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Hello,

When I did "make rebuild", got the following error. Could you please help with that? Thanks.



rm -rfv build
removed 'build/polymer/polymer_main.c'
removed 'build/polymer/fresnel.c'
removed 'build/polymer/clut.c'
removed 'build/polymer/neldermead.html'
removed 'build/polymer/neldermead.c'
removed 'build/polymer/clut.html'
removed directory 'build/polymer'
removed directory 'build'
rm -fv polymer/*.so
auxdata/common/no2_climatology.hdf: OK
auxdata/common/trop_f_no2_200m.hdf: OK
auxdata/common/morel_fq.dat: OK
auxdata/common/AboveRrs_gCoef_w0.dat: OK
auxdata/common/AboveRrs_gCoef_w10.dat: OK
auxdata/common/AboveRrs_gCoef_w5.dat: OK
auxdata/common/aph_bricaud_1995.txt: OK
auxdata/common/aph_bricaud_1998.txt: OK
auxdata/common/morel_buiteveld_bsw.txt: OK
auxdata/common/palmer74.dat: OK
auxdata/common/pope97.dat: OK
auxdata/common/raman_westberry13.txt: OK
auxdata/common/astarmin_average_2015_SLSTR.txt: OK
auxdata/common/astarmin_average.txt: OK
auxdata/common/Matsuoka11_aphy_Table1_JGR.csv: OK
auxdata/common/SOLAR_SPECTRUM_WMO_86: OK
auxdata/common/k_oz.csv: OK
auxdata/generic/LUT.hdf: OK
auxdata/meris/smile/v2/sun_spectral_flux_rr.txt: OK
auxdata/meris/smile/v2/central_wavelen_rr.txt: OK
auxdata/meris/smile/v2/sun_spectral_flux_fr.txt: OK
auxdata/meris/smile/v2/central_wavelen_fr.txt: OK
auxdata/modisa/HMODISA_RSRs.txt: OK
auxdata/seawifs/SeaWiFS_RSRs.txt: OK
auxdata/viirs/VIIRSN_IDPSv3_RSRs.txt: OK
auxdata/msi/S2-SRF_COPE-GSEG-EOPG-TN-15-0007_3.0_S2A.csv: OK
auxdata/msi/S2-SRF_COPE-GSEG-EOPG-TN-15-0007_3.0_S2B.csv: OK
auxdata/oli/Ball_BA_RSR.v1.2.xlsx: OK
python setup.py build_ext --inplace
Compiling polymer/clut.pyx because it changed.
Compiling polymer/neldermead.pyx because it changed.
Compiling polymer/polymer_main.pyx because it changed.
Compiling polymer/water.pyx because it changed.
[1/4] Cythonizing polymer/clut.pyx
/accounts/mzhang11/anaconda3/lib/python3.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /accounts/mzhang11/Rsdata/MODIS/POLYMER/polymer-v4.13/polymer-v4.13/polymer/clut.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
[2/4] Cythonizing polymer/neldermead.pyx
/accounts/mzhang11/anaconda3/lib/python3.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /accounts/mzhang11/Rsdata/MODIS/POLYMER/polymer-v4.13/polymer-v4.13/polymer/neldermead.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
[3/4] Cythonizing polymer/polymer_main.pyx
/accounts/mzhang11/anaconda3/lib/python3.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /accounts/mzhang11/Rsdata/MODIS/POLYMER/polymer-v4.13/polymer-v4.13/polymer/polymer_main.pyx
tree = Parsing.p_module(s, pxd, full_module_name)

Error compiling Cython file:
------------------------------------------------------------
...
# calculate model reflectance at nadir
self.f.init_pixel(
Rprime[i,j,:],
Rprime_noglint[i,j,:],
A[i,j,:,:], pA[i,j,:,:],
if self.normalize:
^
------------------------------------------------------------

polymer/polymer_main.pyx:573:16: Expected an identifier or literal
Traceback (most recent call last):
File "setup.py", line 29, in <module>
annotate=ANNOTATE,
File "/accounts/mzhang11/anaconda3/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1097, in cythonize
cythonize_one(*args)
File "/accounts/mzhang11/anaconda3/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1220, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: polymer/polymer_main.pyx
makefile:9: recipe for target 'main' failed
make: *** [main] Error 1

Hi jared,

These lines of code don't appear like this in the code. Did you modify the source code ?
Cheers,
François

Hi François,

Thanks for your reply. I downloaded the polymer package again and that error disappears. But when I run install-anaconda-deps.sh, got the following error. Sorry for the long error message.
Jared



The following command will be executed:
mamba install -c conda-forge python=3 cython numpy pyhdf scipy netcdf4 pandas pyepr glymur pyproj lxml gdal pygrib bioconda::ecmwfapi cdsapi xarray urllib3 pytest

Getting https://conda.anaconda.org/conda-forge/linux-64
Getting https://conda.anaconda.org/conda-forge/noarch
Getting https://repo.anaconda.com/pkgs/main/linux-64
Getting https://repo.anaconda.com/pkgs/main/noarch
Getting https://repo.anaconda.com/pkgs/r/linux-64
Getting https://repo.anaconda.com/pkgs/r/noarch

Looking for: ['python 3.*', 'cython', 'numpy', 'pyhdf', 'scipy', 'netcdf4', 'pandas', 'pyepr', 'glymur', 'pyproj', 'lxml', 'gdal', 'pygrib', 'ecmwfapi', 'cdsapi', 'xarray', 'urllib3', 'pytest']

Parsing /accounts/mzhang11/anaconda3/pkgs/cache/497deca9.json
184193 packages in https://conda.anaconda.org/conda-forge/linux-64
Parsing /accounts/mzhang11/anaconda3/pkgs/cache/09cdf8bf.json
57416 packages in https://conda.anaconda.org/conda-forge/noarch
Parsing /accounts/mzhang11/anaconda3/pkgs/cache/47929eba.json
22051 packages in https://repo.anaconda.com/pkgs/main/linux-64
Parsing /accounts/mzhang11/anaconda3/pkgs/cache/3e39a7aa.json
3532 packages in https://repo.anaconda.com/pkgs/main/noarch
Parsing /accounts/mzhang11/anaconda3/pkgs/cache/2ce54b42.json
6620 packages in https://repo.anaconda.com/pkgs/r/linux-64
Parsing /accounts/mzhang11/anaconda3/pkgs/cache/4ea078d6.json
5025 packages in https://repo.anaconda.com/pkgs/r/noarch
Allowing downgrade: 1
Creating the solver...
Job: (python >= 3 with python < 4)
Job: cython
Job: numpy
Job: pyhdf
Job: scipy
Job: netcdf4
Job: pandas
Job: pyepr
Job: glymur
Job: pyproj
Job: lxml
Job: gdal
Job: pygrib
Job: ecmwfapi
Job: cdsapi
Job: xarray
Job: urllib3
Job: pytest

Encountered 2 problems.

Problem: package ecmwfapi does not exist
Problem: nothing provides (python_abi[*_cp27mu] >= 2.7 with python_abi[*_cp27mu] < 2.8) needed by pyepr-1.0.0.0-py27h516909a_0

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
File "/accounts/mzhang11/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/accounts/mzhang11/anaconda3/lib/python3.7/site-packages/mamba/mamba.py", line 250, in _wrapped_main
exit_code = do_call(args, p)
File "/accounts/mzhang11/anaconda3/lib/python3.7/site-packages/mamba/mamba.py", line 229, in do_call
exit_code = install(args, parser, 'install')
File "/accounts/mzhang11/anaconda3/lib/python3.7/site-packages/mamba/mamba.py", line 152, in install
to_link, to_unlink = api.solve(channel_json, installed_json_f.name, specs, strict_priority)
RuntimeError: Encountered problems while solving.

`$ /accounts/mzhang11/anaconda3/bin/mamba install -c conda-forge python=3 cython numpy pyhdf scipy netcdf4 pandas pyepr glymur pyproj lxml gdal pygrib bioconda::ecmwfapi cdsapi xarray urllib3 pytest`

environment variables:
CIO_TEST=<not set>
CONDA_DEFAULT_ENV=base
CONDA_EXE=/accounts/mzhang11/anaconda3/bin/conda
CONDA_PREFIX=/accounts/mzhang11/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/accounts/mzhang11/anaconda3/bin/python
CONDA_ROOT=/accounts/mzhang11/anaconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
LD_LIBRARY_PATH=
PATH=/accounts/mzhang11/software/seadas-7.5.3/bin:/accounts/mzhang11/softwa
re/jdk1.8.0_111/bin:/accounts/mzhang11/software/cmake-3.20.0-rc2-linux
-x86_64/bin:/accounts/mzhang11/software/seadas-7.5.3/bin:/accounts/mzh
ang11/software/jdk1.8.0_111/bin:/accounts/mzhang11/ocssw/opt/bin:/acco
unts/mzhang11/ocssw/bin:/accounts/mzhang11/software/cmake-3.20.0-rc2-l
inux-x86_64/bin:/accounts/mzhang11/anaconda3/bin:/accounts/mzhang11/an
aconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sb
in:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-12-ora
cle/bin:/usr/lib/jvm/java-12-oracle/db/bin:/usr/lib/jvm/java-12-oracle
/bin:/usr/lib/jvm/java-12-oracle/db/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=/ssl/cacert.pem
UBUNTU_MENUPROXY=<set>

active environment : base
active env location : /accounts/mzhang11/anaconda3
shell level : 1
user config file : /accounts/mzhang11/.condarc
populated config files :
conda version : 4.10.1
conda-build version : 3.17.8
python version : 3.7.3.final.0
virtual packages : __linux=4.15.0=0
__glibc=2.27=0
__unix=0=0
__archspec=1=x86_64
base environment : /accounts/mzhang11/anaconda3 (writable)
conda av data dir : /accounts/mzhang11/anaconda3/etc/conda
conda av metadata url : https://repo.anaconda.com/pkgs/main
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /accounts/mzhang11/anaconda3/pkgs
/accounts/mzhang11/.conda/pkgs
envs directories : /accounts/mzhang11/anaconda3/envs
/accounts/mzhang11/.conda/envs
platform : linux-64
user-agent : conda/4.10.1 requests/2.21.0 CPython/3.7.3 Linux/4.15.0-140-generic ubuntu/18.04.5 glibc/2.27
UID:GID : 415801708:415801708
netrc file : /accounts/mzhang11/.netrc
offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?

Hi François,

I am sorry but please ignore my last error messages, which disappear after I reinstalled the anaconda. Thanks.
Jared