Closed MinjieHu closed 12 months ago
Could you provide your Python environment information by running the installed_Python_pkgs() function?
Sure. Here are they:
package version requirement channel
1 _libgcc_mutex 0.1 _libgcc_mutex=0.1 conda-forge
2 _openmp_mutex 4.5 _openmp_mutex=4.5 conda-forge
3 anndata 0.9.2 anndata=0.9.2 pypi
4 attmap 0.13.2 attmap=0.13.2 conda-forge
5 attrs 23.1.0 attrs=23.1.0 conda-forge
6 backports 1.0 backports=1.0 conda-forge
7 backports-zoneinfo 0.2.1 backports-zoneinfo=0.2.1 pypi
8 backports.functools_lru_cache 1.6.5 backports.functools_lru_cache=1.6.5 conda-forge
9 binutils_impl_linux-64 2.36.1 binutils_impl_linux-64=2.36.1 conda-forge
10 binutils_linux-64 2.36 binutils_linux-64=2.36 conda-forge
11 biopython 1.81 biopython=1.81 conda-forge
12 bleach 6.0.0 bleach=6.0.0 conda-forge
13 blosc2 2.0.0 blosc2=2.0.0 pypi
14 boltons 23.0.0 boltons=23.0.0 conda-forge
15 brotli-python 1.0.9 brotli-python=1.0.9 conda-forge
16 bzip2 1.0.8 bzip2=1.0.8 conda-forge
17 c-ares 1.19.1 c-ares=1.19.1 conda-forge
18 ca-certificates 2023.7.22 ca-certificates=2023.7.22 conda-forge
19 cattrs 23.1.2 cattrs=23.1.2 conda-forge
20 certifi 2023.7.22 certifi=2023.7.22 conda-forge
21 cffi 1.15.1 cffi=1.15.1 conda-forge
22 cfgv 3.3.1 cfgv=3.3.1 conda-forge
23 charset-normalizer 3.2.0 charset-normalizer=3.2.0 conda-forge
24 cheetah3 3.2.6.post2 cheetah3=3.2.6.post2 conda-forge
25 click 8.1.7 click=8.1.7 conda-forge
26 cmake 3.27.2 cmake=3.27.2 pypi
27 colorama 0.4.6 colorama=0.4.6 conda-forge
28 conda 23.1.0 conda=23.1.0 conda-forge
29 conda-package-handling 2.2.0 conda-package-handling=2.2.0 conda-forge
30 conda-package-streaming 0.9.0 conda-package-streaming=0.9.0 conda-forge
31 contourpy 1.1.0 contourpy=1.1.0 pypi
32 cryptography 41.0.3 cryptography=41.0.3 conda-forge
33 curl 8.2.1 curl=8.2.1 conda-forge
34 cycler 0.11.0 cycler=0.11.0 pypi
35 cython 3.0.0 cython=3.0.0 pypi
36 distlib 0.3.7 distlib=0.3.7 conda-forge
37 docutils 0.20.1 docutils=0.20.1 conda-forge
38 eido 0.2.1 eido=0.2.1 conda-forge
39 exceptiongroup 1.1.3 exceptiongroup=1.1.3 conda-forge
40 fcsparser 0.2.4 fcsparser=0.2.4 pypi
41 filelock 3.12.2 filelock=3.12.2 conda-forge
42 filetype 1.2.0 filetype=1.2.0 conda-forge
43 fonttools 4.42.0 fonttools=4.42.0 pypi
44 future 0.18.3 future=0.18.3 conda-forge
45 galaxy-containers 22.1.1 galaxy-containers=22.1.1 conda-forge
46 galaxy-tool-util 22.1.5 galaxy-tool-util=22.1.5 conda-forge
47 galaxy-util 22.1.2 galaxy-util=22.1.2 conda-forge
48 gcc_impl_linux-64 11.1.0 gcc_impl_linux-64=11.1.0 conda-forge
49 gcc_linux-64 11.1.0 gcc_linux-64=11.1.0 conda-forge
50 gettext 0.21.1 gettext=0.21.1 conda-forge
51 git 2.41.0 git=2.41.0 conda-forge
52 gitdb 4.0.10 gitdb=4.0.10 conda-forge
53 gitpython 3.1.32 gitpython=3.1.32 conda-forge
54 greenlet 2.0.2 greenlet=2.0.2 conda-forge
55 gxx_impl_linux-64 11.1.0 gxx_impl_linux-64=11.1.0 conda-forge
56 gxx_linux-64 11.1.0 gxx_linux-64=11.1.0 conda-forge
57 h5py 3.9.0 h5py=3.9.0 pypi
58 icu 72.1 icu=72.1 conda-forge
59 identify 2.5.26 identify=2.5.26 conda-forge
60 idna 3.4 idna=3.4 conda-forge
61 igraph 0.10.2 igraph=0.10.2 pypi
62 importlib-metadata 6.8.0 importlib-metadata=6.8.0 conda-forge
63 importlib_resources 6.0.1 importlib_resources=6.0.1 conda-forge
64 iniconfig 2.0.0 iniconfig=2.0.0 conda-forge
65 itsdangerous 2.1.2 itsdangerous=2.1.2 conda-forge
66 jax 0.4.13 jax=0.4.13 pypi
67 jaxlib 0.4.13 jaxlib=0.4.13 pypi
68 jaxopt 0.8 jaxopt=0.8 pypi
69 jinja2 3.1.2 jinja2=3.1.2 conda-forge
70 joblib 1.3.2 joblib=1.3.2 pypi
71 jsonpatch 1.32 jsonpatch=1.32 conda-forge
72 jsonpointer 2.0 jsonpointer=2.0 conda-forge
73 jsonschema 4.19.0 jsonschema=4.19.0 conda-forge
74 jsonschema-specifications 2023.7.1 jsonschema-specifications=2023.7.1 conda-forge
75 kernel-headers_linux-64 2.6.32 kernel-headers_linux-64=2.6.32 conda-forge
76 keyutils 1.6.1 keyutils=1.6.1 conda-forge
77 kiwisolver 1.4.4 kiwisolver=1.4.4 pypi
78 krb5 1.21.2 krb5=1.21.2 conda-forge
79 ld_impl_linux-64 2.36.1 ld_impl_linux-64=2.36.1 conda-forge
80 leidenalg 0.10.1 leidenalg=0.10.1 pypi
81 libblas 3.9.0 libblas=3.9.0 conda-forge
82 libcblas 3.9.0 libcblas=3.9.0 conda-forge
83 libcurl 8.2.1 libcurl=8.2.1 conda-forge
84 libedit 3.1.20191231 libedit=3.1.20191231 conda-forge
85 libev 4.33 libev=4.33 conda-forge
86 libexpat 2.5.0 libexpat=2.5.0 conda-forge
87 libffi 3.4.2 libffi=3.4.2 conda-forge
88 libgcc-devel_linux-64 11.1.0 libgcc-devel_linux-64=11.1.0 conda-forge
89 libgcc-ng 13.1.0 libgcc-ng=13.1.0 conda-forge
90 libgfortran-ng 13.1.0 libgfortran-ng=13.1.0 conda-forge
91 libgfortran5 13.1.0 libgfortran5=13.1.0 conda-forge
92 libgomp 13.1.0 libgomp=13.1.0 conda-forge
93 libiconv 1.17 libiconv=1.17 conda-forge
94 liblapack 3.9.0 liblapack=3.9.0 conda-forge
95 libnghttp2 1.52.0 libnghttp2=1.52.0 conda-forge
96 libnsl 2.0.0 libnsl=2.0.0 conda-forge
97 libopenblas 0.3.23 libopenblas=0.3.23 conda-forge
98 libpq 15.4 libpq=15.4 conda-forge
99 libsanitizer 11.1.0 libsanitizer=11.1.0 conda-forge
100 libsqlite 3.42.0 libsqlite=3.42.0 conda-forge
101 libssh2 1.11.0 libssh2=1.11.0 conda-forge
102 libstdcxx-devel_linux-64 11.1.0 libstdcxx-devel_linux-64=11.1.0 conda-forge
103 libstdcxx-ng 13.1.0 libstdcxx-ng=13.1.0 conda-forge
104 libuuid 2.38.1 libuuid=2.38.1 conda-forge
105 libxml2 2.11.5 libxml2=2.11.5 conda-forge
106 libxslt 1.1.37 libxslt=1.1.37 conda-forge
107 libzlib 1.2.13 libzlib=1.2.13 conda-forge
108 llvmlite 0.38.1 llvmlite=0.38.1 pypi
109 logmuse 0.2.6 logmuse=0.2.6 conda-forge
110 loompy 3.0.7 loompy=3.0.7 pypi
111 lxml 4.9.3 lxml=4.9.3 conda-forge
112 markdown 3.4.4 markdown=3.4.4 conda-forge
113 markdown-it-py 3.0.0 markdown-it-py=3.0.0 conda-forge
114 markupsafe 2.1.3 markupsafe=2.1.3 conda-forge
115 matplotlib 3.6.3 matplotlib=3.6.3 pypi
116 mdurl 0.1.0 mdurl=0.1.0 conda-forge
117 mellon 1.3.1 mellon=1.3.1 pypi
118 ml-dtypes 0.2.0 ml-dtypes=0.2.0 pypi
119 msgpack 1.0.5 msgpack=1.0.5 pypi
120 natsort 8.4.0 natsort=8.4.0 pypi
121 ncurses 6.4 ncurses=6.4 conda-forge
122 ndindex 1.7 ndindex=1.7 pypi
123 networkx 3.1 networkx=3.1 pypi
124 nf-core 2.9 nf-core=2.9 bioconda
125 nodeenv 1.8.0 nodeenv=1.8.0 conda-forge
126 numba 0.55.2 numba=0.55.2 pypi
127 numexpr 2.8.5 numexpr=2.8.5 pypi
128 numpy 1.21.6 numpy=1.21.6 pypi
129 numpy-groupies 0.9.22 numpy-groupies=0.9.22 pypi
130 openssl 3.1.2 openssl=3.1.2 conda-forge
131 opt-einsum 3.3.0 opt-einsum=3.3.0 pypi
132 oyaml 1.0 oyaml=1.0 conda-forge
133 packaging 21.3 packaging=21.3 conda-forge
134 palantir 1.3.0 palantir=1.3.0 pypi
135 pandas 1.3.5 pandas=1.3.5 pypi
136 patsy 0.5.3 patsy=0.5.3 pypi
137 pcre2 10.40 pcre2=10.40 conda-forge
138 peppy 0.35.7 peppy=0.35.7 conda-forge
139 perl 5.32.1 perl=5.32.1 conda-forge
140 pillow 10.0.0 pillow=10.0.0 pypi
141 pip 23.2.1 pip=23.2.1 pypi
142 piper 0.12.3 piper=0.12.3 bioconda
143 pipestat 0.5.1 pipestat=0.5.1 conda-forge
144 pkgutil-resolve-name 1.3.10 pkgutil-resolve-name=1.3.10 conda-forge
145 platformdirs 3.10.0 platformdirs=3.10.0 conda-forge
146 pluggy 1.2.0 pluggy=1.2.0 conda-forge
147 pre-commit 3.1.1 pre-commit=3.1.1 conda-forge
148 progressbar2 4.2.0 progressbar2=4.2.0 pypi
149 prompt-toolkit 3.0.39 prompt-toolkit=3.0.39 conda-forge
150 prompt_toolkit 3.0.39 prompt_toolkit=3.0.39 conda-forge
151 psutil 5.9.5 psutil=5.9.5 conda-forge
152 psycopg2 2.9.6 psycopg2=2.9.6 conda-forge
153 psycopg2-binary 2.9.7 psycopg2-binary=2.9.7 pypi
154 py-cpuinfo 9.0.0 py-cpuinfo=9.0.0 pypi
155 pycosat 0.6.4 pycosat=0.6.4 conda-forge
156 pycparser 2.21 pycparser=2.21 conda-forge
157 pydantic 1.10.12 pydantic=1.10.12 conda-forge
158 pyfaidx 0.7.2.1 pyfaidx=0.7.2.1 bioconda
159 pygam 0.8.0 pygam=0.8.0 pypi
160 pygments 2.16.1 pygments=2.16.1 conda-forge
161 pynndescent 0.5.10 pynndescent=0.5.10 pypi
162 pyopenssl 23.2.0 pyopenssl=23.2.0 conda-forge
163 pyparsing 3.1.1 pyparsing=3.1.1 conda-forge
164 pysocks 1.7.1 pysocks=1.7.1 conda-forge
165 pytest 7.4.0 pytest=7.4.0 conda-forge
166 pytest-workflow 2.0.1 pytest-workflow=2.0.1 conda-forge
167 python 3.8.17 python=3.8.17 conda-forge
168 python-dateutil 2.8.2 python-dateutil=2.8.2 conda-forge
169 python-igraph 0.10.2 python-igraph=0.10.2 pypi
170 python-tzdata 2023.3 python-tzdata=2023.3 conda-forge
171 python-utils 3.7.0 python-utils=3.7.0 pypi
172 python_abi 3.8 python_abi=3.8 conda-forge
173 pytz 2023.3 pytz=2023.3 conda-forge
174 pyvcf3 1.0.3 pyvcf3=1.0.3 bioconda
175 pyyaml 6.0 pyyaml=6.0 conda-forge
176 questionary 2.0.0 questionary=2.0.0 conda-forge
177 readline 8.2 readline=8.2 conda-forge
178 referencing 0.30.2 referencing=0.30.2 conda-forge
179 refgenconf 0.12.2 refgenconf=0.12.2 bioconda
180 refgenie 0.12.1 refgenie=0.12.1 bioconda
181 repoze.lru 0.7 repoze.lru=0.7 conda-forge
182 requests 2.31.0 requests=2.31.0 conda-forge
183 requests-cache 1.1.0 requests-cache=1.1.0 conda-forge
184 rich 13.5.1 rich=13.5.1 conda-forge
185 rich-click 1.6.1 rich-click=1.6.1 conda-forge
186 routes 2.5.1 routes=2.5.1 conda-forge
187 rpds-py 0.9.2 rpds-py=0.9.2 conda-forge
188 ruamel.yaml 0.17.32 ruamel.yaml=0.17.32 conda-forge
189 ruamel.yaml.clib 0.2.7 ruamel.yaml.clib=0.2.7 conda-forge
190 scanpy 1.9.3 scanpy=1.9.3 pypi
191 scikit-learn 1.1.2 scikit-learn=1.1.2 pypi
192 scipy 1.10.1 scipy=1.10.1 pypi
193 scvelo 0.2.5 scvelo=0.2.5 pypi
194 seaborn 0.12.2 seaborn=0.12.2 pypi
195 session-info 1.0.0 session-info=1.0.0 pypi
196 setuptools 68.1.0 setuptools=68.1.0 pypi
197 six 1.16.0 six=1.16.0 conda-forge
198 smmap 3.0.5 smmap=3.0.5 conda-forge
199 sortedcontainers 2.4.0 sortedcontainers=2.4.0 conda-forge
200 sqlalchemy 1.4.39 sqlalchemy=1.4.39 pkgs/main
201 sqlalchemy2-stubs 0.0.2a35 sqlalchemy2-stubs=0.0.2a35 conda-forge
202 sqlmodel 0.0.8 sqlmodel=0.0.8 conda-forge
203 statsmodels 0.14.0 statsmodels=0.14.0 pypi
204 stdlib-list 0.9.0 stdlib-list=0.9.0 pypi
205 sysroot_linux-64 2.12 sysroot_linux-64=2.12 conda-forge
206 tables 3.8.0 tables=3.8.0 pypi
207 tabulate 0.9.0 tabulate=0.9.0 conda-forge
208 texttable 1.6.7 texttable=1.6.7 pypi
209 threadpoolctl 3.2.0 threadpoolctl=3.2.0 pypi
210 tk 8.6.12 tk=8.6.12 conda-forge
211 tomli 2.0.1 tomli=2.0.1 conda-forge
212 toolz 0.12.0 toolz=0.12.0 conda-forge
213 tqdm 4.66.1 tqdm=4.66.1 conda-forge
214 typing-extensions 4.7.1 typing-extensions=4.7.1 conda-forge
215 typing_extensions 4.7.1 typing_extensions=4.7.1 conda-forge
216 tzlocal 5.0.1 tzlocal=5.0.1 pypi
217 ubiquerg 0.6.3 ubiquerg=0.6.3 conda-forge
218 ujson 5.7.0 ujson=5.7.0 conda-forge
219 ukkonen 1.0.1 ukkonen=1.0.1 conda-forge
220 umap-learn 0.5.3 umap-learn=0.5.3 pypi
221 url-normalize 1.4.3 url-normalize=1.4.3 conda-forge
222 urllib3 2.0.4 urllib3=2.0.4 conda-forge
223 veracitools 0.1.3 veracitools=0.1.3 conda-forge
224 versioned-hdf5 1.3.14 versioned-hdf5=1.3.14 pypi
225 virtualenv 20.24.3 virtualenv=20.24.3 conda-forge
226 wcwidth 0.2.6 wcwidth=0.2.6 conda-forge
227 webencodings 0.5.1 webencodings=0.5.1 conda-forge
228 wheel 0.41.1 wheel=0.41.1 conda-forge
229 whoosh 2.7.4 whoosh=2.7.4 conda-forge
230 xz 5.2.6 xz=5.2.6 conda-forge
231 yacman 0.9.1 yacman=0.9.1 conda-forge
232 yaml 0.2.5 yaml=0.2.5 conda-forge
233 zipp 3.16.2 zipp=3.16.2 conda-forge
234 zipstream-new 1.1.8 zipstream-new=1.1.8 conda-forge
235 zstandard 0.19.0 zstandard=0.19.0 conda-forge
236 zstd 1.5.2 zstd=1.5.2 conda-forge
This could be a bug in scvelo: https://github.com/theislab/scvelo/pull/1065 https://github.com/theislab/scvelo/issues/1091 https://github.com/theislab/scvelo/issues/1110
There seems to be a conflict between scvelo and pandas > 2.0, but the pandas version in the SCP environment is 1.3.5.
You can try resetting the SCP Python environment by usingPrepareEnv(force = TRUE)
first.
Additionally, reinstalling scvelo from GitHub may also be a potential solution to the issue you're facing:
# Start a new R session
library(SCP)
library(reticulate)
py_install(packages = "git+https://github.com/theislab/scvelo.git@master",pip = TRUE)
If the installation fails, you can also install scvelo manually. Please make sure to use the SCP env's Python to install the package.
Thanks for the instant response.
As you can see in my environment information, the pandas version I had is 1.3.5. I will try to re-install scvelo and see how it goes.
After updating the scvelo, it works now!
Thank you again for the help!
Hi,
Thanks again for the awesome pipeline.
I tried to analysis velocity with the example data and resulted in
Here is the code I am using
And here is the traceback
The package versions loaded are
I have also tried to set up a totally new environment, but still resulted in the same error.
Thanks ahead for the help!
Minjie