Hey,
I have been using RATs recently, mainly with salmon output making use of the fish4rodents function.
It always worked well and I have been working on the same data the whole time (since ~ 1week).
Suddenly I cannot reproduce my results or rather I cannot reproduce because I get an error during the execution of fish4rodents, using the same data using the same code. The only change that might have happened is that with installing a new bioconductor package I updated all other libraries...
But I don't see how this could have influenced the reading of salmon input (as there was no update of wasabi or rats)

The Code
fish4rodents(case.dir.list,control.dir.list,annot,scaleto=libsize)

(first to vars are path lists, annot colnames are as recommended in the vignettes, libsize is a vector of length= length(case.dir.list)+length(control.dir.list))

The Error:

Error in as.data.table.array(h5read(file.path(fil, "abundance.h5"), "/aux/ids")) :
as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used

The error appears after each sample data has already been sucessfully converted as the output tells me.

Tue May 8 11:05:53 2018
[1] "Successfully converted sailfish / salmon results in salmon_withBootstrap/1234 to kallisto HDF5 format"

I checked the code of the function and also went to check the wasabi code of the prepareFishForSleuth() functions. No error comes up during the call of this function. It seems to go all well until line
104 in RATS/R/input.R
ids <- as.data.table( h5read(file.path(fil, "abundance.h5"), "/aux/ids") )

I unfortunately have no knowledge about h5 files and their structure but it seems that they were created in a wrong way during conversion even though no error was caught before?

I attached my session info.
I hope provided all necessary information, if not please let me know.

Thanks in advance

sessionInfo.txt