Creation of TiledbArray fails on Linux ARM64

[martin-g]

Hello,

The CMD build of TileDBArray fails on Linux ARM64 with the following error:

 ~/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data TileDBArray
* checking for file ‘TileDBArray/DESCRIPTION’ ... OK
* preparing ‘TileDBArray’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘userguide.Rmd’ using rmarkdown
Quitting from lines 35-38 (userguide.Rmd) 
Error: processing vignette 'userguide.Rmd' failed with diagnostics:
Expecting an external pointer: [type=NULL].
--- failed re-building ‘userguide.Rmd’

SUMMARY: processing the following file failed:
  ‘userguide.Rmd’

Error: Vignette re-building failed.
Execution halted

I have also tested with as(X, "TileDBArray") and it fails the same way:

* creating vignettes ... ERROR
--- re-building ‘userguide.Rmd’ using rmarkdown
Quitting from lines 43-44 (userguide.Rmd) 
Error: processing vignette 'userguide.Rmd' failed with diagnostics:
Expecting an external pointer: [type=NULL].
--- failed re-building ‘userguide.Rmd’

Do you have any ideas what could be the problem ?

[LTLA]

Hm. And the tiledb package itself builds/checks okay on Arm? Because I don't do anything with external pointers in this package's C++ code, so it must be coming from a tiledb function.

The only thing I can imagine is that I'm not using a tiledb function in the correct way, or I'm using an obsolete function; but it's hard to imagine that doing so in a manner that only causes failures on Arm.

[martin-g]

Thanks for the answer, @LTLA !

It might be related to TileDB-Inc/TileDB-R#520 where we decided to use the Ubuntu package of tiledb and not build it from source because the stock tiledb does not support Linux ARM64. The Ubuntu package maintainers add the support but also the version of tiledb is a bit old...

[eddelbuettel]

If I recall correctly we waiting for CI runners to be come available so that we can make it part of the usual workflow.

As for 'newer Ubuntu builds', there is only so much we (TileDB) can do about a distro having six-month snapshots or two years for LTS. If you CI process needs it now on a different platform maybe you just have to build it from source. I don't see many other options.