Error en if (sum(filter_bool) == 0) {: valor ausente donde TRUE/FALSE es necesario

[vancampra]

Good afternoon,

I have been using the same pipeline with sleuth for the last 2 years, and this time along, I encountered this problem which I don't understand. I have recently updated R to version 4.5.0 and many packages along with it, so I guess this can be the reason. But not sure how to get around it. I was still using sleuth 0.30.1. I updated ti to 0.30.2, but the problem persists.

My metada is of the shape:

Sample|Group|Type|Batch
P100_p1_quant | P_CH | Porta | 1
P105_p1_quant | P_CT | Porta | 1
P106_p1_quant | P_CT | Porta | 1
P109_p1_quant | P_CH | Porta | 1
P111_p1_quant | P_CH | Porta | 1
P112_p1_quant | P_CH_PVT | Porta | 1

And the code I have been using is:

P_CH_fixat_genemode <- sleuth_prep (metadata,
target_mapping = tg2unique,
aggregation_column = 'ens_gene',
gene_mode = TRUE,
read_bootstrap_tpm = TRUE,
extra_bootstrap_summary = TRUE,
transformation_function = function(x) log2(x + 0.5),
num_cores = 2)

And the error:
'gene_mode' is TRUE. Sleuth will do counts aggregation at the gene level for downstream normalization, transformation, and modeling steps, as well as for plotting and results.
Warning in check_num_cores(num_cores) :
It appears that you are running Sleuth from within Rstudio.
Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
If you wish to take advantage of multiple cores, please consider running sleuth from the command line.
reading in kallisto results
dropping unused factor levels
............................................
Warning in check_target_mapping(tmp_names, target_mapping, !is.null(aggregation_column)) :
intersection between target_id from kallisto runs and the target_mapping is empty. attempted to fix problem by removing .N from target_id, then merging back into target_mapping. please check obj$target_mapping to ensure this new mapping is correct.
normalizing est_counts
Error en if (sum(filter_bool) == 0) {:
valor ausente donde TRUE/FALSE es necesario
Error durante el wrapup: no hay tantas estructuras en la pila
Error: no more error handlers available (recursive errors?); invoking 'abort' restart

The problem with the target IDs has been appearing since the beginning. Is that now giving the problem?

Thanks in advance for any input!