Closed JJJaneeee closed 4 months ago
name: r-41
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- _r-mutex=1.0.1=anacondar_1
- anyio=4.2.0=pyhd8ed1ab_0
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- r-spatstat.random=3.1_5=r41ha503ecb_0
- r-spatstat.sparse=3.0_1=r41h133d619_0
- r-spatstat.utils=3.0_3=r41h57805ef_0
- r-squarem=2021.1=r41hc72bb7e_1
- r-stringi=1.7.12=r41hc0c3e09_1
- r-stringr=1.5.0=r41h785f33e_0
- r-survival=3.5_5=r41h133d619_0
- r-sys=3.4.2=r41h57805ef_0
- r-systemfonts=1.0.4=r41h0ff29ef_1
- r-tensor=1.5=r41hc72bb7e_1004
- r-textshaping=0.3.6=r41h24cd192_5
- r-tibble=3.2.1=r41h133d619_1
- r-tidyr=1.3.0=r41h38f115c_0
- r-tidyselect=1.2.0=r41hc72bb7e_0
- r-tidyverse=2.0.0=r41h785f33e_0
- r-timechange=0.2.0=r41h38f115c_0
- r-timedate=4022.108=r41hc72bb7e_0
- r-tinytex=0.45=r41hc72bb7e_0
- r-triebeard=0.4.1=r41h38f115c_0
- r-ttr=0.24.3=r41h06615bd_1
- r-tzdb=0.4.0=r41ha503ecb_0
- r-urltools=1.7.3=r41h7525677_3
- r-utf8=1.2.3=r41h133d619_0
- r-uuid=1.1_0=r41h06615bd_1
- r-uwot=0.1.14=r41h7525677_1
- r-vctrs=0.6.2=r41ha503ecb_0
- r-viridislite=0.4.1=r41hc72bb7e_1
- r-vroom=1.6.3=r41ha503ecb_0
- r-withr=2.5.0=r41hc72bb7e_1
- r-xfun=0.39=r41ha503ecb_0
- r-xml2=1.3.4=r41h1ad5fc0_1
- r-xtable=1.8_4=r41hc72bb7e_4
- r-xts=0.13.1=r41h133d619_0
- r-yaml=2.3.7=r41h133d619_0
- r-zoo=1.8_12=r41h133d619_0
- readline=8.2=h8228510_1
- referencing=0.32.1=pyhd8ed1ab_0
- requests=2.31.0=pyhd8ed1ab_0
- rfc3339-validator=0.1.4=pyhd8ed1ab_0
- rfc3986-validator=0.1.1=pyh9f0ad1d_0
- rpds-py=0.17.1=py312h4b3b743_0
- sed=4.8=he412f7d_0
- send2trash=1.8.2=pyh41d4057_0
- setuptools=69.0.3=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- sniffio=1.3.0=pyhd8ed1ab_0
- soupsieve=2.5=pyhd8ed1ab_1
- stack_data=0.6.2=pyhd8ed1ab_0
- sysroot_linux-64=2.12=he073ed8_16
- terminado=0.18.0=pyh0d859eb_0
- tinycss2=1.2.1=pyhd8ed1ab_0
- tk=8.6.13=noxft_h4845f30_101
- tktable=2.10=h0c5db8f_5
- tomli=2.0.1=pyhd8ed1ab_0
- tornado=6.3.3=py312h98912ed_1
- traitlets=5.14.1=pyhd8ed1ab_0
- types-python-dateutil=2.8.19.20240106=pyhd8ed1ab_0
- typing-extensions=4.9.0=hd8ed1ab_0
- typing_extensions=4.9.0=pyha770c72_0
- typing_utils=0.1.0=pyhd8ed1ab_0
- tzdata=2023d=h0c530f3_0
- uri-template=1.3.0=pyhd8ed1ab_0
- urllib3=2.1.0=pyhd8ed1ab_0
- wcwidth=0.2.13=pyhd8ed1ab_0
- webcolors=1.13=pyhd8ed1ab_0
- webencodings=0.5.1=pyhd8ed1ab_2
- websocket-client=1.7.0=pyhd8ed1ab_0
- wheel=0.42.0=pyhd8ed1ab_0
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.1.1=hd590300_0
- xorg-libsm=1.2.4=h7391055_0
- xorg-libx11=1.8.7=h8ee46fc_0
- xorg-libxau=1.0.11=hd590300_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxrender=0.9.11=hd590300_0
- xorg-libxt=1.3.0=hd590300_1
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h0b41bf4_1003
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.6=h166bdaf_0
- yaml=0.2.5=h7f98852_2
- zeromq=4.3.5=h59595ed_0
- zipp=3.17.0=pyhd8ed1ab_0
- zlib=1.2.13=hd590300_5
- zstd=1.5.5=hfc55251_0
prefix: /data/users/tanliwei/conda/envs/r-41
Here is a conda environment definition, I can run h5ad2rds.R successfully on it, you can copy into a file, like env.yml
, and run the command below to create a new conda environment and try again
conda env create -n r-env -f env.yml
Hey guys! When I run 'h5ad2rds.R' to convert h5ad file to .rds format, I met error"Error in UpdateKey(key = layer) : could not find function "UpdateKey". Maybe "UpdateKey" function is a function in"SeuratDisk", and I have installed the package"SeuratDisk" v0.0.0.9015, It's the latest version, but there is no function"UpdateKey". I want to know how can I use this R script for data conversion?
Thanks for help!