Closed noah-chongsiriwatana closed 1 year ago
EricThomson
commented
1 year ago Did you get this sorted? You should have 1.9.16 if you install using conda/mamba and follow the quickstart guide on the main caiman page: https://github.com/flatironinstitute/CaImAn
noah-chongsiriwatana
commented
1 year ago When I try to run
mamba create -n caiman -c conda-forge caiman
I get
Transaction
Prefix: C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\envs\caiman
Updating specs:
- caiman
Package Version Build Channel Size
--------------------------------------------------------------------------------------------------------------
Install:
--------------------------------------------------------------------------------------------------------------
+ absl-py 2.0.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ anyio 3.7.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ aom 3.6.1 h63175ca_0 conda-forge/win-64 Cached
+ argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ argon2-cffi-bindings 21.2.0 py37hcc03f2d_2 conda-forge/win-64 Cached
+ astor 0.8.1 pyh9f0ad1d_0 conda-forge/noarch Cached
+ attrs 23.1.0 pyh71513ae_1 conda-forge/noarch Cached
+ backcall 0.2.0 pyh9f0ad1d_0 conda-forge/noarch Cached
+ backports 1.0 pyhd8ed1ab_3 conda-forge/noarch Cached
+ backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge/noarch Cached
+ beautifulsoup4 4.12.2 pyha770c72_0 conda-forge/noarch Cached
+ bleach 6.1.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ blosc 1.21.5 hdccc3a2_0 conda-forge/win-64 Cached
+ bokeh 2.4.3 pyhd8ed1ab_3 conda-forge/noarch Cached
+ brotli 1.1.0 hcfcfb64_1 conda-forge/win-64 Cached
+ brotli-bin 1.1.0 hcfcfb64_1 conda-forge/win-64 Cached
+ brotli-python 1.0.9 py37hf2a7229_7 conda-forge/win-64 Cached
+ bzip2 1.0.8 h8ffe710_4 conda-forge/win-64 Cached
+ c-ares 1.20.1 hcfcfb64_0 conda-forge/win-64 Cached
+ ca-certificates 2023.7.22 h56e8100_0 conda-forge/win-64 Cached
+ caiman 1.9.8 py37h9386db6_0 conda-forge/win-64 Cached
...
+ sqlite 3.43.2 hcfcfb64_0 conda-forge/win-64 Cached
+ svt-av1 1.4.1 h63175ca_0 conda-forge/win-64 Cached
+ tbb 2021.10.0 h91493d7_2 conda-forge/win-64 157kB
+ tensorboard 1.14.0 py37_0 conda-forge/win-64 Cached
+ tensorflow 1.14.0 h1f41ff6_0 conda-forge/win-64 Cached
+ tensorflow-base 1.14.0 py37hc8dfbb8_0 conda-forge/win-64 Cached
+ tensorflow-estimator 1.14.0 py37h5ca1d4c_0 conda-forge/win-64 Cached
+ termcolor 2.3.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ terminado 0.17.0 pyh08f2357_0 conda-forge/noarch CachedI've tried reinstalling mamba from scratch and clearing all packages and caches. This is my system info:
pgunn
commented
1 year ago Hello, I see from the above that every single package is coming from conda-forge. That doesn't work on Windows with anything that needs tensorflow.
Try this instead:
mamba create -n caiman --override-channels -c base -c conda-forge caiman
That should get mamba looking in both places and hopefully will let it find the newer tensorflow.
noah-chongsiriwatana
commented
1 year ago Thank you for the suggestion, I tried that instead but am still seeing tensorflow 1.14 from conda-forge. I previously tried getting tensorflow from the anaconda channel, but the package seemed to be corrupted from that channel.
pgunn
commented
1 year ago Hm. Do you get the same results with this?
mamba create -n caiman --override-channels -c conda-forge -c base caiman
noah-chongsiriwatana
commented
1 year ago Unfortunately yes. I noticed in the Gitter chat that another user encountered the same issue as me. I also had the same @lru_cache issue, but I have already been using mambaforge (specifically miniforge-pypy3).
pgunn
commented
1 year ago I was pretty sure that was the case; we need to convince mambaforge to use both the defaults channel and the conda-forge channel in order to get this to resolve correctly. Let me see if I can figure out the right way to do that.
noah-chongsiriwatana
commented
1 year ago Looking at the mambaforge github, I notice that as of September mambaforge is discouraged, and miniforge is apparently identical to it now. This may be the issue, as I was able to install and use caiman earlier in the summer on the same machine, and only recently broke it trying to update caiman.
pgunn
commented
1 year ago What happens if we specifically tell it what tensorflow to use?
e.g.
mamba create -n caiman -c base -c conda-forge caiman tensorflow=2.12.0
pgunn
commented
1 year ago Sorry, that'll have to be
mamba create -n caiman -c base -c conda-forge caiman tensorflow=2.10.0
Looks like they're a little behind on packaging on Windows right now in base
noah-chongsiriwatana
commented
1 year ago This is the result:
$ mamba create -n caiman -c base -c conda-forge caiman tensorflow=2.10.0
conda-forge/win-64 Using cache
conda-forge/noarch Using cache
Looking for: ['caiman', 'tensorflow=2.10.0']
Could not solve for environment specs
The following package could not be installed
└─ tensorflow 2.10.0** does not exist (perhaps a typo or a missing channel).I have previously tried creating an environment, installing tensorflow first via https://anaconda.org/anaconda/tensorflow, then installing caiman, but this resulted in corrupted tensorflow package.
pgunn
commented
1 year ago Oh goodness I am an idiot.
Try this:
mamba create -n caiman -c defaults -c conda-forge caiman tensorflow=2.10.0
Sorry, for some reason I was pulling up the wrong word.
noah-chongsiriwatana
commented
1 year ago This is progress as it does attempt to install the correct versions of tensorflow and caiman. However in the verifying transaction stage, there are corrupted packages and the install fails:
Looking for: ['caiman', 'tensorflow=2.10.0']
Downloading and Extracting Packages
Preparing transaction: ...working... done
Verifying transaction: ...working... failed
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/AffineMemoryOpInterfacesIncGen/mlir/Dialect/Affine/IR/AffineMemoryOpInterfaces.cpp.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/AffineMemoryOpInterfacesIncGen/mlir/Dialect/Affine/IR/AffineMemoryOpInterfaces.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/AllocationOpInterfaceIncGen/mlir/Dialect/Bufferization/IR/AllocationOpInterface.cpp.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/AllocationOpInterfaceIncGen/mlir/Dialect/Bufferization/IR/AllocationOpInterface.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/BufferizableOpInterfaceIncGen/mlir/Dialect/Bufferization/IR/BufferizableOpInterface.cpp.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/BufferizableOpInterfaceIncGen/mlir/Dialect/Bufferization/IR/BufferizableOpInterface.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/BufferizationBaseIncGen/mlir/Dialect/Bufferization/IR/BufferizationOpsDialect.cpp.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/BufferizationBaseIncGen/mlir/Dialect/Bufferization/IR/BufferizationOpsDialect.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/DerivedAttributeOpInterfaceIncGen/mlir/Interfaces/DerivedAttributeOpInterface.cpp.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/DerivedAttributeOpInterfaceIncGen/mlir/Interfaces/DerivedAttributeOpInterface.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/LLVMIntrinsicConversionIncGen/mlir/Dialect/LLVMIR/LLVMIntrinsicToLLVMIROpPairs.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/ParallelCombiningOpInterfaceIncGen/mlir/Interfaces/ParallelCombiningOpInterface.cpp.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/ParallelCombiningOpInterfaceIncGen/mlir/Interfaces/ParallelCombiningOpInterface.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/SparseTensorAttrDefsIncGen/mlir/Dialect/SparseTensor/IR/SparseTensorAttrDefs.cpp.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/SparseTensorAttrDefsIncGen/mlir/Dialect/SparseTensor/IR/SparseTensorAttrDefs.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/SparseTensorOpsIncGen/mlir/Dialect/SparseTensor/IR/SparseTensorOpsDialect.cpp.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/compose_set_interface_inc_gen/mlir-hlo/Dialect/gml_st/transforms/compose_set_interface.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/fusion_interface_inc_gen/mlir-hlo/Dialect/gml_st/transforms/fusion_interface.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/lhlo_gpu_ops_attrdefs_inc_gen/mlir-hlo/Dialect/lhlo_gpu/IR/lhlo_gpu_ops_attrdefs.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/lhlo_gpu_ops_dialect_inc_gen/mlir-hlo/Dialect/lhlo_gpu/IR/lhlo_gpu_ops_dialect.h.inc'
specified in the package manifest cannot be found.
The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/lhlo_gpu_ops_enums_inc_gen/mlir-hlo/Dialect/lhlo_gpu/IR/lhlo_gpu_ops_enums.h.inc'
specified in the package manifest cannot be found.
This transaction has incompatible packages due to a shared path.
packages: conda-forge/win-64::libsqlite-3.43.2-hcfcfb64_0, defaults/win-64::sqlite-3.41.2-h2bbff1b_0
path: 'library/bin/sqlite3.dll'
This transaction has incompatible packages due to a shared path.
packages: conda-forge/win-64::libsqlite-3.43.2-hcfcfb64_0, defaults/win-64::sqlite-3.41.2-h2bbff1b_0
path: 'library/include/sqlite3.h'
This transaction has incompatible packages due to a shared path.
packages: conda-forge/win-64::libsqlite-3.43.2-hcfcfb64_0, defaults/win-64::sqlite-3.41.2-h2bbff1b_0
path: 'library/include/sqlite3ext.h'
This transaction has incompatible packages due to a shared path.
packages: conda-forge/win-64::libsqlite-3.43.2-hcfcfb64_0, defaults/win-64::sqlite-3.41.2-h2bbff1b_0
path: 'library/lib/sqlite3.lib'
This transaction has incompatible packages due to a shared path.
packages: defaults/win-64::notebook-6.5.4-py310haa95532_1, defaults/win-64::notebook-6.5.4-py310haa95532_1
path: 'menu/notebook.json'
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/AffineMemoryOpInterfacesIncGen/mlir/Dialect/Affine/IR/AffineMemoryOpInterfaces.cpp.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/AffineMemoryOpInterfacesIncGen/mlir/Dialect/Affine/IR/AffineMemoryOpInterfaces.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/AllocationOpInterfaceIncGen/mlir/Dialect/Bufferization/IR/AllocationOpInterface.cpp.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/AllocationOpInterfaceIncGen/mlir/Dialect/Bufferization/IR/AllocationOpInterface.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/BufferizableOpInterfaceIncGen/mlir/Dialect/Bufferization/IR/BufferizableOpInterface.cpp.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/BufferizableOpInterfaceIncGen/mlir/Dialect/Bufferization/IR/BufferizableOpInterface.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/BufferizationBaseIncGen/mlir/Dialect/Bufferization/IR/BufferizationOpsDialect.cpp.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/BufferizationBaseIncGen/mlir/Dialect/Bufferization/IR/BufferizationOpsDialect.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/DerivedAttributeOpInterfaceIncGen/mlir/Interfaces/DerivedAttributeOpInterface.cpp.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/DerivedAttributeOpInterfaceIncGen/mlir/Interfaces/DerivedAttributeOpInterface.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/LLVMIntrinsicConversionIncGen/mlir/Dialect/LLVMIR/LLVMIntrinsicToLLVMIROpPairs.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/ParallelCombiningOpInterfaceIncGen/mlir/Interfaces/ParallelCombiningOpInterface.cpp.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/ParallelCombiningOpInterfaceIncGen/mlir/Interfaces/ParallelCombiningOpInterface.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/SparseTensorAttrDefsIncGen/mlir/Dialect/SparseTensor/IR/SparseTensorAttrDefs.cpp.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/SparseTensorAttrDefsIncGen/mlir/Dialect/SparseTensor/IR/SparseTensorAttrDefs.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/external/llvm-project/mlir/_virtual_includes/SparseTensorOpsIncGen/mlir/Dialect/SparseTensor/IR/SparseTensorOpsDialect.cpp.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/compose_set_interface_inc_gen/mlir-hlo/Dialect/gml_st/transforms/compose_set_interface.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/fusion_interface_inc_gen/mlir-hlo/Dialect/gml_st/transforms/fusion_interface.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/lhlo_gpu_ops_attrdefs_inc_gen/mlir-hlo/Dialect/lhlo_gpu/IR/lhlo_gpu_ops_attrdefs.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/lhlo_gpu_ops_dialect_inc_gen/mlir-hlo/Dialect/lhlo_gpu/IR/lhlo_gpu_ops_dialect.h.inc'
specified in the package manifest cannot be found.
CondaVerificationError: The package for tensorflow-base located at C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\pkgs\tensorflow-base-2.10.0-mkl_py310h6a7f48e_0
appears to be corrupted. The path 'Lib/site-packages/tensorflow/include/tensorflow/compiler/mlir/hlo/_virtual_includes/lhlo_gpu_ops_enums_inc_gen/mlir-hlo/Dialect/lhlo_gpu/IR/lhlo_gpu_ops_enums.h.inc'
specified in the package manifest cannot be found.
ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/win-64::libsqlite-3.43.2-hcfcfb64_0, defaults/win-64::sqlite-3.41.2-h2bbff1b_0
path: 'library/bin/sqlite3.dll'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/win-64::libsqlite-3.43.2-hcfcfb64_0, defaults/win-64::sqlite-3.41.2-h2bbff1b_0
path: 'library/include/sqlite3.h'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/win-64::libsqlite-3.43.2-hcfcfb64_0, defaults/win-64::sqlite-3.41.2-h2bbff1b_0
path: 'library/include/sqlite3ext.h'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/win-64::libsqlite-3.43.2-hcfcfb64_0, defaults/win-64::sqlite-3.41.2-h2bbff1b_0
path: 'library/lib/sqlite3.lib'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: defaults/win-64::notebook-6.5.4-py310haa95532_1, defaults/win-64::notebook-6.5.4-py310haa95532_1
path: 'menu/notebook.json'This is similar to what I had encountered when I tried installing tensorflow from anaconda channel.
noah-chongsiriwatana
commented
1 year ago A similar issue is found here: https://github.com/conda/conda/issues/10767
pgunn
commented
1 year ago In that issue they tell you how to enable long path names on Windows; you'll want to do that. After that you can repeat the operation and it should work without problems.
noah-chongsiriwatana
commented
1 year ago Thank you, I solved the long file path issue. Changing the registry value and group policy didn't help, so I had to install the packages in a higher level folder as a workaround. Now I am getting an error at the executing transaction stage:
$ mamba create -n caiman -c defaults -c conda-forge caiman tensorflow=2.10.0
Transaction
Prefix: C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\envs\caiman
Updating specs:
- caiman
- tensorflow=2.10.0
Package Version Build Channel Size
-----------------------------------------------------------------------------------------
Install:
-----------------------------------------------------------------------------------------
+ _tflow_select 2.3.0 mkl pkgs/main 3kB
+ ucrt 10.0.20348.0 haa95532_0 pkgs/main 543kB
+ blas 1.0 mkl pkgs/main 6kB
+ icc_rt 2022.1.0 h6049295_2 pkgs/main 7MB
+ ca-certificates 2023.08.22 haa95532_0 pkgs/main 126kB
+ winpty 0.4.3 4 pkgs/main 695kB
+ python_abi 3.10 4_cp310 conda-forge 7kB
+ vc14_runtime 14.36.32532 hdcecf7f_17 conda-forge 739kB
+ vs2015_runtime 14.36.32532 h05e6639_17 conda-forge 17kB
...
+ tensorflow 2.10.0 mkl_py310hd99672f_0 pkgs/main 4kB
+ notebook 6.5.4 py310haa95532_1 pkgs/main 572kB
+ jupyterlab 3.6.3 py310haa95532_0 pkgs/main 4MB
+ jupyter 1.0.0 py310haa95532_8 pkgs/main 8kB
+ caiman 1.9.16 py310h00ffb61_0 conda-forge 118MB
Summary:
Install: 317 packages
Total download: 964MB
-----------------------------------------------------------------------------------------
Confirm changes: [Y/n]
Looking for: ['caiman', 'tensorflow=2.10.0']
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
ERROR conda.core.link:_execute(945): An error occurred while installing package 'defaults::scikit-learn-1.3.0-py310h4ed8f06_0'.
Rolling back transaction: ...working... done
post-link script failed for package defaults::scikit-learn-1.3.0-py310h4ed8f06_0
location of failed script: C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\envs\caiman\Scripts\.scikit-learn-post-link.bat
==> script messages <==
<None>
==> script output <==
stdout:
stderr: 'conda' is not recognized as an internal or external command,
operable program or batch file.
return code: 255
()
LinkError: post-link script failed for package defaults::scikit-learn-1.3.0-py310h4ed8f06_0
location of failed script: C:\Users\nschong.AD\AppData\Local\miniforge-pypy3\envs\caiman\Scripts\.scikit-learn-post-link.bat
==> script messages <==
<None>
==> script output <==
stdout:
stderr: 'conda' is not recognized as an internal or external command,
operable program or batch file.
return code: 255
()Does miniforge somehow not give you a conda command?
noah-chongsiriwatana
commented
1 year ago Not sure, I'm going to try a fresh install of miniforge without pypy.
pgunn
commented
1 year ago You might just try miniconda instead.
noah-chongsiriwatana
commented
1 year ago Thank you, it seems like there are some issues with mamba. Switching to conda seems to have solved things. Thanks very much for the help.
Hello,
I am trying to run caiman on windows. In a clean conda environment I ran
mamba install -c conda-forge caimanwhich shows the packages and versions to be installed. I noticed that the version for caiman is 1.9.8, and found that this is because the conda-forge channel for windows supports tensorflow version at 1 rather than 2. Do you have any recommendations on how to use the most up to date version of caiman?Thank you!
Your setup: