Comments (13)
Try again. I think, a trouble shooting guide for the installation would be helpful. I think most people will fail because of the python2/3 mess
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If I do
install_sjSDM()
I now get
Error in reticulate::py_install(packages = c(stringr::str_split_fixed(unlist(packages), :
object 'python_version' not found
3.
conda_install(envname, packages = packages, conda = conda, python_version = python_version,
...)
2.
reticulate::py_install(packages = c(stringr::str_split_fixed(unlist(packages),
" ", n = Inf)[1, ], "sjSDM_py"), envname = envname, method = method,
conda = conda, pip = TRUE, python_version = python_version) at install.R#102
1.
install_sjSDM()
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Regardless of improving the install functions, I wonder if we should provide manual install instructions in case the automatic install fails? I think it will be very hard to ensure a proper functioning of the install function on all OS / settings.
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Yes, I will add instructions. PyTorch is more challenging than tensorflow.
Maybe change your python_version to 3.6? Do you have conda installed?
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I have Python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46)
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
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Okay, maybe sjSDM::install_sjSDM(python_version=3.6) works. But its a good reminder, we have to change the behaviour so that it only checks the minimal requirement of python >= 3.6.
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I think the problem in my code is that the code wants python_version, but the function interface has conda_python_version
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yes, changing this it runs
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Now I have have this ;)
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /anaconda3/envs/r-sjSDM
added / updated specs:
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2020.1.1 | 0 125 KB
certifi-2019.11.28 | py36_0 153 KB
libcxx-4.0.1 | hcfea43d_1 947 KB
libcxxabi-4.0.1 | hcfea43d_1 350 KB
libedit-3.1.20181209 | hb402a30_0 136 KB
ncurses-6.1 | h0a44026_1 732 KB
openssl-1.1.1d | h1de35cc_4 2.2 MB
pip-20.0.2 | py36_1 1.7 MB
python-3.6.10 | h359304d_0 17.1 MB
readline-7.0 | h1de35cc_5 316 KB
setuptools-45.2.0 | py36_0 511 KB
sqlite-3.31.1 | ha441bb4_0 1.2 MB
tk-8.6.8 | ha441bb4_0 2.8 MB
wheel-0.34.2 | py36_0 50 KB
xz-5.2.4 | h1de35cc_4 239 KB
zlib-1.2.11 | h1de35cc_3 90 KB
------------------------------------------------------------
Total: 28.6 MB
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-py36_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_4
pip pkgs/main/osx-64::pip-20.0.2-py36_1
python pkgs/main/osx-64::python-3.6.10-h359304d_0
readline pkgs/main/osx-64::readline-7.0-h1de35cc_5
setuptools pkgs/main/osx-64::setuptools-45.2.0-py36_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-py36_0
xz pkgs/main/osx-64::xz-5.2.4-h1de35cc_4
zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3
Downloading and Extracting Packages
sqlite-3.31.1 | 1.2 MB | ########## | 100%
zlib-1.2.11 | 90 KB | ########## | 100%
ncurses-6.1 | 732 KB | ########## | 100%
libedit-3.1.20181209 | 136 KB | ########## | 100%
readline-7.0 | 316 KB | ########## | 100%
python-3.6.10 | 17.1 MB | ########## | 100%
wheel-0.34.2 | 50 KB | ########## | 100%
pip-20.0.2 | 1.7 MB | ########## | 100%
xz-5.2.4 | 239 KB | ########## | 100%
ca-certificates-2020 | 125 KB | ########## | 100%
certifi-2019.11.28 | 153 KB | ########## | 100%
tk-8.6.8 | 2.8 MB | ########## | 100%
libcxx-4.0.1 | 947 KB | ########## | 100%
setuptools-45.2.0 | 511 KB | ########## | 100%
libcxxabi-4.0.1 | 350 KB | ########## | 100%
openssl-1.1.1d | 2.2 MB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
# $ conda activate r-sjSDM
#
# To deactivate an active environment, use
#
# $ conda deactivate
ERROR: Could not open requirements file: [Errno 2] No such file or directory: 'pytorch'
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I'm still getting
> install_sjSDM()
Error in strsplit(unlist(package), " ", fixed = TRUE) :
non-character argument
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We have to see how the installation vignette works for the users. Since most of the errors in this issue are solved and provide no help for the users, I will close this issue.
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installation via conda is still buggy
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It's probably not possible to consider all issues that could occur. What I would do is to make sure that we have an error message that always works and directs to a good help file (I think we have this), and add in the help, maybe even in the error message, that people should create an issue here in case they have a problem. This will reduce frustration, and also, we will get an idea about what the typical problems are.
Maybe you should add the think with deleting the environments though, as this could be a frequent problem.
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Related Issues (20)
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