> /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo/gdal.py to gdal.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo/__init__.py to __init__.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo/gdalnumeric.py to gdalnumeric.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo/gdalconst.py to gdalconst.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo/ogr.py to ogr.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo/gdal_array.py to gdal_array.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo/osr.py to osr.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/gdalconst.py to gdalconst.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osr.py to osr.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/ogr.py to ogr.cpython-35.pyc
    byte-compiling /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/gdal.py to gdal.cpython-35.pyc
    running install_egg_info
    running egg_info
    writing GDAL.egg-info/PKG-INFO
    writing top-level names to GDAL.egg-info/top_level.txt
    writing dependency_links to GDAL.egg-info/dependency_links.txt
    reading manifest file 'GDAL.egg-info/SOURCES.txt'
    writing manifest file 'GDAL.egg-info/SOURCES.txt'
    Copying GDAL.egg-info to /home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/GDAL-1.11.2-py3.5.egg-info
    running install_scripts
    writing list of installed files to '/tmp/pip-s3n06txp-record/install-record.txt'
done
  Removing source in /tmp/pip-build-2mhax_53/gdal
Successfully installed gdal-1.11.2
Cleaning up...

Still, there is some linking problem:

(r35_test) $ python -c "import osgeo"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo/__init__.py", line 21, in <module>
    _gdal = swig_import_helper()
  File "/home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/site-packages/osgeo/__init__.py", line 17, in swig_import_helper
    _mod = imp.load_module('_gdal', fp, pathname, description)
  File "/home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/imp.py", line 242, in load_module
    return load_dynamic(name, filename, file)
  File "/home/juanlu/.miniconda36/envs/r35_test/lib/python3.5/imp.py", line 342, in load_dynamic
    return _load(spec)
ImportError: libcom_err.so.3: cannot open shared object file: No such file or directory

Which can nonetheless be trivially solved:

https://stackoverflow.com/a/36295620/554319

(r35_test) $ ln -s  /usr/lib/libcom_err.so.2 ~/.miniconda36/envs/r35_test/lib/libcom_err.so.3
(r35_test) $ python -c "import osgeo"
(r35_test) $ 

Ideas?

[astrojuanlu]

There are probably two separate issues here. I'm first concerned with the fact that conda env create does not properly install pip packages. Perhaps there's no activation right before? Do you think this belongs to conda/conda @kalefranz?

[astrojuanlu]

I reported the linking problem separately: #4788

[astrojuanlu]

And the conda-env failure in https://github.com/conda/conda/issues/5901. Closing this.