Open teng-gao opened 2 years ago
Relevant code:
https://github.com/YuLab-SMU/treeio/blob/master/R/method-as-phylo.R#L1-L3
> tree = readRDS("tree_final_1")
> ape::as.phylo(tree)
Error in UseMethod("as.phylo") :
no applicable method for 'as.phylo' applied to an object of class "c('tbl_graph', 'igraph')"
> treeio::as.phylo(tree)
Error: C stack usage 7969664 is too close to the limit
In addition: Warning message:
The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Using compatibility `.name_repair`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Somewhere there is very deep recursion happening to be fixed.
I remember tracing the error back to this line
https://github.com/YuLab-SMU/treeio/blob/master/R/method-as-phylo.R#L28-L31
Most likely occurred in treeio:::.write.tree4
.
@xiangpin
Relevant issue here: https://github.com/kharchenkolab/numbat/issues/30
At some point, there's a recursive function which recurses too deeply, creating a stack overflow.
It's possible the fix belongs in ape
...I haven't explored this properly yet.
Just following up on this - do you think this is an ape
issue or treeio
issue? This fix in ape
last week that seems relevant:
https://github.com/emmanuelparadis/ape/issues/53
Yes, I'm working with Teng above---we are working on this package: https://github.com/kharchenkolab/numbat
The dependencies are ape
and treeio
. We're trying to figure out where the error is and how to best fix it. We should really CC the relevant ape
authors: @KlausVigo @emmanuelparadis
I'm happy to put in time for a PR to fix these issues, but (like Teng) I'm trying to figure out where to begin.
Everyone's insight here would be really helpful.
Thanks, Evan
Hey,
I am getting an error when trying to plot the heatmap while running Numbat: Mem used: 5.84Gb INFO [2022-06-17 00:24:06] Using 3 CNVs to construct phylogeny INFO [2022-06-17 00:25:14] Using UPGMA tree as seed.. INFO [2022-06-17 00:25:16] Mem used: 5.84Gb INFO [2022-06-17 00:25:25] Iter 2 -2575.81224322793 9.6s INFO [2022-06-17 00:25:36] opt_move:17a->9d, cost=886 INFO [2022-06-17 00:25:46] Found 2111 normal cells.. WARN [2022-06-17 00:25:50] Plotting phylo-heatmap failed, continuing.. INFO [2022-06-17 00:25:50] All done!
BTW I managed to infer the heatmap and phylogeny in another dataset with 2 CNVs:
Mem used: 9.9Gb INFO [2022-06-02 05:09:48] Using 2 CNVs to construct phylogeny INFO [2022-06-02 06:13:03] Using UPGMA tree as seed.. INFO [2022-06-02 06:13:05] Mem used: 9.9Gb INFO [2022-06-02 06:14:27] Iter 2 -3793.82482404086 82s INFO [2022-06-02 06:15:45] opt_move:5b->8a, cost=2820 INFO [2022-06-02 06:17:05] Found 2359 normal cells.. INFO [2022-06-02 06:17:42] All done!
Please notice that the cost value is significantly lower in the first case. Is this causing the problem?'
I'd appreciate any insights on this one!
Best, Tonia
Hi @GuangchuangYu,
I think the above error is caused by as.phylo
(as reported in my original issue). Please let me know if there would be a fix soon!
Thanks, Teng
@xiangpin do you have some times to look into this?
I think the problem is caused by the internal function check_edgelist
and .write.tree4
. I have modified the check_edgelist
, but the .write.tree4
(seems to be caused by the recursive) might need some time.
I think the problem is caused by the internal function
check_edgelist
and.write.tree4
. I have modified thecheck_edgelist
, but the.write.tree4
(seems to be caused by the recursive) might need some time.
Thanks! A similar issue may have been fixed in ape
(although haven't looked too closely):
https://github.com/emmanuelparadis/ape/commit/defb6d2d1300e4173b22d4ea73d3eaab6ea06fb8
Hi @xiangpin,
Just wanted to follow up on this. Thanks in advance!
Best, Teng
Hi,
When converting from igraph to phylo, I run into the issue of C stack overflow for very deep trees.
Reproducible example: tree_final_1.rds.zip
This is probably similar to the
ape
issue that is address here: https://github.com/emmanuelparadis/ape/issues/54Would really appreciate your help!
Thanks, Teng