Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Magic issue with mkl #202

Open
abhay0305 opened this issue May 11, 2022 · 0 comments
Open

Magic issue with mkl #202

abhay0305 opened this issue May 11, 2022 · 0 comments
Labels

Comments

@abhay0305
Copy link

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Standalone code to reproduce the error

Expected behavior
A clear and concise description of what you expected to happen.

Actual behavior
Please include the full traceback of any errors

System information:

Output of magic.__version__:

python -c 'import magic'
/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/numpy/init.py:143: UserWarning: mkl-service package failed to import, therefore Intel(R) MKL initialization ensuring its correct out-of-the box operation under condition when Gnu OpenMP had already been loaded by Python process is not assured. Please install mkl-service package, see http://github.com/IntelPython/mkl-service
from . import _distributor_init
Traceback (most recent call last):
File "", line 1, in
File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/magic/init.py", line 1, in
from .magic import MAGIC
File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/magic/magic.py", line 9, in
from . import utils
File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/magic/utils.py", line 1, in
from scipy import sparse
File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/scipy/init.py", line 67, in
from numpy import show_config as show_numpy_config
File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/numpy/init.py", line 326, in
import mkl
ModuleNotFoundError: No module named 'mkl'

Output of pd.show_versions():

python -c 'import pandas as pd'
/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/numpy/__init__.py:143: UserWarning: mkl-service package failed to import, therefore Intel(R) MKL initialization ensuring its correct out-of-the box operation under condition when Gnu OpenMP had already been loaded by Python process is not assured. Please install mkl-service package, see http://github.com/IntelPython/mkl-service
  from . import _distributor_init
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/pandas/__init__.py", line 16, in <module>
    raise ImportError(
ImportError: Unable to import required dependencies:
numpy: No module named 'mkl'


Output of sessionInfo():

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] Rmagic_2.0.3 Matrix_1.4-1

loaded via a namespace (and not attached):
[1] nlme_3.1-157 matrixStats_0.62.0 spatstat.sparse_2.1-1 RcppAnnoy_0.0.19
[5] RColorBrewer_1.1-3 httr_1.4.2 rprojroot_2.0.3 sctransform_0.3.3
[9] tools_4.1.2 utf8_1.2.2 R6_2.5.1 irlba_2.3.5
[13] rpart_4.1.16 KernSmooth_2.23-20 uwot_0.1.11 mgcv_1.8-40
[17] rgeos_0.5-9 DBI_1.1.2 lazyeval_0.2.2 colorspace_2.0-3
[21] sp_1.4-7 tidyselect_1.1.2 gridExtra_2.3 compiler_4.1.2
[25] progressr_0.10.0 cli_3.3.0 plotly_4.10.0 Seurat_4.1.1
[29] scales_1.2.0 lmtest_0.9-40 spatstat.data_2.2-0 ggridges_0.5.3
[33] pbapply_1.5-0 goftest_1.2-3 stringr_1.4.0 digest_0.6.29
[37] spatstat.utils_2.3-0 pkgconfig_2.0.3 htmltools_0.5.2 parallelly_1.31.1
[41] fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.0.2 shiny_1.7.1
[45] generics_0.1.2 zoo_1.8-10 jsonlite_1.8.0 spatstat.random_2.2-0
[49] ica_1.0-2 dplyr_1.0.9 magrittr_2.0.3 patchwork_1.1.1
[53] Rcpp_1.0.8.3 munsell_0.5.0 fansi_1.0.3 abind_1.4-5
[57] reticulate_1.24-9000 lifecycle_1.0.1 stringi_1.7.6 MASS_7.3-57
[61] Rtsne_0.16 plyr_1.8.7 grid_4.1.2 parallel_4.1.2
[65] listenv_0.8.0 promises_1.2.0.1 ggrepel_0.9.1 crayon_1.5.1
[69] deldir_1.0-6 miniUI_0.1.1.1 lattice_0.20-45 cowplot_1.1.1
[73] splines_4.1.2 tensor_1.5 pillar_1.7.0 igraph_1.3.1
[77] spatstat.geom_2.4-0 future.apply_1.9.0 reshape2_1.4.4 codetools_0.2-18
[81] leiden_0.3.10 glue_1.6.2 SeuratObject_4.1.0 data.table_1.14.2
[85] png_0.1-7 vctrs_0.4.1 httpuv_1.6.5 polyclip_1.10-0
[89] gtable_0.3.0 RANN_2.6.1 purrr_0.3.4 spatstat.core_2.4-2
[93] tidyr_1.2.0 scattermore_0.8 future_1.25.0 assertthat_0.2.1
[97] ggplot2_3.3.6 mime_0.12 xtable_1.8-4 later_1.3.0
[101] survival_3.3-1 viridisLite_0.4.0 tibble_3.1.7 cluster_2.1.3
[105] globals_0.14.0 fitdistrplus_1.1-8 ellipsis_0.3.2 here_1.0.1
[109] ROCR_1.0-11

Output of reticulate::py_discover_config(required_module = "magic"):

python: /usr/bin/python3
libpython: /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/config-3.8-darwin/libpython3.8.dylib
pythonhome: /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8:/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8
version: 3.8.2 (default, Jun 8 2021, 11:59:35) [Clang 12.0.5 (clang-1205.0.22.11)]
numpy: /Users/abhaykanodia/Library/Python/3.8/lib/python/site-packages/numpy
numpy_version: 1.22.3
magic: [NOT FOUND]

NOTE: Python version was forced by use_python function


Output of Rmagic::check_pymagic_version():

Rmagic::check_pymagic_version()
Error: 'check_pymagic_version' is not an exported object from 'namespace:Rmagic'


</details>

**Additional context**
Add any other context about the problem here.
@abhay0305 abhay0305 added the bug label May 11, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant