proton0803
commented
8 months ago I had a same problem with sleuth_prep(). (sleuth 0.30.1 on R 4.3.2)
> so <- sleuth_prep(s2c, extra_bootstrap_summary = T, target_mapping = t2g, aggregation_column = 'gene_id', gene_mode = T)
'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.
reading in kallisto results
dropping unused factor levels
......
normalizing est_counts
25264 targets passed the filter
normalizing tpm
merging in metadata
aggregating by column: geneid
18671 genes passed the filter
summarizing bootstraps
......Error in order(indices) : unimplemented type 'list' in 'orderVector1'
In addition: Warning messages:
1: `select()was deprecated in dplyr 0.7.0. ℹ Please useselect()instead. ℹ The deprecated feature was likely used in the sleuth package. Please report the issue at <https://github.com/pachterlab/sleuth/issues>. This warning is displayed once every 8 hours. Calllifecycle::last_lifecycle_warnings()` to see where this warning was generated.
2: In parallel::mclapply(x, y, mc.cores = num_cores) :
scheduled core 3 did not deliver a result, all values of the job will be affected
ℹ Please use
spread()instead. ℹ The deprecated feature was likely used in the sleuth package. Please report the issue at https://github.com/pachterlab/sleuth/issues.