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brycefrank / pyfor

Tools for analyzing aerial point clouds of forest data.
MIT License
94 stars 19 forks source link

Conda forge gdal issue #78

Open bw4sz opened 4 years ago

bw4sz commented 4 years ago

Hey Bryce. I'm debugging a pyfor install issue. I'll document here in case it happens to others. gdal and rasterio are failing on your conda forge build, but not only rasterio alone. Here is what I have so far.

Rasterio builds fine on its own. OSX.

 MacBook-Pro:NEON_crown_maps ben$ conda --version
conda 4.8.1
MacBook-Pro:NEON_crown_maps ben$ conda create python=3.7 --name rasterio_only
Collecting package metadata (current_repodata.json): |done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.1
  latest version: 4.8.2

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /Users/ben/miniconda3/envs/rasterio_only

  added / updated specs:
    - python=3.7

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    python-3.7.6               |       h5c2c468_2        22.6 MB  conda-forge
    readline-8.0               |       hcfe32e1_0         415 KB  conda-forge
    sqlite-3.30.1              |       h93121df_0         2.5 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        25.5 MB

The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2019.11.28-hecc5488_0
  certifi            conda-forge/osx-64::certifi-2019.11.28-py37_0
  libcxx             conda-forge/osx-64::libcxx-9.0.1-1
  libffi             conda-forge/osx-64::libffi-3.2.1-h6de7cb9_1006
  ncurses            conda-forge/osx-64::ncurses-6.1-h0a44026_1002
  openssl            conda-forge/osx-64::openssl-1.1.1d-h0b31af3_0
  pip                conda-forge/noarch::pip-20.0.2-py_2
  python             conda-forge/osx-64::python-3.7.6-h5c2c468_2
  readline           conda-forge/osx-64::readline-8.0-hcfe32e1_0
  setuptools         conda-forge/osx-64::setuptools-45.1.0-py37_0
  sqlite             conda-forge/osx-64::sqlite-3.30.1-h93121df_0
  tk                 conda-forge/osx-64::tk-8.6.10-hbbe82c9_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xz                 conda-forge/osx-64::xz-5.2.4-h1de35cc_1001
  zlib               conda-forge/osx-64::zlib-1.2.11-h0b31af3_1006

Proceed ([y]/n)? y
Invalid choice: cony
Proceed ([y]/n)? y

Downloading and Extracting Packages
readline-8.0         | 415 KB    | #################################################################### | 100%
python-3.7.6         | 22.6 MB   | #################################################################### | 100%
sqlite-3.30.1        | 2.5 MB    | #################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate rasterio_only
#
# To deactivate an active environment, use
#
#     $ conda deactivate

MacBook-Pro:NEON_crown_maps ben$ conda activate rasterio_only
(rasterio_only) MacBook-Pro:NEON_crown_maps ben$ conda config --add channels conda-forge

Warning: 'conda-forge' already in 'channels' list, moving to the top
(rasterio_only) MacBook-Pro:NEON_crown_maps ben$
(rasterio_only) MacBook-Pro:NEON_crown_maps ben$ conda install rasterio
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.1
  latest version: 4.8.2

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /Users/ben/miniconda3/envs/rasterio_only

  added / updated specs:
    - rasterio

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    boost-cpp-1.70.0           |       h75728bb_2        19.0 MB  conda-forge
    cairo-1.16.0               |    he1c11cd_1002         1.3 MB  conda-forge
    cfitsio-3.470              |       h84d2f63_2         1.4 MB  conda-forge
    expat-2.2.9                |       h4a8c4bd_2         126 KB  conda-forge
    fontconfig-2.13.1          |    h6b1039f_1001         270 KB  conda-forge
    geos-3.8.0                 |       h4a8c4bd_0         898 KB  conda-forge
    geotiff-1.5.1              |       hc9fff18_8         125 KB  conda-forge
    giflib-5.2.1               |       h0b31af3_1          64 KB  conda-forge
    glib-2.58.3                |py37h577aef8_1002         3.1 MB  conda-forge
    hdf4-4.2.13                |    h84186c3_1003         882 KB  conda-forge
    hdf5-1.10.5                |nompi_h3e39495_1104         3.0 MB  conda-forge
    icu-64.2                   |       h6de7cb9_1        12.3 MB  conda-forge
    kealib-1.4.10              |    h6659575_1005         162 KB  conda-forge
    krb5-1.16.4                |       h1752a42_0         1.1 MB  conda-forge
    libdap4-3.20.4             |       habf5908_0        12.7 MB  conda-forge
    libedit-3.1.20170329       |    hcfe32e1_1001         152 KB  conda-forge
    libgdal-3.0.4              |       hf96e369_0        17.2 MB  conda-forge
    libgfortran-4.0.0          |                2         716 KB  conda-forge
    libnetcdf-4.7.3            |nompi_hda4e5f1_101         1.2 MB  conda-forge
    libopenblas-0.3.7          |       h3d69b6c_7         8.2 MB  conda-forge
    libpq-12.1                 |       h31a01ba_0         2.5 MB  conda-forge
    libspatialite-4.3.0a       |    h9c28a66_1034         3.1 MB  conda-forge
    libtiff-4.1.0              |       ha78913b_3         567 KB  conda-forge
    libwebp-1.0.2              |       hd3bf737_5         841 KB  conda-forge
    libxml2-2.9.10             |       h53d96d6_0         1.2 MB  conda-forge
    llvm-openmp-9.0.1          |       h28b9765_2         265 KB  conda-forge
    openjpeg-2.3.1             |       hcdae239_3         377 KB  conda-forge
    pcre-8.43                  |       h4a8c4bd_0         222 KB  conda-forge
    poppler-0.67.0             |       h16886b5_8         1.6 MB  conda-forge
    postgresql-12.1            |       h26bc10f_0         4.5 MB  conda-forge
    proj-6.3.0                 |       h773a61f_0        10.2 MB  conda-forge
    rasterio-1.1.2             |   py37he71f6a4_0         8.1 MB  conda-forge
    tiledb-1.7.0               |       hd5e958f_2         2.3 MB  conda-forge
    tzcode-2019a               |    h01d97ff_1002         429 KB  conda-forge
    xerces-c-3.2.2             |    h8f8adb3_1004         1.5 MB  conda-forge
    zstd-1.4.4                 |       he7fca8b_1         1.0 MB  conda-forge
    ------------------------------------------------------------
                                           Total:       122.6 MB

The following NEW packages will be INSTALLED:

  affine             conda-forge/noarch::affine-2.3.0-py_0
  attrs              conda-forge/noarch::attrs-19.3.0-py_0
  boost-cpp          conda-forge/osx-64::boost-cpp-1.70.0-h75728bb_2
  bzip2              conda-forge/osx-64::bzip2-1.0.8-h0b31af3_2
  cairo              conda-forge/osx-64::cairo-1.16.0-he1c11cd_1002
  cfitsio            conda-forge/osx-64::cfitsio-3.470-h84d2f63_2
  click              conda-forge/noarch::click-7.0-py_0
  click-plugins      conda-forge/noarch::click-plugins-1.1.1-py_0
  cligj              conda-forge/noarch::cligj-0.5.0-py_0
  curl               conda-forge/osx-64::curl-7.68.0-h8754def_0
  expat              conda-forge/osx-64::expat-2.2.9-h4a8c4bd_2
  fontconfig         conda-forge/osx-64::fontconfig-2.13.1-h6b1039f_1001
  freetype           conda-forge/osx-64::freetype-2.10.0-h24853df_1
  freexl             conda-forge/osx-64::freexl-1.0.5-h1de35cc_1002
  geos               conda-forge/osx-64::geos-3.8.0-h4a8c4bd_0
  geotiff            conda-forge/osx-64::geotiff-1.5.1-hc9fff18_8
  gettext            conda-forge/osx-64::gettext-0.19.8.1-h46ab8bc_1002
  giflib             conda-forge/osx-64::giflib-5.2.1-h0b31af3_1
  glib               conda-forge/osx-64::glib-2.58.3-py37h577aef8_1002
  hdf4               conda-forge/osx-64::hdf4-4.2.13-h84186c3_1003
  hdf5               conda-forge/osx-64::hdf5-1.10.5-nompi_h3e39495_1104
  icu                conda-forge/osx-64::icu-64.2-h6de7cb9_1
  jpeg               conda-forge/osx-64::jpeg-9c-h1de35cc_1001
  json-c             conda-forge/osx-64::json-c-0.13.1-h1de35cc_1001
  kealib             conda-forge/osx-64::kealib-1.4.10-h6659575_1005
  krb5               conda-forge/osx-64::krb5-1.16.4-h1752a42_0
  libblas            conda-forge/osx-64::libblas-3.8.0-14_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-14_openblas
  libcurl            conda-forge/osx-64::libcurl-7.68.0-h709d2b2_0
  libdap4            conda-forge/osx-64::libdap4-3.20.4-habf5908_0
  libedit            conda-forge/osx-64::libedit-3.1.20170329-hcfe32e1_1001
  libgdal            conda-forge/osx-64::libgdal-3.0.4-hf96e369_0
  libgfortran        conda-forge/osx-64::libgfortran-4.0.0-2
  libiconv           conda-forge/osx-64::libiconv-1.15-h01d97ff_1005
  libkml             conda-forge/osx-64::libkml-1.3.0-hed7d534_1010
  liblapack          conda-forge/osx-64::liblapack-3.8.0-14_openblas
  libnetcdf          conda-forge/osx-64::libnetcdf-4.7.3-nompi_hda4e5f1_101
  libopenblas        conda-forge/osx-64::libopenblas-0.3.7-h3d69b6c_7
  libpng             conda-forge/osx-64::libpng-1.6.37-h2573ce8_0
  libpq              conda-forge/osx-64::libpq-12.1-h31a01ba_0
  libspatialite      conda-forge/osx-64::libspatialite-4.3.0a-h9c28a66_1034
  libssh2            conda-forge/osx-64::libssh2-1.8.2-hcdc9a53_2
  libtiff            conda-forge/osx-64::libtiff-4.1.0-ha78913b_3
  libwebp            conda-forge/osx-64::libwebp-1.0.2-hd3bf737_5
  libxml2            conda-forge/osx-64::libxml2-2.9.10-h53d96d6_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-9.0.1-h28b9765_2
  lz4-c              conda-forge/osx-64::lz4-c-1.8.3-h6de7cb9_1001
  numpy              conda-forge/osx-64::numpy-1.18.1-py37hde6bac1_0
  openjpeg           conda-forge/osx-64::openjpeg-2.3.1-hcdae239_3
  pcre               conda-forge/osx-64::pcre-8.43-h4a8c4bd_0
  pixman             conda-forge/osx-64::pixman-0.38.0-h01d97ff_1003
  poppler            conda-forge/osx-64::poppler-0.67.0-h16886b5_8
  poppler-data       conda-forge/noarch::poppler-data-0.4.9-1
  postgresql         conda-forge/osx-64::postgresql-12.1-h26bc10f_0
  proj               conda-forge/osx-64::proj-6.3.0-h773a61f_0
  pyparsing          conda-forge/noarch::pyparsing-2.4.6-py_0
  rasterio           conda-forge/osx-64::rasterio-1.1.2-py37he71f6a4_0
  snuggs             conda-forge/noarch::snuggs-1.4.7-py_0
  tbb                conda-forge/osx-64::tbb-2018.0.5-h2d50403_0
  tiledb             conda-forge/osx-64::tiledb-1.7.0-hd5e958f_2
  tzcode             conda-forge/osx-64::tzcode-2019a-h01d97ff_1002
  xerces-c           conda-forge/osx-64::xerces-c-3.2.2-h8f8adb3_1004
  zstd               conda-forge/osx-64::zstd-1.4.4-he7fca8b_1

Proceed ([y]/n)? y

Downloading and Extracting Packages
pcre-8.43            | 222 KB    | #################################################################### | 100%
libspatialite-4.3.0a | 3.1 MB    | #################################################################### | 100%
libopenblas-0.3.7    | 8.2 MB    | #################################################################### | 100%
hdf5-1.10.5          | 3.0 MB    | #################################################################### | 100%
rasterio-1.1.2       | 8.1 MB    | #################################################################### | 100%
boost-cpp-1.70.0     | 19.0 MB   | #################################################################### | 100%
zstd-1.4.4           | 1.0 MB    | #################################################################### | 100%
libwebp-1.0.2        | 841 KB    | #################################################################### | 100%
libgdal-3.0.4        | 17.2 MB   | #################################################################### | 100%
openjpeg-2.3.1       | 377 KB    | #################################################################### | 100%
fontconfig-2.13.1    | 270 KB    | #################################################################### | 100%
glib-2.58.3          | 3.1 MB    | #################################################################### | 100%
postgresql-12.1      | 4.5 MB    | #################################################################### | 100%
cairo-1.16.0         | 1.3 MB    | #################################################################### | 100%
krb5-1.16.4          | 1.1 MB    | #################################################################### | 100%
xerces-c-3.2.2       | 1.5 MB    | #################################################################### | 100%
libgfortran-4.0.0    | 716 KB    | #################################################################### | 100%
libedit-3.1.20170329 | 152 KB    | #################################################################### | 100%
libpq-12.1           | 2.5 MB    | #################################################################### | 100%
libnetcdf-4.7.3      | 1.2 MB    | #################################################################### | 100%
poppler-0.67.0       | 1.6 MB    | #################################################################### | 100%
proj-6.3.0           | 10.2 MB   | #################################################################### | 100%
geos-3.8.0           | 898 KB    | #################################################################### | 100%
expat-2.2.9          | 126 KB    | #################################################################### | 100%
tzcode-2019a         | 429 KB    | #################################################################### | 100%
hdf4-4.2.13          | 882 KB    | #################################################################### | 100%
tiledb-1.7.0         | 2.3 MB    | #################################################################### | 100%
cfitsio-3.470        | 1.4 MB    | #################################################################### | 100%
llvm-openmp-9.0.1    | 265 KB    | #################################################################### | 100%
icu-64.2             | 12.3 MB   | #################################################################### | 100%
kealib-1.4.10        | 162 KB    | #################################################################### | 100%
geotiff-1.5.1        | 125 KB    | #################################################################### | 100%
libxml2-2.9.10       | 1.2 MB    | #################################################################### | 100%
libdap4-3.20.4       | 12.7 MB   | #################################################################### | 100%
giflib-5.2.1         | 64 KB     | #################################################################### | 100%
libtiff-4.1.0        | 567 KB    | #################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Rasterio imports fine.

(rasterio_only) MacBook-Pro:NEON_crown_maps ben$ python
Python 3.7.6 | packaged by conda-forge | (default, Jan  7 2020, 22:05:27)
[Clang 9.0.1 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import rasterio
>>>

But within pyfor conda build it emerges.

MacBook-Pro:NEON_crown_maps ben$ conda create python=3.7 --name pyfor
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.1
  latest version: 4.8.2

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /Users/ben/miniconda3/envs/pyfor

  added / updated specs:
    - python=3.7

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/osx-64::certifi-2019.11.28-py37_0
  libcxx             pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
  libcxxabi          pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.2.1-h475c297_4
  ncurses            pkgs/main/osx-64::ncurses-6.1-h0a44026_1
  openssl            pkgs/main/osx-64::openssl-1.1.1d-h1de35cc_3
  pip                pkgs/main/osx-64::pip-20.0.2-py37_1
  python             pkgs/main/osx-64::python-3.7.6-h359304d_2
  readline           pkgs/main/osx-64::readline-7.0-h1de35cc_5
  setuptools         pkgs/main/osx-64::setuptools-45.1.0-py37_0
  sqlite             pkgs/main/osx-64::sqlite-3.31.1-ha441bb4_0
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  wheel              pkgs/main/osx-64::wheel-0.34.2-py37_0
  xz                 pkgs/main/osx-64::xz-5.2.4-h1de35cc_4
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate pyfor
#
# To deactivate an active environment, use
#
#     $ conda deactivate

MacBook-Pro:NEON_crown_maps ben$ conda activate pyfor
(pyfor) MacBook-Pro:NEON_crown_maps ben$ conda install -c conda-forge pyfor
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.1
  latest version: 4.8.2

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /Users/ben/miniconda3/envs/pyfor

  added / updated specs:
    - pyfor

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2019.11.28         |           py37_0         148 KB  conda-forge
    curl-7.68.0                |       h8754def_0         130 KB  conda-forge
    libblas-3.8.0              |      14_openblas          10 KB  conda-forge
    libcblas-3.8.0             |      14_openblas          10 KB  conda-forge
    liblapack-3.8.0            |      14_openblas          10 KB  conda-forge
    libopenblas-0.3.7          |       hd44dcd8_1         8.4 MB  conda-forge
    matplotlib-2.2.4           |           py37_1           6 KB  conda-forge
    postgresql-11.2            |       h051b688_0         3.2 MB
    tbb-2018.0.5               |       h2d50403_0         150 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        12.1 MB

The following NEW packages will be INSTALLED:

  affine             conda-forge/noarch::affine-2.3.0-py_0
  attrs              conda-forge/noarch::attrs-19.3.0-py_0
  boost-cpp          conda-forge/osx-64::boost-cpp-1.70.0-hd59e818_1
  bzip2              conda-forge/osx-64::bzip2-1.0.8-h0b31af3_2
  cairo              conda-forge/osx-64::cairo-1.16.0-h0ab9d94_1001
  cfitsio            conda-forge/osx-64::cfitsio-3.470-h389770f_2
  click              conda-forge/noarch::click-7.0-py_0
  click-plugins      conda-forge/noarch::click-plugins-1.1.1-py_0
  cligj              conda-forge/noarch::cligj-0.5.0-py_0
  curl               conda-forge/osx-64::curl-7.68.0-h8754def_0
  cycler             conda-forge/noarch::cycler-0.10.0-py_2
  expat              pkgs/main/osx-64::expat-2.2.6-h0a44026_0
  fiona              pkgs/main/osx-64::fiona-1.8.11-py37heeaa653_0
  fontconfig         conda-forge/osx-64::fontconfig-2.13.1-h1027ab8_1000
  freetype           conda-forge/osx-64::freetype-2.10.0-h24853df_1
  freexl             conda-forge/osx-64::freexl-1.0.5-h1de35cc_1002
  gdal               pkgs/main/osx-64::gdal-3.0.2-py37hbe65578_0
  geopandas          conda-forge/noarch::geopandas-0.6.2-py_0
  geos               pkgs/main/osx-64::geos-3.8.0-h0a44026_0
  geotiff            pkgs/main/osx-64::geotiff-1.5.1-h0b0f252_0
  gettext            conda-forge/osx-64::gettext-0.19.8.1-h46ab8bc_1002
  giflib             conda-forge/osx-64::giflib-5.1.7-h01d97ff_1
  glib               conda-forge/osx-64::glib-2.58.3-h9d45998_1002
  hdf4               conda-forge/osx-64::hdf4-4.2.13-hf3c6af0_1002
  hdf5               conda-forge/osx-64::hdf5-1.10.4-nompi_h0cbb7df_1106
  icu                conda-forge/osx-64::icu-58.2-h0a44026_1000
  joblib             conda-forge/noarch::joblib-0.14.1-py_0
  jpeg               conda-forge/osx-64::jpeg-9c-h1de35cc_1001
  json-c             conda-forge/osx-64::json-c-0.13.1-h1de35cc_1001
  kealib             conda-forge/osx-64::kealib-1.4.10-hecf890f_1003
  kiwisolver         conda-forge/osx-64::kiwisolver-1.1.0-py37h770b8ee_0
  krb5               pkgs/main/osx-64::krb5-1.16.4-hddcf347_0
  laspy              conda-forge/noarch::laspy-1.6.0-pyh5ca1d4c_0
  lastools           conda-forge/osx-64::lastools-20171231-h0a44026_1000
  laxpy              conda-forge/noarch::laxpy-0.2.2-py_0
  libblas            conda-forge/osx-64::libblas-3.8.0-14_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-14_openblas
  libcurl            conda-forge/osx-64::libcurl-7.68.0-h709d2b2_0
  libdap4            pkgs/main/osx-64::libdap4-3.19.1-h3d3e54a_0
  libgdal            pkgs/main/osx-64::libgdal-3.0.2-h42cfeda_0
  libgfortran        conda-forge/osx-64::libgfortran-3.0.1-0
  libiconv           conda-forge/osx-64::libiconv-1.15-h01d97ff_1005
  libkml             conda-forge/osx-64::libkml-1.3.0-hed7d534_1010
  liblapack          conda-forge/osx-64::liblapack-3.8.0-14_openblas
  libnetcdf          conda-forge/osx-64::libnetcdf-4.6.2-h6b88ef6_1001
  libopenblas        conda-forge/osx-64::libopenblas-0.3.7-hd44dcd8_1
  libpng             conda-forge/osx-64::libpng-1.6.37-h2573ce8_0
  libpq              pkgs/main/osx-64::libpq-11.2-h051b688_0
  libspatialindex    pkgs/main/osx-64::libspatialindex-1.9.3-h0a44026_0
  libspatialite      pkgs/main/osx-64::libspatialite-4.3.0a-h5142b36_0
  libssh2            conda-forge/osx-64::libssh2-1.8.2-hcdc9a53_2
  libtiff            pkgs/main/osx-64::libtiff-4.1.0-hcb84e12_0
  libxml2            pkgs/main/osx-64::libxml2-2.9.9-hf6e021a_1
  llvmlite           pkgs/main/osx-64::llvmlite-0.31.0-py37h1341992_0
  lz4-c              conda-forge/osx-64::lz4-c-1.8.3-h6de7cb9_1001
  matplotlib         conda-forge/osx-64::matplotlib-2.2.4-py37_1
  matplotlib-base    conda-forge/osx-64::matplotlib-base-2.2.4-py37h31f9439_1
  munch              conda-forge/noarch::munch-2.5.0-py_0
  numba              pkgs/main/osx-64::numba-0.48.0-py37h6c726b0_0
  numpy              conda-forge/osx-64::numpy-1.18.1-py37hde6bac1_0
  openjpeg           conda-forge/osx-64::openjpeg-2.3.1-hdc36067_1
  pandas             conda-forge/osx-64::pandas-0.25.1-py37h86efe34_0
  pcre               pkgs/main/osx-64::pcre-8.43-h0a44026_0
  pixman             conda-forge/osx-64::pixman-0.38.0-h01d97ff_1003
  plyfile            conda-forge/noarch::plyfile-0.7.1-py_0
  poppler            conda-forge/osx-64::poppler-0.67.0-hd5eb092_7
  poppler-data       conda-forge/noarch::poppler-data-0.4.9-1
  postgresql         pkgs/main/osx-64::postgresql-11.2-h051b688_0
  proj               pkgs/main/osx-64::proj-6.2.1-hfd5b9e3_0
  pyfor              conda-forge/noarch::pyfor-0.3.6-py_0
  pyparsing          conda-forge/noarch::pyparsing-2.4.6-py_0
  pyproj             conda-forge/osx-64::pyproj-2.4.2.post1-py37h03a428a_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  pytz               conda-forge/noarch::pytz-2019.3-py_0
  rasterio           pkgs/main/osx-64::rasterio-1.1.0-py37heeaa653_0
  rtree              conda-forge/osx-64::rtree-0.9.3-py37h7b0cdae_0
  scipy              conda-forge/osx-64::scipy-1.2.1-py37hbd7caa9_1
  shapely            conda-forge/osx-64::shapely-1.7.0-py37h999ffa5_0
  six                conda-forge/osx-64::six-1.14.0-py37_0
  snuggs             conda-forge/noarch::snuggs-1.4.7-py_0
  tbb                conda-forge/osx-64::tbb-2018.0.5-h2d50403_0
  tiledb             pkgs/main/osx-64::tiledb-1.6.3-h29f752d_0
  tornado            conda-forge/osx-64::tornado-6.0.3-py37h0b31af3_0
  xerces-c           conda-forge/osx-64::xerces-c-3.2.2-h4db8090_1003
  zstd               pkgs/main/osx-64::zstd-1.3.7-h5bba6e5_0

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates     pkgs/main::ca-certificates-2020.1.1-0 --> conda-forge::ca-certificates-2019.11.28-hecc5488_0
  certifi                                         pkgs/main --> conda-forge
  openssl              pkgs/main::openssl-1.1.1d-h1de35cc_3 --> conda-forge::openssl-1.1.1d-h0b31af3_0

Proceed ([y]/n)? y

Downloading and Extracting Packages
postgresql-11.2      | 3.2 MB    | #################################################################### | 100%
libopenblas-0.3.7    | 8.4 MB    | #################################################################### | 100%
certifi-2019.11.28   | 148 KB    | #################################################################### | 100%
libcblas-3.8.0       | 10 KB     | #################################################################### | 100%
curl-7.68.0          | 130 KB    | #################################################################### | 100%
libblas-3.8.0        | 10 KB     | #################################################################### | 100%
tbb-2018.0.5         | 150 KB    | #################################################################### | 100%
liblapack-3.8.0      | 10 KB     | #################################################################### | 100%
matplotlib-2.2.4     | 6 KB      | #################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(pyfor) MacBook-Pro:NEON_crown_maps ben$ python
Python 3.7.6 (default, Jan  8 2020, 13:42:34)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyfor
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/ben/miniconda3/envs/pyfor/lib/python3.7/site-packages/pyfor/__init__.py", line 5, in <module>
    from pyfor import cloud
  File "/Users/ben/miniconda3/envs/pyfor/lib/python3.7/site-packages/pyfor/cloud.py", line 7, in <module>
    from pyfor import rasterizer
  File "/Users/ben/miniconda3/envs/pyfor/lib/python3.7/site-packages/pyfor/rasterizer.py", line 5, in <module>
    from pyfor import gisexport
  File "/Users/ben/miniconda3/envs/pyfor/lib/python3.7/site-packages/pyfor/gisexport.py", line 2, in <module>
    import rasterio
  File "/Users/ben/miniconda3/envs/pyfor/lib/python3.7/site-packages/rasterio/__init__.py", line 22, in <module>
    from rasterio._base import gdal_version
ImportError: dlopen(/Users/ben/miniconda3/envs/pyfor/lib/python3.7/site-packages/rasterio/_base.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libpoppler.76.dylib
  Referenced from: /Users/ben/miniconda3/envs/pyfor/lib/libgdal.26.dylib
  Reason: image not found

There was an earlier issue that seems to be resolved for this same issue. @lwasser (hi! go earth lab/NEON) any recent problems? https://github.com/conda-forge/rasterio-feedstock/issues/118

My interpretation is something about the pyfor conda forge build is conflicting with gdal and rasterio. All ideas welcome.

bw4sz commented 4 years ago

Something to do with cache. Hard to pin down, but its solved, hopefully save some time for someone else. I was only 1 minor version off up conda latest, but who knows.

conda update conda
conda clean --all
MacBook-Pro:NEON_crown_maps ben$ conda create python=3.7 --name test
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/ben/miniconda3/envs/test

  added / updated specs:
    - python=3.7

The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2019.11.28-hecc5488_0
  certifi            conda-forge/osx-64::certifi-2019.11.28-py37_0
  libcxx             conda-forge/osx-64::libcxx-9.0.1-1
  libffi             conda-forge/osx-64::libffi-3.2.1-h6de7cb9_1006
  ncurses            conda-forge/osx-64::ncurses-6.1-h0a44026_1002
  openssl            conda-forge/osx-64::openssl-1.1.1d-h0b31af3_0
  pip                conda-forge/noarch::pip-20.0.2-py_2
  python             conda-forge/osx-64::python-3.7.6-h5c2c468_2
  readline           conda-forge/osx-64::readline-8.0-hcfe32e1_0
  setuptools         conda-forge/osx-64::setuptools-45.1.0-py37_0
  sqlite             conda-forge/osx-64::sqlite-3.30.1-h93121df_0
  tk                 conda-forge/osx-64::tk-8.6.10-hbbe82c9_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xz                 conda-forge/osx-64::xz-5.2.4-h1de35cc_1001
  zlib               conda-forge/osx-64::zlib-1.2.11-h0b31af3_1006

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate test
#
# To deactivate an active environment, use
#
#     $ conda deactivate

MacBook-Pro:NEON_crown_maps ben$ conda activate test
(test) MacBook-Pro:NEON_crown_maps ben$ conda install -c conda-forge pyfor
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/ben/miniconda3/envs/test

  added / updated specs:
    - pyfor

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    fiona-1.8.13               |   py37he71f6a4_0         1.0 MB  conda-forge
    gdal-3.0.4                 |   py37h97c3584_0         1.5 MB  conda-forge
    kiwisolver-1.1.0           |   py37ha1b3eb9_0          56 KB  conda-forge
    libspatialindex-1.9.3      |       h4a8c4bd_1         397 KB  conda-forge
    llvmlite-0.31.0            |   py37h05045ef_0         250 KB  conda-forge
    matplotlib-3.1.3           |           py37_0           7 KB  conda-forge
    matplotlib-base-3.1.3      |   py37h11da6c2_0         6.6 MB  conda-forge
    numba-0.48.0               |   py37h4f17bb1_0         3.2 MB  conda-forge
    pandas-1.0.1               |   py37h4f17bb1_0        10.1 MB  conda-forge
    pyproj-2.4.2.post1         |   py37hf8af742_1         308 KB  conda-forge
    scipy-1.4.1                |   py37h82752d6_0        18.9 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        42.3 MB

The following NEW packages will be INSTALLED:

  affine             conda-forge/noarch::affine-2.3.0-py_0
  attrs              conda-forge/noarch::attrs-19.3.0-py_0
  boost-cpp          conda-forge/osx-64::boost-cpp-1.70.0-h75728bb_2
  bzip2              conda-forge/osx-64::bzip2-1.0.8-h0b31af3_2
  cairo              conda-forge/osx-64::cairo-1.16.0-he1c11cd_1002
  cfitsio            conda-forge/osx-64::cfitsio-3.470-h84d2f63_2
  click              conda-forge/noarch::click-7.0-py_0
  click-plugins      conda-forge/noarch::click-plugins-1.1.1-py_0
  cligj              conda-forge/noarch::cligj-0.5.0-py_0
  curl               conda-forge/osx-64::curl-7.68.0-h8754def_0
  cycler             conda-forge/noarch::cycler-0.10.0-py_2
  expat              conda-forge/osx-64::expat-2.2.9-h4a8c4bd_2
  fiona              conda-forge/osx-64::fiona-1.8.13-py37he71f6a4_0
  fontconfig         conda-forge/osx-64::fontconfig-2.13.1-h6b1039f_1001
  freetype           conda-forge/osx-64::freetype-2.10.0-h24853df_1
  freexl             conda-forge/osx-64::freexl-1.0.5-h1de35cc_1002
  gdal               conda-forge/osx-64::gdal-3.0.4-py37h97c3584_0
  geopandas          conda-forge/noarch::geopandas-0.6.2-py_0
  geos               conda-forge/osx-64::geos-3.8.0-h4a8c4bd_0
  geotiff            conda-forge/osx-64::geotiff-1.5.1-hc9fff18_8
  gettext            conda-forge/osx-64::gettext-0.19.8.1-h46ab8bc_1002
  giflib             conda-forge/osx-64::giflib-5.2.1-h0b31af3_1
  glib               conda-forge/osx-64::glib-2.58.3-py37h577aef8_1002
  hdf4               conda-forge/osx-64::hdf4-4.2.13-h84186c3_1003
  hdf5               conda-forge/osx-64::hdf5-1.10.5-nompi_h3e39495_1104
  icu                conda-forge/osx-64::icu-64.2-h6de7cb9_1
  joblib             conda-forge/noarch::joblib-0.14.1-py_0
  jpeg               conda-forge/osx-64::jpeg-9c-h1de35cc_1001
  json-c             conda-forge/osx-64::json-c-0.13.1-h1de35cc_1001
  kealib             conda-forge/osx-64::kealib-1.4.10-h6659575_1005
  kiwisolver         conda-forge/osx-64::kiwisolver-1.1.0-py37ha1b3eb9_0
  krb5               conda-forge/osx-64::krb5-1.16.4-h1752a42_0
  laspy              conda-forge/noarch::laspy-1.6.0-pyh5ca1d4c_0
  lastools           conda-forge/osx-64::lastools-20171231-h0a44026_1000
  laxpy              conda-forge/noarch::laxpy-0.2.2-py_0
  libblas            conda-forge/osx-64::libblas-3.8.0-14_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-14_openblas
  libcurl            conda-forge/osx-64::libcurl-7.68.0-h709d2b2_0
  libdap4            conda-forge/osx-64::libdap4-3.20.4-habf5908_0
  libedit            conda-forge/osx-64::libedit-3.1.20170329-hcfe32e1_1001
  libgdal            conda-forge/osx-64::libgdal-3.0.4-hf96e369_0
  libgfortran        conda-forge/osx-64::libgfortran-4.0.0-2
  libiconv           conda-forge/osx-64::libiconv-1.15-h01d97ff_1005
  libkml             conda-forge/osx-64::libkml-1.3.0-hed7d534_1010
  liblapack          conda-forge/osx-64::liblapack-3.8.0-14_openblas
  libllvm8           conda-forge/osx-64::libllvm8-8.0.1-h770b8ee_0
  libnetcdf          conda-forge/osx-64::libnetcdf-4.7.3-nompi_hda4e5f1_101
  libopenblas        conda-forge/osx-64::libopenblas-0.3.7-h3d69b6c_7
  libpng             conda-forge/osx-64::libpng-1.6.37-h2573ce8_0
  libpq              conda-forge/osx-64::libpq-12.1-h31a01ba_0
  libspatialindex    conda-forge/osx-64::libspatialindex-1.9.3-h4a8c4bd_1
  libspatialite      conda-forge/osx-64::libspatialite-4.3.0a-h9c28a66_1034
  libssh2            conda-forge/osx-64::libssh2-1.8.2-hcdc9a53_2
  libtiff            conda-forge/osx-64::libtiff-4.1.0-ha78913b_3
  libwebp            conda-forge/osx-64::libwebp-1.0.2-hd3bf737_5
  libxml2            conda-forge/osx-64::libxml2-2.9.10-h53d96d6_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-9.0.1-h28b9765_2
  llvmlite           conda-forge/osx-64::llvmlite-0.31.0-py37h05045ef_0
  lz4-c              conda-forge/osx-64::lz4-c-1.8.3-h6de7cb9_1001
  matplotlib         conda-forge/osx-64::matplotlib-3.1.3-py37_0
  matplotlib-base    conda-forge/osx-64::matplotlib-base-3.1.3-py37h11da6c2_0
  munch              conda-forge/noarch::munch-2.5.0-py_0
  numba              conda-forge/osx-64::numba-0.48.0-py37h4f17bb1_0
  numpy              conda-forge/osx-64::numpy-1.18.1-py37hde6bac1_0
  openjpeg           conda-forge/osx-64::openjpeg-2.3.1-hcdae239_3
  pandas             conda-forge/osx-64::pandas-1.0.1-py37h4f17bb1_0
  pcre               conda-forge/osx-64::pcre-8.43-h4a8c4bd_0
  pixman             conda-forge/osx-64::pixman-0.38.0-h01d97ff_1003
  plyfile            conda-forge/noarch::plyfile-0.7.1-py_0
  poppler            conda-forge/osx-64::poppler-0.67.0-h16886b5_8
  poppler-data       conda-forge/noarch::poppler-data-0.4.9-1
  postgresql         conda-forge/osx-64::postgresql-12.1-h26bc10f_0
  proj               conda-forge/osx-64::proj-6.3.0-h773a61f_0
  pyfor              conda-forge/noarch::pyfor-0.3.6-py_0
  pyparsing          conda-forge/noarch::pyparsing-2.4.6-py_0
  pyproj             conda-forge/osx-64::pyproj-2.4.2.post1-py37hf8af742_1
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  pytz               conda-forge/noarch::pytz-2019.3-py_0
  rasterio           conda-forge/osx-64::rasterio-1.1.2-py37he71f6a4_0
  rtree              conda-forge/osx-64::rtree-0.9.3-py37h7b0cdae_0
  scipy              conda-forge/osx-64::scipy-1.4.1-py37h82752d6_0
  shapely            conda-forge/osx-64::shapely-1.7.0-py37h999ffa5_0
  six                conda-forge/osx-64::six-1.14.0-py37_0
  snuggs             conda-forge/noarch::snuggs-1.4.7-py_0
  tbb                conda-forge/osx-64::tbb-2018.0.5-h2d50403_0
  tiledb             conda-forge/osx-64::tiledb-1.7.0-hd5e958f_2
  tornado            conda-forge/osx-64::tornado-6.0.3-py37h0b31af3_0
  tzcode             conda-forge/osx-64::tzcode-2019a-h01d97ff_1002
  xerces-c           conda-forge/osx-64::xerces-c-3.2.2-h8f8adb3_1004
  zstd               conda-forge/osx-64::zstd-1.4.4-he7fca8b_1

Proceed ([y]/n)? y

Downloading and Extracting Packages
matplotlib-3.1.3     | 7 KB      | #################################################################### | 100%
numba-0.48.0         | 3.2 MB    | #################################################################### | 100%
libspatialindex-1.9. | 397 KB    | #################################################################### | 100%
fiona-1.8.13         | 1.0 MB    | #################################################################### | 100%
llvmlite-0.31.0      | 250 KB    | #################################################################### | 100%
pyproj-2.4.2.post1   | 308 KB    | #################################################################### | 100%
kiwisolver-1.1.0     | 56 KB     | #################################################################### | 100%
pandas-1.0.1         | 10.1 MB   | #################################################################### | 100%
matplotlib-base-3.1. | 6.6 MB    | #################################################################### | 100%
scipy-1.4.1          | 18.9 MB   | #################################################################### | 100%
gdal-3.0.4           | 1.5 MB    | #################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(test) MacBook-Pro:NEON_crown_maps ben$ python
Python 3.7.6 | packaged by conda-forge | (default, Jan  7 2020, 22:05:27)
[Clang 9.0.1 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyfor
>>> import rasterio
>>> quit()

Success.

brycefrank commented 4 years ago

Thanks Ben!

I may have time to look at this next month. Glad it is resolved all the same. The conda-forge stuff has been a very steep learning curve.

bw4sz commented 4 years ago

Just as a heads up, I also needed to downgrade the numpy version to get laspy to work.

(test) MacBook-Pro:NEON_crown_maps ben$ conda install  numpy==1.16.4
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/ben/miniconda3/envs/test

  added / updated specs:
    - numpy==1.16.4

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    numpy-1.16.4               |   py37h6b0580a_0         4.1 MB
 conda-forge
    ------------------------------------------------------------
                                           Total:         4.1 MB

The following packages will be DOWNGRADED:

  numpy                               1.18.1-py37hde6bac1_0 -->
1.16.4-py37h6b0580a_0

Proceed ([y]/n)? y

Downloading and Extracting Packages
numpy-1.16.4         | 4.1 MB    |
#################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

seems to be a known thing. https://github.com/laspy/laspy/issues/112

You might want to set a numpy== in the setup.py or conda yml.

On Thu, Feb 6, 2020 at 3:58 PM Bryce Frank notifications@github.com wrote:

Thanks Ben!

I may have time to look at this next month. Glad it is resolved all the same. The conda-forge stuff has been a very steep learning curve.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/brycefrank/pyfor/issues/78?email_source=notifications&email_token=AAJHBLEWJ6V3BIJMITZMIJLRBSPY7A5CNFSM4KRFLV42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELBHNGI#issuecomment-583169689, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJHBLGWOI5BF6BXQBLTMZLRBSPY7ANCNFSM4KRFLV4Q .

-- Ben Weinstein, Ph.D. Postdoctoral Fellow University of Florida http://benweinstein.weebly.com/

brycefrank commented 4 years ago

Going to re-open, I will take a closer look in the coming weeks

lwasser commented 4 years ago

hi @bw4sz et al 👋 👋 👋 👋 !! fingers crossed ...gdal has been behaving nicely for me lately and i have been using rasterio and updating environments without any issue. if for some reason i notice any other bugs however i will let you guys know because i haven't done a bit envt update in maybe a week or so? I hope this can be resolved!! i know gdal installs w python can be super tricky!!

bw4sz commented 4 years ago

Confirmed that I had to downgrade to numpy 1.16.4 from numpy 1.18 on a second machine. This time a linux HPC machine.

BilyBrown commented 1 year ago

Hello, I think I am experiencing a similar issue with Laspy v2.4.1 Reading into it it looks like some issue with Laspy v2 broke some of the functionality of Laspy v1. After running:

import pyfor

tile = pyfor.cloud.Cloud(r"C:\Users\****\Documents\python_scripts\las-trial\laz\20120310_scdnr_mccormick_6716_01.las")

print(tile)

I get this error:

laspy.errors.LaspyException: You are using laspy 2.0, which has several improvements over 1.x
            but with several breaking changes.
            To stay on laspy 1.x: `pip install laspy<2.0.0`

            In short:
              - To read a file do: las = laspy.read('somefile.laz')
              - To create a new LAS data do: las = laspy.create(point_format=2, file_version='1.2')
              - To write a file previously read or created: las.write('somepath.las')
            See the documentation for more information about the changes https://laspy.readthedocs.io/en/latest/