Error - cannot make plots #101
Description
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