Autopkgtest of r-bioc-gsva fails on Salsa CI

[Andreas Tille <andreas@an3as.eu>]

Hi,

I've just realised that autopkgtest of r-bioc-gsva fails with:

...
Error in as(m, "dMatrix") : 
  no method or default for coercing “matrix” to “dMatrix”
In addition: Warning messages:
1: In .local(expr, gset.idx.list, ...) :
  Using 'HDF5Array' objects as input is still in an experimental stage.
2: In .gsva(expr, mapped.gset.idx.list, method, kcdf, rnaseq, abs.ranking,  :
  Using 'DelayedArray' objects as input is still in an experimental stage.
3: Argument 'center' should be of the same length as number of rows of 'x'. Use of a scalar value is deprecated: 1 != 1000 
4: In .local(expr, gset.idx.list, ...) :
  Using 'HDF5Array' objects as input is still in an experimental stage.
5: In .gsva(expr, mapped.gset.idx.list, method, kcdf, rnaseq, abs.ranking,  :
  Using 'DelayedArray' objects as input is still in an experimental stage.
6: Argument 'center' should be of the same length as number of rows of 'x'. Use of a scalar value is deprecated: 1 != 1000 
7: In .local(expr, gset.idx.list, ...) :
  Using 'HDF5Array' objects as input is still in an experimental stage.
8: In .gsva(expr, mapped.gset.idx.list, method, kcdf, rnaseq, abs.ranking,  :
  Using 'DelayedArray' objects as input is still in an experimental stage.
9: In .local(expr, gset.idx.list, ...) :
  Using 'dgCMatrix' objects as input is still in an experimental stage.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
RUNIT TEST PROTOCOL -- Wed Sep 14 07:11:01 2022 
*********************************************** 
Number of test functions: 4 
Number of errors: 1 

Feel free to check the full log[1].

I'm not sure whether this is an hdf5 issue or something else.
Any idea how to fix this before asking upstream?

Kind regards

    Andreas.


[1] https://salsa.debian.org/r-pkg-team/r-bioc-gsva/-/jobs/3234485

-- 
http://fam-tille.de