Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Get errors when retrieving information from the BioMart database #215

Open
ZyRose1 opened this issue Dec 1, 2023 · 1 comment
Open

Get errors when retrieving information from the BioMart database #215

ZyRose1 opened this issue Dec 1, 2023 · 1 comment

Comments

@ZyRose1
Copy link

ZyRose1 commented Dec 1, 2023

This is My error and Package ‘biomaRt’ version 2.56.1 cannot be unloaded :

ht <- FeatureHeatmap(
+   srt = pancreas_sub, group.by = "celltype", features = DEGs$gene, feature_split = DEGs$group1,
+   species = "Homo_sapiens", db = c("GO_BP","KEGG"), anno_terms = TRUE,
+   feature_annotation = c("CSPA"), feature_annotation_palcolor = list(c("gold")),
+   height = 5, width = 4
+ )
Warning in FeatureHeatmap(srt = pancreas_sub, group.by = "celltype", features = DEGs$gene,  :
  The values in the 'counts' slot are non-integer. Set the library size to 1.
[2023-12-02 00:55:42.461781] Start Enrichment
Workers: 6
Species: Homo_sapiens
Loading cached db: GO_BP version:3.17.0 nterm:15960 created:2023-08-23 10:35:32.644541
Loading cached db: KEGG version:Release 108.0+/11-26, Nov 23 nterm:356 created:2023-11-26 22:33:54.616616
Convert ID types for the database: KEGG
Connect to the Ensembl archives...
Using the 103 version of biomart...
Connecting to the biomart...
Searching the dataset hsapiens ...
Connecting to the dataset hsapiens_gene_ensembl ...
Converting the geneIDs...
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Get errors when retrieving information from the BioMart database
Retrying...
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Get errors when retrieving information from the BioMart database
Retrying...
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
@synapse73
Copy link

downgrading dbplyr solves this issue for me (devtools::install_version("dbplyr", version = "2.3.4"))

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants