Ubuntu系统biomaRt+dbplyr调用getBM时collect报错求助

在Ubuntu系统使用biomaRt获取Ensembl注释时，已更新所有相关包，但仍反复触发相同错误，Mac系统下无此问题。

运行代码 #

ensembl <- useMart(
  "ENSEMBL_MART_ENSEMBL",
  dataset = "hsapiens_gene_ensembl", 
  host="https://may2021.archive.ensembl.org"
)
ids <- as.vector(row.names(OS_total))
ids
listAttributes(ensembl)
annot <- getBM(
  attributes=c(
    "ensembl_gene_id",
    "transcript_length", 
    "percentage_gene_gc_content",
    "gene_biotype",
    "chromosome_name", 
    "start_position",
    "end_position",
    "external_gene_name",
    "external_gene_source"
  ),
  filters="ensembl_gene_id",
  values=ids,
  mart=ensembl
)

错误详情 #

rlang::last_trace()
<error/rlang_error>
Error in collect():
! 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?

回溯信息 #

1. ├─biomaRt::getBM(...)
2. │ └─BiocFileCache::BiocFileCache(cache, ask = FALSE)
3. │ └─BiocFileCache:::.sql_create_db(bfc)
4. │ └─BiocFileCache:::.sql_validate_version(bfc)
5. │ └─BiocFileCache:::.sql_schema_version(bfc)
6. │ ├─base::tryCatch(...)
7. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. │ └─tbl(src, "metadata") %>% collect(Inf)
9. ├─dplyr::collect(., Inf)
10. └─dbplyr:::collect.tbl_sql(., Inf)
11. ├─base::tryCatch(...)
12. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. └─dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)

已尝试操作 #

• 查阅BiocFileCache与新版dbplyr兼容性相关内容
• 从GitHub更新所有相关包

解决建议 #

• 降级dbplyr到兼容版本：新版dbplyr的collect函数参数逻辑变更，导致BiocFileCache调用报错，安装dbplyr 2.3.4版本：

  install.packages("dbplyr", version = "2.3.4")
  

• 清理BiocFileCache缓存：清除旧缓存避免数据库schema冲突：

  BiocFileCache::bfcpurge()
  

• 指定临时缓存目录：调用useMart时指定临时目录作为缓存，绕过现有缓存问题：

  ensembl <- useMart(
    "ENSEMBL_MART_ENSEMBL",
    dataset = "hsapiens_gene_ensembl", 
    host="https://may2021.archive.ensembl.org",
    cache = tempdir()
  )
  

• 检查系统依赖：Ubuntu系统确保安装libsqlite3-dev依赖：

  sudo apt-get install libsqlite3-dev
  

内容的提问来源于stack exchange，提问作者Roberto Salatino