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dynverse / dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages šŸ¦•
https://dynverse.github.io/dyno
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Error with Singularity 3.30 x Docker version 19.03.8 unknown flag: --containall #82

Open tiagobrc opened 4 years ago

tiagobrc commented 4 years ago

Hi, Thanks for this amazing project on TI. I am trying to run the ti_paga as suggested by the shiny tool. But I am getting a singularity error. It looks to me that it is related to a version incompatibility? Would you be able to tell me/guide me through the issue?

Thanks !

after running the command šŸ‘Ž model <- infer_trajectory(dataset = dataset, method = ti_paga())


Running singularity exec 'docker://dynverse/ti_paga:v0.9.9.05' echo hi
Running /usr/local/bin/singularity exec --containall -B \
  '/tmp/folders/yb/fr3srvpx3f19zyd4fx52836r0000gn/T//Rtmp0PRKPF/filebab83110c43c/:/copy_mount,/tmp/folders/yb/fr3srvpx3f19zyd4fx52836r0000gn/T//Rtmp0PRKPF/filebab843c3584e/tmp:/tmp2' \
  'docker://dynverse/ti_paga:v0.9.9.05' cp /code/definition.yml /copy_mount/

Error: Error for command "exec": unknown flag: --containall Options for exec command: -B, --bind strings a user-bind path specification. spec has the format src[:dest[:opts]], where src and dest are outside and inside paths. If dest is not given, it is set equal to src. Mount options ('opts') may be specified as 'ro' (read-only) or 'rw' (read/write, which is the default). Multiple bind paths can be given by a comma separated list. --disable-cache dont use cache, and dont create cache --docker-login login to a Docker Repository interactively -h, --help help for exec -H, --home string a home directory specification. spec can either be a src path or src:dest pair. src is the source path of the home directory outside the container
tiagobrc commented 4 years ago

I am using a MacBook pro running Catalina. By running the singularity test command I get another error: > dynwrap::test_singularity_installation(detailed = TRUE)


> dynwrap::test_singularity_installation(detailed = TRUE)
āœ” Singularity is installed
āœ” Singularity is at correct version (>=3.0): 3.3.0-rc.1.658.g7427b73f1.dirty is installed
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:5d20c808ce198565ff70b3ed23a991dd49afac45dece63474b27ce6ed036adc6
 2.01 MiB / 2.01 MiB  0s
Copying config sha256:54c9afe02933973b548088d74fca8dc95f0c3ae0d1bc765efbf2673c31a8e627
 585 B / 585 B  0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
Error in dynwrap::test_singularity_installation(detailed = TRUE) : 
  āŒ Singularity is unable to run pull and run a container from Dockerhub.
zy-fang commented 2 years ago

Hi,

I have same problem. Did you solve it ?