使用biomaRt时遇mutate()与dplyr::select()错误求助

问题详情 #

使用biomaRt包获取Ensembl注释信息时，调用getBM()出现异常错误，重新加载包无法解决。

运行代码及报错 #

> library("biomaRt")
> # release 88 of Ensembl is March 2017
> ensembl <- useEnsembl(biomart = "ensembl", 
+                       dataset = "hsapiens_gene_ensembl", 
+                       mirror = "useast")
> annot2 <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position', 'end_position', 'description', 'strand','external_gene_name'), 
+                 #filters ='ensembl_gene_id', 
+                 #values = gene_ids, 
+                 mart = ensembl)
Error in `mutate()`:
! Problem while computing `rpath = unname(bfcrpath(x, rids = rids))`.
Caused by error in `dplyr::select()`:
! <text>:1:7: unexpected symbol
1: Using an
          ^
Run `rlang::last_error()` to see where the error occurred.
> rlang::last_error()
<error/dplyr:::mutate_error>
Error in `mutate()`:
! Problem while computing `rpath = unname(bfcrpath(x, rids = rids))`.
Caused by error in `dplyr::select()`:
! <text>:1:7: unexpected symbol
1: Using an
          ^
---
Backtrace:
  1. biomaRt::getBM(...)
22. dplyr:::select.data.frame(., rid, field)

环境信息 #

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.46.3      BiocManager_1.30.20 dplyr_1.0.9        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9           dbplyr_2.2.1         pillar_1.8.1         compiler_4.0.3       prettyunits_1.1.1    progress_1.2.2       tools_4.0.3         
 [8] bit_4.0.5            BiocFileCache_1.14.0 RSQLite_2.2.15       memoise_2.0.1        lifecycle_1.0.1      tibble_3.1.7         pkgconfig_2.0.3     
[15] rlang_1.0.4          DBI_1.1.3            cli_3.4.0            rstudioapi_0.14      curl_5.0.0           parallel_4.0.3       xfun_0.31           
[22] fastmap_1.1.1        withr_2.5.0          xml2_1.3.3           httr_1.4.5           stringr_1.4.1        rappdirs_0.3.3       askpass_1.1         
[29] hms_1.1.2            IRanges_2.24.1       generics_0.1.3       vctrs_0.4.1          S4Vectors_0.28.1     stats4_4.0.3         bit64_4.0.5         
[36] tidyselect_1.2.0     glue_1.6.2           Biobase_2.50.0       R6_2.5.1             fansi_1.0.3          AnnotationDbi_1.52.0 XML_3.99-0.13       
[43] limma_3.46.0         purrr_0.3.4          blob_1.2.3           magrittr_2.0.3       ellipsis_0.3.2       BiocGenerics_0.36.1  assertthat_0.2.1    
[50] utf8_1.2.3           tinytex_0.44         stringi_1.7.6        openssl_2.0.3        cachem_1.0.6         crayon_1.5.2        

解决步骤 #

这个错误源于BiocFileCache处理缓存元数据时的解析异常，可按以下顺序尝试解决：

• 清除缓存
  删除现有BiocFileCache缓存文件，让包重新生成：

  library(BiocFileCache)
  bfc <- BiocFileCache()
  bfcpurge(bfc, ask = FALSE)
  

  执行后重新运行你的biomaRt代码。

• 指定新缓存目录
  若清除缓存无效，手动指定一个新的可读写目录作为缓存路径：

  Sys.setenv("BIOCFILECACHE_DIR" = "/your/new/cache/path")
  

  替换路径后重启R再运行代码。

• 更新兼容包版本
  当前R版本4.0.3对应Bioconductor 3.12，dplyr 1.0.9与部分旧版Bioconductor包可能存在兼容问题，更新相关包：

  BiocManager::install(c("BiocFileCache", "biomaRt"), update = FALSE)
  

• 直接指定Ensembl版本
  调用Ensembl 88时，直接用version参数指定而非依赖镜像，避免镜像连接问题：

  ensembl <- useEnsembl(biomart = "ensembl", 
                         dataset = "hsapiens_gene_ensembl", 
                         version = 88)
  

内容的提问来源于stack exchange，提问作者Chiara