list.files("/opt/R") returning character(0) on 1.x

[hughjonesd]

On a fresh container of 1.x, running /opt/R/1.0.0/bin/R (or other versions):

> list.files("/opt/R")
character(0)
> list.files("/usr/lib/perl")
character(0)

Is this a permissions issue? I'm logged in as root and bash ls returns the expected result. Other directories also return a normal result:

> list.files("/usr/lib/mime/packages/")
[1] "debianutils" "groff-base"  "less"        "tar"         "util-linux" 

[gaborcsardi]

I think that's a bug in Docker, when you run an i386 container on aarch64 processor, unfortunately.

[hughjonesd]

Do you by chance know if there's an issue for this on Docker?

[gaborcsardi]

I don't remember. Not many people use the i386 arch on Docker or qemu.

If you have a script to run, it is best to run it on GH actions, which is intel, or I can also run it.

[gaborcsardi]

I have some memories that it has to do with the file system (?) using large integers, which is not handled by the OS. Something like this.

[gaborcsardi]

I found this: docker/buildx#395

Somewhere I read that this is an Issue with qemu emulating an 32bit system on an 64bit host.

This is a good way to reproduce, because R ignores the system errors in list.files() (!):

56d7cfb548b9:~# find /opt/R
/opt/R
find: /opt/R: Value too large for defined data type

[gaborcsardi]

I possibly found a silly workaround. If you bind mount a volume, and copy the whole of /opt/R over there, then remove /opt/R and then symlink it to the mounted volume, then things seems to work better.

[gaborcsardi]

Still an issue with Docker 24.0.6 on macOS. I don't think this is going to be fixed.

But I found a workaround based on https://www.mjr19.org.uk/sw/inodes64.html It works pretty well, I am going to add it to the Docker images, or possibly to the DEB packages even:

77d2f1f438e2:~# echo 'list.files("/opt/R")' | /opt/R/1.0.0/bin/R  -q --vanilla
> list.files("/opt/R")
character(0)
> 
77d2f1f438e2:~# echo 'list.files("/opt/R")' | fix32 /opt/R/1.0.0/bin/R  -q --vanilla
> list.files("/opt/R")
 [1] "1.0.0" "1.0.1" "1.1.0" "1.1.1" "1.2.0" "1.2.1" "1.2.2" "1.2.3" "1.3.0"
[10] "1.3.1" "1.4.0" "1.4.1" "1.5.0" "1.5.1" "1.6.0" "1.6.1" "1.6.2" "1.7.0"
[19] "1.7.1" "1.8.0" "1.8.1" "1.9.0" "1.9.1"

[gaborcsardi]

This should be fixed now and work OOTB.

[hughjonesd]

I'm still getting the list.files() problem on 1.x. Should I be using a special command to run R?

[gaborcsardi]

This is macOS arm64:

❯ docker run --pull always -it ghcr.io/r-hub/evercran/1.x bash
latest: Pulling from r-hub/evercran/1.x
Digest: sha256:6c71408ee75154439519f9f7e69ec31ea9bfe5b9e18b95e92f786ee9ff392866
Status: Image is up to date for ghcr.io/r-hub/evercran/1.x:latest
WARNING: The requested image's platform (linux/386) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

b0e5c274aa4f:~# /opt/R/1.9.1/bin/R -q
> list.files("/opt/R")
 [1] "1.0.0" "1.0.1" "1.1.0" "1.1.1" "1.2.0" "1.2.1" "1.2.2" "1.2.3" "1.3.0"
[10] "1.3.1" "1.4.0" "1.4.1" "1.5.0" "1.5.1" "1.6.0" "1.6.1" "1.6.2" "1.7.0"
[19] "1.7.1" "1.8.0" "1.8.1" "1.9.0" "1.9.1"
> list.files("/usr/lib/perl")
[1] "5.8"   "5.8.4"

[gaborcsardi]

Can you share some details about your platform? OS vesion (sw_vers), docker version?