Error: 'separate_longer_delim' is not an exported object from 'namespace:tidyr'

[fahmadimoughari]

Hi,

I ran run_numbat using the following code:
allele <- read.table(paste0(outdir, the.sample, "_allele_counts.tsv.gz"), sep = "\t", header = TRUE);
seu <- readRDS(file.path(data.dir, the.sample, "clustered_seurat_.rds"));
counts <- GetAssayData(seu, slot = "counts", assay = "RNA");
out <- run_numbat( count_mat = counts, lambdas_ref = ref_hca, df_allele = allele, genome = "hg38", t = 1e-5, ncores = 16, plot = TRUE, out_dir = outdir );

And it ran for 3 hours and generated bulk_clones_1.tsv, bulk_subtrees_1.tsv, gex_roll_wide.tsv, hc.rds, sc_refs.rds and segs_consensus_1.tsv files, but it stopped and. gave the following error:

Running HMMs on 3 cell groups..
Testing for multi-allelic CNVs ..
1 multi-allelic CNVs found: 11c
Evaluating CNV per cell ..
Mem used: 10.2Gb
All cells succeeded
Expanding allelic states..
Error: 'separate_longer_delim' is not an exported object from 'namespace:tidyr'
In addition: Warning message:
In asMethod(object) :
sparse->dense coercion: allocating vector of size 1.1 GiB
Execution halted
srun: error: node01: task 0: Exited with exit code 1

Any idea what the reason is and how can I address the issue?

[fahmadimoughari]

I managed to debug it and get to this point that it works perfectly by setting multi_allelic = FALSE
And the reason id, when multi_allelic = TRUE, it logs as '0 multi-allelic CNVs found so it would run'
and then it will run test_multi_allelic, in which it will run this line n_states = ifelse(cnv_state == 'neu', 0, 1), which means all n_states in segs_consensus would be 0 & 1. This is how my segs_consensus look like:

>table(segs_consensus$n_states)
 0  1 
25 37 

so, by the time it gets to run exp_post = expand_states(exp_post, segs_consensus)
there is no n_states > 1; therefore, running expand_states function breaks
because dimension of segs_consensus %>% filter(n_states > 1) would be 0

> dim(segs_consensus%>% filter(n_states > 1))
[1]  0 29

so it will stop at this line

segs_multi = segs_consensus %>% filter(n_states > 1) %>%
        select(seg = seg_cons, cnv_states, n_states) %>%
        tidyr::separate_longer_delim(cnv_states, ',') %>%
        rename(cnv_state = cnv_states)

in expand_states function and return
Error: 'separate_longer_delim' is not an exported object from 'namespace:tidyr'

because all n_states has been set to 0 & 1 and technically, there is no way to get past
this step unless we set multi_allelic = FALSE. It seems to me that the code is written
in a way that if multi_allelic == TRUE, there is no way to run it successfully unless
you actually have some multi-allelic CNVs.

[teng-gao]

Does upgrading to tidyr 1.3.0 solve the issue? Prior versions do not have this function separate_longer_delim.

https://www.tidyverse.org/blog/2023/01/tidyr-1-3-0/