Error - cannot make plots

[mariaUCL]

When I run cellxgene I get the button and everythiing but when I try to make a violin plot or any other plot I get an error. This is what I get after running cellxgene launch --host localhost --port 5005 --disable-annotations -var feature_name --verbose https://datasets.cellxgene.cziscience.com/676c47a4-bd2c-4f09-82cb-2dfcd54be04a.h5ad :

ERROR @server: Traceback (most recent call last): File "/Users/usr/anaconda3/envs/VIP/lib/python3.8/site-packages/server/app/VIPInterface.py", line 62, in route setTimeStamp(data) File "/Users/usr/anaconda3/envs/VIP/lib/python3.8/site-packages/server/app/VIPInterface.py", line 1501, in setTimeStamp Path(strF).touch() File "/Users/usr/anaconda3/envs/VIP/lib/python3.8/pathlib.py", line 1274, in touch fd = self._raw_open(flags, mode) File "/Users/usr/anaconda3/envs/VIP/lib/python3.8/pathlib.py", line 1083, in _raw_open return self._accessor.open(self, flags, mode) FileNotFoundError: [Errno 2] No such file or directory: 'https:/datasets.cellxgene.cziscience.com/676c47a4-bd2c-4f09-82cb-2dfcd54be04a.timestamp'

Someone suggested I might not have the necessary R packages but I don't think this is it. I also ran R -q -e 'installed.packages()' to check that I have all the packages which I do. I am not sure what is causing this. I got errors installing hexbin and Cairo so installed them with the below code and still I am getting this error:

R -q -e 'install.packages("hexbin", repos = "http://bioconductor.org/biocLite.R")' R -q -e 'install.packages("hexbin", repos = "http://cran.us.r-project.org/", INSTALL_opts = "--build")' brew install Cairo

See packages below: devtools version: 2.4.5

check_and_print_version("Cairo") Cairo is not installed. check_and_print_version("foreign") foreign version: 0.8.86 check_and_print_version("ggpubr") ggpubr version: 0.6.0 check_and_print_version("ggrastr") ggrastr version: 1.0.2 check_and_print_version("arrow") arrow version: 14.0.0.2 check_and_print_version("Seurat") Seurat version: 5.0.1 check_and_print_version("rmarkdown") rmarkdown version: 2.25 check_and_print_version("tidyverse") tidyverse version: 2.0.0 check_and_print_version("viridis") viridis version: 0.6.4 check_and_print_version("hexbin") hexbin version: 1.28.3 check_and_print_version("ggforce") ggforce version: 0.4.1 check_and_print_version("RcppRoll") RcppRoll version: 0.3.0 check_and_print_version("fastmatch") fastmatch version: 1.1.4 check_and_print_version("BiocManager") BiocManager version: 1.30.22 check_and_print_version("fgsea") fgsea version: 1.28.0 check_and_print_version("rtracklayer") rtracklayer version: 1.62.0 check_and_print_version("rjson") rjson version: 0.2.21 check_and_print_version("ComplexHeatmap") ComplexHeatmap version: 2.18.0 check_and_print_version("dbplyr") dbplyr version: 2.4.0 check_and_print_version("RColorBrewer") RColorBrewer version: 1.1.3 check_and_print_version("glue") glue version: 1.6.2 check_and_print_version("gridExtra") gridExtra version: 2.3 check_and_print_version("ggrepel") ggrepel version: 0.9.4 check_and_print_version("MASS") MASS version: 7.3.60 check_and_print_version("data.table") data.table version: 1.14.8

[z5ouyang]

Please checkout the newest commit and update.VIPInterface.sh. Let me know if the issue still persists.