Khris
Reputation: 3212
Fail to install basemap 1.2.1 with conda due to package conflicts, how to resolve?
I installed Basemap on Conda (Win 10 64, Python 3.7.3) in a non-root environment but I ended up with the problem that there is no epsg in the proj folder. Following the advice from github I found out I had version 1.2.0 and tried to install 1.2.1 without success.
EDIT: Apparently it is an incompatibility issue with proj as can be seen when trying this:
conda create -n test python proj basemap=1.2.1 -c defaults -c conda-forge
First I set channel conda-forge to highest priority and half of my environment got updated due to this, Basemap didn't however.
Then I tried to force an install of 1.2.1 which lead to a detailed report of what packages are in conflict with each other:
Package llvm-meta conflicts for:
arrow-cpp -> numpy[version='>=1.16,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
parquet-cpp -> arrow-cpp=0.5 -> numpy[version='>=1.16,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
fastparquet -> numpy[version='>=1.11'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
statsmodels -> numpy=1.11 -> libblas[version='>=3.8.0,<4.0a0'] -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
pandas -> numpy[version='>=1.11.*'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
wordcloud -> numpy -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
mkl-service -> numpy[version='>=1.11.3,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
bokeh -> numpy[version='>=1.7.1'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
blas -> openblas -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
nltk -> numpy -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
liblapack -> libblas==3.8.0=14_openblas -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
matplotlib-base -> numpy[version='>=1.14.6,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
scipy -> blas==1.0=mkl -> libblas==3.8.0=10_mkl -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
libblas -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
scikit-learn -> libcblas[version='>=3.8.0,<4.0a0'] -> libblas==3.8.0=14_openblas -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
basemap=1.2.1 -> numpy[version='>=1.14.6,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
seaborn -> numpy -> libblas[version='>=3.8.0,<4.0a0'] -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
pyarrow -> numpy=1.11 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
libcblas -> libblas==3.8.0=14_openblas -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
matplotlib -> numpy -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
patsy -> numpy[version='>=1.4.0'] -> libblas[version='>=3.8.0,<4.0a0'] -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
numba -> numpy[version='>=1.11,<1.12.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
numpy -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> llvm-meta[version='5.0.0|5.0.0.*']
Package clangdev conflicts for:
libblas -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
basemap=1.2.1 -> numpy[version='>=1.14.6,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
scikit-learn -> libcblas[version='>=3.8.0,<4.0a0'] -> libblas==3.8.0=14_openblas -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
matplotlib-base -> numpy[version='>=1.14.6,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
seaborn -> numpy -> libblas[version='>=3.8.0,<4.0a0'] -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
blas -> openblas -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
libcblas -> libblas==3.8.0=14_openblas -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
bokeh -> numpy[version='>=1.7.1'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
wordcloud -> numpy -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
matplotlib -> numpy -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
fastparquet -> numpy[version='>=1.11'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
numpy -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
numba -> numpy[version='>=1.11,<1.12.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
nltk -> numpy -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
scipy -> blas==1.0=mkl -> libblas==3.8.0=10_mkl -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
mkl-service -> numpy[version='>=1.11.3,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
pyarrow -> numpy=1.11 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
parquet-cpp -> arrow-cpp=0.5 -> numpy[version='>=1.16,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
pandas -> numpy[version='>=1.11.*'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
liblapack -> libblas==3.8.0=14_openblas -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
arrow-cpp -> numpy[version='>=1.16,<2.0a0'] -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
statsmodels -> numpy=1.11 -> libblas[version='>=3.8.0,<4.0a0'] -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
patsy -> numpy[version='>=1.4.0'] -> libblas[version='>=3.8.0,<4.0a0'] -> libopenblas==0.3.7=h29e5d5d_0 -> libflang[version='>=5.0.0'] -> openmp==5.0.0 -> clangdev[version='5.0.0|5.0.0.*']
I'm at a loss what I should do next, neither llvm-meta nor clangdev are even installed in the environment, so why are there conflicts with non-existing packages?
When installing Basemap 1.2.0 none of those packages are installed either, so unless dependencies changed in version 1.2.1 this makes no sense to me.
I also have no idea which github to report this to, any advice would be helpful.
Here's the output of conda list:
# Name Version Build Channel
alabaster 0.7.12 py_0 conda-forge
arrow-cpp 0.15.0 py37h5c295ed_0 conda-forge
asn1crypto 1.2.0 py37_0 conda-forge
astroid 2.3.2 py37_0 conda-forge
attrs 19.3.0 py_0 conda-forge
babel 2.7.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
beautifulsoup4 4.8.1 py37_0 conda-forge
blas 1.0 mkl
bleach 3.1.0 py_0 conda-forge
bokeh 1.3.4 py37_0 conda-forge
boost-cpp 1.70.0 h6a4c333_2 conda-forge
brotli 1.0.7 he025d50_1000 conda-forge
bzip2 1.0.8 hfa6e2cd_1 conda-forge
c-ares 1.15.0 h2fa13f4_1001 conda-forge
ca-certificates 2019.9.11 hecc5488_0 conda-forge
certifi 2019.6.16 py37_1 conda-forge
cffi 1.13.1 py37hb32ad35_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
cloudpickle 1.2.2 py_0 conda-forge
colorama 0.4.1 py_0 conda-forge
console_shortcut 0.1.1 3
cryptography 2.7 py37hb32ad35_0 conda-forge
cycler 0.10.0 py_2 conda-forge
cython 0.29.13 py37h6538335_0 conda-forge
decorator 4.4.1 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
docopt 0.6.2 pypi_0 pypi
docutils 0.15.2 py37_0 conda-forge
double-conversion 3.1.5 h6538335_1 conda-forge
easyprocess 0.2.7 pypi_0 pypi
entrypoints 0.3 py37_1000 conda-forge
et_xmlfile 1.0.1 py_1001 conda-forge
fastcache 1.1.0 py37hfa6e2cd_0 conda-forge
fastparquet 0.3.2 py37hc8d92b1_0 conda-forge
freetype 2.10.0 h563cfd7_1 conda-forge
future 0.18.1 py37_0 conda-forge
fuzzywuzzy 0.17.0 py_0 conda-forge
gflags 2.2.2 he025d50_1002 conda-forge
glog 0.4.0 he025d50_1 conda-forge
googletrans 2.4.0 pypi_0 pypi
grpc-cpp 1.23.0 h4d7d3fa_0 conda-forge
hdfs 2.5.8 pypi_0 pypi
ibm_db 3.0.1 py37hfa6e2cd_1 conda-forge
icc_rt 2019.0.0 h0cc432a_1
icu 64.2 he025d50_1 conda-forge
idna 2.8 py37_1000 conda-forge
imagesize 1.1.0 py_0 conda-forge
importlib_metadata 0.23 py37_0 conda-forge
intel-openmp 2019.4 245
ipykernel 5.1.3 py37h5ca1d4c_0 conda-forge
ipython 7.9.0 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
isort 4.3.21 py37_0 conda-forge
jdcal 1.4.1 py_0 conda-forge
jedi 0.15.1 py37_0 conda-forge
jinja2 2.10.3 py_0 conda-forge
joblib 0.14.0 py_0 conda-forge
jpeg 9c hfa6e2cd_1001 conda-forge
jsonschema 3.1.1 py37_0 conda-forge
jupyter_client 5.3.3 py37_1 conda-forge
jupyter_core 4.5.0 py_0 conda-forge
keyring 19.2.0 py37_0 conda-forge
kiwisolver 1.1.0 py37he980bc4_0 conda-forge
langid 1.1.6 pypi_0 pypi
lazy-object-proxy 1.4.3 py37hfa6e2cd_0 conda-forge
libblas 3.8.0 14_mkl conda-forge
libcblas 3.8.0 14_mkl conda-forge
libclang 9.0.0 h74a9793_1 conda-forge
liblapack 3.8.0 14_mkl conda-forge
libpng 1.6.37 h7602738_0 conda-forge
libprotobuf 3.8.0 h1a1b453_0 conda-forge
libsodium 1.0.17 h2fa13f4_0 conda-forge
libtiff 4.0.10 h6512ee2_1003 conda-forge
llvmlite 0.30.0 py37_0 conda-forge
lz4-c 1.8.3 he025d50_1001 conda-forge
markupsafe 1.1.1 py37hfa6e2cd_0 conda-forge
matplotlib 3.1.1 py37_1 conda-forge
matplotlib-base 3.1.1 py37h2852a4a_1 conda-forge
mccabe 0.6.1 py_1 conda-forge
mistune 0.8.4 py37hfa6e2cd_1000 conda-forge
mkl 2019.4 245
mkl-service 2.3.0 py37hfa6e2cd_0 conda-forge
more-itertools 7.2.0 py_0 conda-forge
mpmath 1.1.0 py_0 conda-forge
nbconvert 5.6.1 py37_0 conda-forge
nbformat 4.4.0 py_1 conda-forge
networkx 2.4 py_0 conda-forge
nltk 3.4.4 py_0 conda-forge
numba 0.46.0 py37hf9181ef_0
numpy 1.17.3 py37hc71023c_0 conda-forge
numpydoc 0.9.1 py_0 conda-forge
olefile 0.46 py_0 conda-forge
openpyxl 3.0.0 py_0 conda-forge
openssl 1.1.1c hfa6e2cd_0 conda-forge
packaging 19.2 py_0 conda-forge
pandas 0.25.2 py37he350917_0 conda-forge
pandoc 2.7.3 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parquet 1.2 pypi_0 pypi
parquet-cpp 1.5.1 2 conda-forge
parso 0.5.1 py_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pickleshare 0.7.5 py37_1000 conda-forge
pillow 6.2.1 py37h643dfcc_0 conda-forge
pip 19.3.1 py37_0 conda-forge
ply 3.11 pypi_0 pypi
powershell_shortcut 0.0.1 2
proj 6.2.0 ha7a8c7b_1 conda-forge
prompt_toolkit 2.0.10 py_0 conda-forge
psutil 5.6.3 py37hfa6e2cd_0 conda-forge
pure-sasl 0.6.1 py_0 conda-forge
pyarrow 0.15.0 py37h803c963_1 conda-forge
pycodestyle 2.5.0 py_0 conda-forge
pycparser 2.19 py37_1 conda-forge
pyflakes 2.1.1 py_0 conda-forge
pygments 2.4.2 py_0 conda-forge
pyhive 0.6.1 py37_0
pylint 2.4.3 py37_0 conda-forge
pyopenssl 19.0.0 py37_0 conda-forge
pyparsing 2.4.2 py_0 conda-forge
pyqt 5.12.3 py37h6538335_0 conda-forge
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtwebengine 5.12.1 pypi_0 pypi
pyrsistent 0.15.5 py37hfa6e2cd_0 conda-forge
pysocks 1.7.1 py37_0 conda-forge
python 3.7.3 h510b542_1 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
python-levenshtein 0.12.0 py37hfa6e2cd_1001 conda-forge
python-snappy 0.5.4 py37hd25c944_0 conda-forge
pytz 2019.3 py_0 conda-forge
pyunpack 0.1.2 pypi_0 pypi
pywin32 224 py37hfa6e2cd_1000 conda-forge
pywin32-ctypes 0.2.0 py37_1000 conda-forge
pyyaml 5.1.2 py37hfa6e2cd_0 conda-forge
pyzmq 18.1.0 py37h16f9016_0 conda-forge
qt 5.12.5 h7ef1ec2_0 conda-forge
qtawesome 0.6.0 py_0 conda-forge
qtconsole 4.5.5 py_0 conda-forge
qtpy 1.9.0 py_0 conda-forge
re2 2019.09.01 vc14h6538335_0 [vc14] conda-forge
regex 2019.08.19 py37hfa6e2cd_0 conda-forge
requests 2.22.0 py37_1 conda-forge
rope 0.14.0 py_0 conda-forge
scikit-learn 0.21.3 py37h7208079_0 conda-forge
scipy 1.3.1 py37h29ff71c_0
seaborn 0.9.0 py_1 conda-forge
setuptools 41.6.0 py37_0 conda-forge
six 1.12.0 py37_1000 conda-forge
snappy 1.1.7 h6538335_1002 conda-forge
snowballstemmer 2.0.0 py_0 conda-forge
soupsieve 1.9.4 py37_0 conda-forge
sphinx 2.2.1 py_0 conda-forge
sphinxcontrib-applehelp 1.0.1 py_0 conda-forge
sphinxcontrib-devhelp 1.0.1 py_0 conda-forge
sphinxcontrib-htmlhelp 1.0.2 py_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.2 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.3 py_0 conda-forge
spyder 3.3.6 py37_1 conda-forge
spyder-kernels 0.5.2 py37_0 conda-forge
sqlalchemy 1.3.10 py37hfa6e2cd_0 conda-forge
sqlite 3.30.1 hfa6e2cd_0 conda-forge
statsmodels 0.10.1 py37hfa6e2cd_1 conda-forge
sympy 1.4 py37_0 conda-forge
tbb 2019.9 he980bc4_0 conda-forge
testpath 0.4.2 py_1001 conda-forge
thrift 0.11.0 py37h6538335_1001 conda-forge
thrift-cpp 0.12.0 hd042d19_1004 conda-forge
thrift_sasl 0.3.0 py37hfa6e2cd_1001 conda-forge
thriftpy 0.3.9 pypi_0 pypi
tk 8.6.9 hfa6e2cd_1003 conda-forge
tornado 6.0.3 py37hfa6e2cd_0 conda-forge
tqdm 4.36.1 py_0 conda-forge
traitlets 4.3.3 py37_0 conda-forge
unidecode 1.1.1 py_0 conda-forge
uriparser 0.9.3 he025d50_1 conda-forge
urllib3 1.25.6 py37_0 conda-forge
vc 14.1 h0510ff6_4
vs2015_runtime 14.16.27012 hf0eaf9b_0
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.33.6 py37_0 conda-forge
win_inet_pton 1.1.0 py37_0 conda-forge
wincertstore 0.2 py37_1002 conda-forge
wordcloud 1.5.0 py37hfa6e2cd_1000 conda-forge
wrapt 1.11.2 py37hfa6e2cd_0 conda-forge
xlrd 1.2.0 py_0 conda-forge
xlsxwriter 1.2.2 py_0 conda-forge
xmljson 0.2.0 pypi_0 pypi
xmltodict 0.12.0 py_0 conda-forge
xz 5.2.4 h2fa13f4_1001 conda-forge
yaml 0.1.7 hfa6e2cd_1001 conda-forge
zeromq 4.3.2 h6538335_2 conda-forge
zipp 0.6.0 py_0 conda-forge
zlib 1.2.11 h2fa13f4_1006 conda-forge
zstd 1.4.0 hd8a0e53_0 conda-forge
Upvotes: 0
Views: 1833
Answers (2)
Khris
Reputation: 3212
After a long search in different githubs and experimenting I found that there were two separate issues here:
First it was an issue with Spyder/Anaconda/Miniconda, specifically with the automatically created Windows-Shortcut on creating a new Conda environment. Starting Spyder using that shortcut for some reason does not set the PROJ_LIB environment variable while starting Spyder from the console from the active environment gets rid of the error.
Second I found my installed versions were these:
basemap 1.2.0 py37h4e5d7af_0
proj 6.2.0 ha7a8c7b_1 conda-forge
pyproj 2.4.0 py37h77f86b8_0 conda-forge
And apparently that was a botched install as there was no espg file anywhere in the environment.
I created a new testing environment where everything was working and looked at the versions installed there:
basemap 1.2.1 py37h79c95a4_1 conda-forge
proj4 5.2.0 ha925a31_1
pyproj 1.9.6 py37h6782396_0
After removing the old versions and specifically installing those versions now everything works.
Upvotes: 2
James
Reputation: 36623
You may want to try destroying your environment and starting fresh. Also, it looks like you have almost cloned the base environment, are you sure you need all of those packages?
To remove the environment:
conda env remove -n <env name>
To create it from scratch, you can specify multiple channels to search within. The conda-forge channel has the latest releases, but they are not always stable. The recommendation is to use the default channels when you can. Try creating the environment using:
conda create -n bmap python ipython matplotlib pandas basemap=1.2.1 -c defaults -c conda-forge
It looks like someone didn't check the dependencies when compiling proj. If you run
conda search proj=6.2.0 --info -c conda-forge
it shows it a constraint of - proj4 ==999999999999.
Upvotes: 1
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