pyfor
pyfor copied to clipboard
Published
20 hours ago •
brycefrank
brycefrank
Conda forge gdal issue
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.
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.
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.
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 [email protected] 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/
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!!
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.
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/
