Hi, I'm getting three errors trying to run phate(). I've tried removing and restarting the environment, installing/uninstalling numpy, and updating packages. Any help is very appreciated!
-->Errors:
Error in py_module_import(module, convert = convert) :
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
Run reticulate::py_last_error() for details.
Error in py_module_import(module, convert = convert) :
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
Run reticulate::py_last_error() for details.
Error in pyphate()$PHATE : $ operator is invalid for atomic vectors
-->data: rows are subjects, columns are genes
1 R2249549 7 1 34 13 22 0 2 7
2 R9307768 50 2 61 32 37 0 1 14
3 R5756103 14 2 60 29 28 0 1 8
4 R4689636 21 6 120 94 85 2 4 42
5 R2845830 111 6 223 148 79 2 1 58
6 R1913204 47 3 124 118 71
-->R code:
library(phateR)
library(ggplot2)
library(readr)
library(viridis)
library(Rmagic)
psych <- read.csv("pseudobulk_counts_type_Astro.csv")
data_phate <- phate(psych)
-->Output of phate.version:
python -c "import phate; print(phate.version)"
Traceback (most recent call last):
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/swig/layout.py", line 17, in swig_import_helper
return importlib.import_module(mname)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/courteneymattison/anaconda3/lib/python3.11/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 1204, in _gcd_import
File "", line 1176, in _find_and_load
File "", line 1140, in _find_and_load_unlocked
ModuleNotFoundError: No module named 's_gd2.swig._layout'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "", line 1, in
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/phate/init.py", line 3, in
from .phate import PHATE
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/phate/phate.py", line 19, in
from . import utils, vne, mds
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/phate/mds.py", line 14, in
import s_gd2
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/init.py", line 1, in
from .s_gd2 import *
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/s_gd2.py", line 1, in
from .swig import layout as cpp
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/swig/layout.py", line 21, in
_layout = swig_import_helper()
^^^^^^^^^^^^^^^^^^^^
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/swig/layout.py", line 19, in swig_import_helper
return importlib.import_module("_layout")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/courteneymattison/anaconda3/lib/python3.11/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: dlopen(/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_layout.cpython-311-darwin.so, 0x0002): tried: '/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_layout.cpython-311-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_layout.cpython-311-darwin.so' (no such file), '/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_layout.cpython-311-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64'))
-->Output of pd.show_versions():
'import pandas as pd; pd.show_versions()'
/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_distutils_hack/init.py:33: UserWarning: Setuptools is replacing distutils.
warnings.warn("Setuptools is replacing distutils.")
INSTALLED VERSIONS
commit : 2e218d10984e9919f0296931d92ea851c6a6faf5
python : 3.11.5.final.0
python-bits : 64
OS : Darwin
OS-release : 23.6.0
Version : Darwin Kernel Version 23.6.0: Mon Jul 29 21:14:30 PDT 2024; root:xnu-10063.141.2~1/RELEASE_ARM64_T6030
machine : arm64
processor : arm
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8
pandas : 1.5.3
numpy : 1.24.4
pytz : 2024.2
dateutil : 2.9.0.post0
setuptools : 68.0.0
pip : 23.2.1
Cython : 3.0.8
pytest : 7.4.0
hypothesis : None
sphinx : 5.0.2
blosc : None
feather : None
xlsxwriter : None
lxml.etree : 4.9.3
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 3.1.2
IPython : 8.15.0
pandas_datareader: None
bs4 : 4.12.2
bottleneck : 1.3.6
brotli :
fastparquet : None
fsspec : 2024.5.0
gcsfs : None
matplotlib : 3.9.2
numba : 0.60.0
numexpr : 2.8.4
odfpy : None
openpyxl : 3.0.10
pandas_gbq : None
pyarrow : 11.0.0
pyreadstat : None
pyxlsb : None
s3fs : 0.4.2
scipy : 1.10.1
snappy :
sqlalchemy : 1.4.39
tables : 3.8.0
tabulate : 0.8.10
xarray : 2023.12.0
xlrd : None
xlwt : None
zstandard : 0.19.0
tzdata : 2024.2
-->Output of sessionInfo():
sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rmagic_2.0.3 viridis_0.6.5 viridisLite_0.4.2 readr_2.1.5 ggplot2_3.5.1 phateR_1.0.7 Matrix_1.6-5
[8] SeuratObject_5.0.2 sp_2.1-4
loaded via a namespace (and not attached):
[1] future_1.34.0 generics_0.1.3 lattice_0.22-6 listenv_0.9.1 hms_1.1.3 digest_0.6.37
[7] magrittr_2.0.3 evaluate_1.0.3 grid_4.3.2 fastmap_1.2.0 rprojroot_2.0.4 jsonlite_1.8.9
[13] gridExtra_2.3 spam_2.11-1 scales_1.3.0 codetools_0.2-20 cli_3.6.4 rlang_1.1.5
[19] parallelly_1.42.0 future.apply_1.11.3 munsell_0.5.1 withr_3.0.2 cachem_1.1.0 tools_4.3.2
[25] parallel_4.3.2 tzdb_0.4.0 memoise_2.0.1 dplyr_1.1.4 colorspace_2.1-1 here_1.0.1
[31] globals_0.16.3 reticulate_1.40.0 vctrs_0.6.5 R6_2.6.1 png_0.1-8 lifecycle_1.0.4
[37] pkgconfig_2.0.3 progressr_0.15.1 pillar_1.10.1 gtable_0.3.6 glue_1.8.0 Rcpp_1.0.14
[43] xfun_0.50 tibble_3.2.1 tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.49 dotCall64_1.2
[49] compiler_4.3.2
--> reticulate::py_discover_config(required_module = "phate")
python: /Users/courteneymattison/.virtualenvs/r-reticulate/bin/python
libpython: /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-darwin/libpython3.9.dylib
pythonhome: /Users/courteneymattison/.virtualenvs/r-reticulate:/Users/courteneymattison/.virtualenvs/r-reticulate
version: 3.9.6 (default, Nov 10 2023, 13:38:27) [Clang 15.0.0 (clang-1500.1.0.2.5)]
numpy: /Users/courteneymattison/.virtualenvs/r-reticulate/lib/python3.9/site-packages/numpy
numpy_version: 2.0.2
phate: /Users/courteneymattison/.virtualenvs/r-reticulate/lib/python3.9/site-packages/phate
NOTE: Python version was forced by VIRTUAL_ENV
--> phateR::check_pyphate_version()
Error in pyphate()$__version__ :
$ operator is invalid for atomic vectors
Hi, I'm getting three errors trying to run phate(). I've tried removing and restarting the environment, installing/uninstalling numpy, and updating packages. Any help is very appreciated!
-->Errors:
Error in py_module_import(module, convert = convert) :
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
Run
reticulate::py_last_error()for details.Error in py_module_import(module, convert = convert) :
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
Run
reticulate::py_last_error()for details.Error in pyphate()$PHATE : $ operator is invalid for atomic vectors
-->data: rows are subjects, columns are genes
1 R2249549 7 1 34 13 22 0 2 7
2 R9307768 50 2 61 32 37 0 1 14
3 R5756103 14 2 60 29 28 0 1 8
4 R4689636 21 6 120 94 85 2 4 42
5 R2845830 111 6 223 148 79 2 1 58
6 R1913204 47 3 124 118 71
-->R code:
library(phateR)
library(ggplot2)
library(readr)
library(viridis)
library(Rmagic)
psych <- read.csv("pseudobulk_counts_type_Astro.csv")
data_phate <- phate(psych)
-->Output of phate.version:
python -c "import phate; print(phate.version)"
Traceback (most recent call last):
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/swig/layout.py", line 17, in swig_import_helper
return importlib.import_module(mname)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/courteneymattison/anaconda3/lib/python3.11/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 1204, in _gcd_import
File "", line 1176, in _find_and_load
File "", line 1140, in _find_and_load_unlocked
ModuleNotFoundError: No module named 's_gd2.swig._layout'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "", line 1, in
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/phate/init.py", line 3, in
from .phate import PHATE
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/phate/phate.py", line 19, in
from . import utils, vne, mds
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/phate/mds.py", line 14, in
import s_gd2
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/init.py", line 1, in
from .s_gd2 import *
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/s_gd2.py", line 1, in
from .swig import layout as cpp
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/swig/layout.py", line 21, in
_layout = swig_import_helper()
^^^^^^^^^^^^^^^^^^^^
File "/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/s_gd2/swig/layout.py", line 19, in swig_import_helper
return importlib.import_module("_layout")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/courteneymattison/anaconda3/lib/python3.11/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: dlopen(/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_layout.cpython-311-darwin.so, 0x0002): tried: '/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_layout.cpython-311-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_layout.cpython-311-darwin.so' (no such file), '/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_layout.cpython-311-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64'))
-->Output of pd.show_versions():
'import pandas as pd; pd.show_versions()'
/Users/courteneymattison/anaconda3/lib/python3.11/site-packages/_distutils_hack/init.py:33: UserWarning: Setuptools is replacing distutils.
warnings.warn("Setuptools is replacing distutils.")
INSTALLED VERSIONS
commit : 2e218d10984e9919f0296931d92ea851c6a6faf5
python : 3.11.5.final.0
python-bits : 64
OS : Darwin
OS-release : 23.6.0
Version : Darwin Kernel Version 23.6.0: Mon Jul 29 21:14:30 PDT 2024; root:xnu-10063.141.2~1/RELEASE_ARM64_T6030
machine : arm64
processor : arm
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8
pandas : 1.5.3
numpy : 1.24.4
pytz : 2024.2
dateutil : 2.9.0.post0
setuptools : 68.0.0
pip : 23.2.1
Cython : 3.0.8
pytest : 7.4.0
hypothesis : None
sphinx : 5.0.2
blosc : None
feather : None
xlsxwriter : None
lxml.etree : 4.9.3
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 3.1.2
IPython : 8.15.0
pandas_datareader: None
bs4 : 4.12.2
bottleneck : 1.3.6
brotli :
fastparquet : None
fsspec : 2024.5.0
gcsfs : None
matplotlib : 3.9.2
numba : 0.60.0
numexpr : 2.8.4
odfpy : None
openpyxl : 3.0.10
pandas_gbq : None
pyarrow : 11.0.0
pyreadstat : None
pyxlsb : None
s3fs : 0.4.2
scipy : 1.10.1
snappy :
sqlalchemy : 1.4.39
tables : 3.8.0
tabulate : 0.8.10
xarray : 2023.12.0
xlrd : None
xlwt : None
zstandard : 0.19.0
tzdata : 2024.2
-->Output of sessionInfo():
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rmagic_2.0.3 viridis_0.6.5 viridisLite_0.4.2 readr_2.1.5 ggplot2_3.5.1 phateR_1.0.7 Matrix_1.6-5
[8] SeuratObject_5.0.2 sp_2.1-4
loaded via a namespace (and not attached):
[1] future_1.34.0 generics_0.1.3 lattice_0.22-6 listenv_0.9.1 hms_1.1.3 digest_0.6.37
[7] magrittr_2.0.3 evaluate_1.0.3 grid_4.3.2 fastmap_1.2.0 rprojroot_2.0.4 jsonlite_1.8.9
[13] gridExtra_2.3 spam_2.11-1 scales_1.3.0 codetools_0.2-20 cli_3.6.4 rlang_1.1.5
[19] parallelly_1.42.0 future.apply_1.11.3 munsell_0.5.1 withr_3.0.2 cachem_1.1.0 tools_4.3.2
[25] parallel_4.3.2 tzdb_0.4.0 memoise_2.0.1 dplyr_1.1.4 colorspace_2.1-1 here_1.0.1
[31] globals_0.16.3 reticulate_1.40.0 vctrs_0.6.5 R6_2.6.1 png_0.1-8 lifecycle_1.0.4
[37] pkgconfig_2.0.3 progressr_0.15.1 pillar_1.10.1 gtable_0.3.6 glue_1.8.0 Rcpp_1.0.14
[43] xfun_0.50 tibble_3.2.1 tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.49 dotCall64_1.2
[49] compiler_4.3.2
--> reticulate::py_discover_config(required_module = "phate")
python: /Users/courteneymattison/.virtualenvs/r-reticulate/bin/python
libpython: /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-darwin/libpython3.9.dylib
pythonhome: /Users/courteneymattison/.virtualenvs/r-reticulate:/Users/courteneymattison/.virtualenvs/r-reticulate
version: 3.9.6 (default, Nov 10 2023, 13:38:27) [Clang 15.0.0 (clang-1500.1.0.2.5)]
numpy: /Users/courteneymattison/.virtualenvs/r-reticulate/lib/python3.9/site-packages/numpy
numpy_version: 2.0.2
phate: /Users/courteneymattison/.virtualenvs/r-reticulate/lib/python3.9/site-packages/phate
NOTE: Python version was forced by VIRTUAL_ENV
--> phateR::check_pyphate_version()
Error in pyphate()$
__version__:$ operator is invalid for atomic vectors