ArchRBrowser error message gio: http://127.0.0.1:7711: Operation not supported

[wshands]

I am attempting to run the ArchBrowser from a Docker container with this command:
docker run --workdir /mnt/ArchR/app_test -v /mnt/ArchR:/mnt/ArchR -v /tmp/.X11-unix:/tmp/.X11-unix --net=host archr-app:latest <project dir>

Docker file snippet:

FROM rocker/tidyverse:4.1.1
...
ENTRYPOINT ["Rscript", "/opt/run_archr_app.R"]
CMD ["Rscript", "/opt/run_archr_app.R"]

R script in container that calls ArchRBrowser is essentially this:

message(paste("Loading ArchR project in project directory:", opt$project_directory))
proj <- loadArchRProject(path = opt$project_directory)
message(paste("Calling ArchR browser"))
ArchRBrowser(ArchRProj = proj, logFile = createLogFile(name = "ArchRBrowser", logDir = paste(opt$project_directory,"ArchRLogs", sep = "/")))

I see this in output:

Calling ArchR browser
ArchR logging to : /mnt/ArchR/new_test_data_from_matt_run/1956686d45a88c099ef8384ecf9f1329/SciTest//ArchRLogs/ArchR-ArchRBrowser-13614181c-Date-2021-11-16_Time-16-09-00.log
If there is an issue, please report to github with logFile!
Listening on http://127.0.0.1:7711
gio: http://127.0.0.1:7711: Operation not supported

However this command

docker run -v /tmp/.X11-unix:/tmp/.X11-unix --net=host archr-app:latest

will launch the firefox browser with this statement in the Dockerfile

CMD /usr/bin/firefox

The log file looks like this:

Logging With ArchR!
Start Time : 2021-11-16 16:09:00
------- ArchR Info
ArchRThreads = 1
------- System Info
Computer OS = unix
------- Session Info
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ArchR_1.0.2 magrittr_2.0.1
[3] rhdf5_2.38.0 Matrix_1.3-4
[5] data.table_1.14.2 SummarizedExperiment_1.24.0
[7] Biobase_2.54.0 GenomicRanges_1.46.0
[9] GenomeInfoDb_1.30.0 IRanges_2.28.0
[11] S4Vectors_0.32.2 BiocGenerics_0.40.0
[13] MatrixGenerics_1.6.0 matrixStats_0.61.0
[15] ggplot2_3.3.5 optparse_1.7.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 XVector_0.34.0 pillar_1.6.4
[4] compiler_4.1.1 rhdf5filters_1.6.0 zlibbioc_1.40.0
[7] tools_4.1.1 bitops_1.0-7 lattice_0.20-44
[10] lifecycle_1.0.1 tibble_3.1.6 gtable_0.3.0
[13] pkgconfig_2.0.3 rlang_0.4.12 DelayedArray_0.20.0
[16] DBI_1.1.1 GenomeInfoDbData_1.2.7 stringr_1.4.0
[19] withr_2.4.2 dplyr_1.0.7 generics_0.1.1
[22] vctrs_0.3.8 grid_4.1.1 getopt_1.20.3
[25] tidyselect_1.1.1 glue_1.5.0 R6_2.5.1
[28] fansi_0.5.0 Rhdf5lib_1.16.0 purrr_0.3.4
[31] scales_1.1.1 ellipsis_0.3.2 assertthat_0.2.1
[34] colorspace_2.0-2 utf8_1.2.2 stringi_1.7.5
[37] RCurl_1.98-1.5 munsell_0.5.0 crayon_1.4.2
------- Log Info
2021-11-16 16:09:00 : ArchRBrowser Input-Parameters, Class = list
ArchRBrowser Input-Parameters$ArchRProj: length = 1
ArchRBrowser Input-Parameters$features: length = 0
NULL
ArchRBrowser Input-Parameters$loops: length = 0
NULL
ArchRBrowser Input-Parameters$minCells: length = 1
[1] 25
ArchRBrowser Input-Parameters$baseSize: length = 1
[1] 10
ArchRBrowser Input-Parameters$borderWidth: length = 1
[1] 0.5
ArchRBrowser Input-Parameters$tickWidth: length = 1
[1] 0.5
ArchRBrowser Input-Parameters$facetbaseSize: length = 1
[1] 12
ArchRBrowser Input-Parameters$browserTheme: length = 1
[1] "cosmo"
ArchRBrowser Input-Parameters$threads: length = 1
[1] 1
ArchRBrowser Input-Parameters$verbose: length = 1
[1] TRUE
ArchRBrowser Input-Parameters$verbose: length = 1
[1] TRUE
ArchRBrowser Input-Parameters$logFile: length = 1
[1] "/mnt/ArchR/new_test_data_from_matt_run/1956686d45a88c099ef8384ecf9f1329/SciTest//ArchRLogs/ArchR-ArchRBrowser-13614181c-Date-2021-11-16_Time-16-09-00.log"
1,0-1 Top

Has anyone seen the gio Operation not supported error before and found out how to fix it? Maybe its an incomplete ArchR project?

[rcorces]

My assumption would be that this is related to containerization. We have been playing around with containers for ArchR but I'm not sure we've ever used the ArchRBrowser from within the container. I'm unfortunately not very fluent with containers and dont think I'll be of much help here.

[wshands]

I think I figured out a Dockerfile and installation files (there are probably extraneous packages that could be removed) that work to enable one to start a Docker container with an rstudio server with ArchR packages installed.
Get the files:
git clone https://github.com/wshands/archr-rstudio-server.git
Build the Docker image as usual
docker build -t archr-rstudio-server:latest ./docker
You need to start the container with something like the following, where you use your container name and a password of your chosing:
docker run --rm -p 8787:8787 -e PASSWORD=password archr-rstudio-server:latest
Then open a browser on the same machine and navigate to http://localhost:8787
Login as user 'rstudio' and use your chosen password
An rstudio environment should load into the browser
Run library(Archr) to load ArchR and enable the R session for ArchR commands

PS you can find more example commands for running the rstudio server at https://hub.docker.com/r/rocker/rstudio which works for a container based on the tidyverse image even though the instructions are on the rstudio image page.

[rcorces]

thanks for sharing!