无法通过 RStudio 服务器在 Linux 上安装 SingleCellExperiment R 包

如何解决无法通过 RStudio 服务器在 Linux 上安装 SingleCellExperiment R 包

我尝试使用

在 Linux 服务器上安装 SingleCellExperiment

if (!requireNamespace("BiocManager",quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("SingleCellExperiment")

然而，我得到了这样的错误信息，似乎错误是关于不匹配的插槽类。我是单细胞分析的新手，不知道如何解决这个问题。

Error in makePrototypeFromClassDef(properties,ClassDef,immediate,where) : 
  in making the prototype for class “SingleCellExperiment” elements of the prototype Failed to match the corresponding slot class: rowRanges (class "genomicrangesORGRangesList" )
Error: unable to load R code in package ‘SingleCellExperiment’
Execution halted

我的会话信息如下：

R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (nitrogen)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

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

attached base packages:
[1] parallel  stats4    stats     graphics  Grdevices utils    
[7] datasets  methods   base     

other attached packages:
 [1] SummarizedExperiment_1.6.5 DelayedArray_0.2.7        
 [3] matrixStats_0.57.0         Biobase_2.36.2            
 [5] genomicranges_1.38.0       GenomeInfoDb_1.22.1       
 [7] XVector_0.26.0             IRanges_2.20.2            
 [9] S4Vectors_0.24.4           Biocgenerics_0.32.0       

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5             BiocInstaller_1.26.1  
 [3] pillar_1.4.4           compiler_3.6.0        
 [5] BiocManager_1.30.10    bitops_1.0-6          
 [7] tools_3.6.0            zlibbioc_1.22.0       
 [9] lattice_0.20-38        lifecycle_0.2.0       
[11] tibble_3.0.1           gtable_0.3.0          
[13] pkgconfig_2.0.3        rlang_0.4.9           
[15] Matrix_1.2-17          cli_2.2.0             
[17] rstudioapi_0.13        ggrepel_0.9.0         
[19] GenomeInfoDbData_1.2.2 dplyr_1.0.0           
[21] generics_0.1.0         vctrs_0.3.1           
[23] grid_3.6.0             tidyselect_1.1.0      
[25] glue_1.4.2             R6_2.5.0              
[27] fansi_0.4.1            ggplot2_3.3.2         
[29] purrr_0.3.4            magrittr_2.0.1        
[31] scales_1.1.1           ellipsis_0.3.1        
[33] assertthat_0.2.1       colorspace_2.0-0      
[35] RCurl_1.95-4.11        munsell_0.5.0         
[37] Crayon_1.3.4  

安装时来自控制台的更多信息：

Bioconductor version 3.10 (BiocManager 1.30.10),R 3.6.0 (2019-04-26)
Installing package(s) 'SingleCellExperiment'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/SingleCellExperiment_1.8.0.tar.gz'
Content type 'application/x-gzip' length 614930 bytes (600 KB)
==================================================
downloaded 600 KB

* installing *source* package ‘SingleCellExperiment’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: no function found corresponding to methods exports from ‘DelayedArray’ for: ‘acbind’,‘arbind’ 
2: multiple methods tables found for ‘type’ 
3: multiple methods tables found for ‘rowSums’ 
4: multiple methods tables found for ‘colSums’ 
5: multiple methods tables found for ‘rowMeans’ 
6: multiple methods tables found for ‘colMeans’ 
7: multiple methods tables found for ‘splitAsList’ 
8: replacing prevIoUs import ‘Biocgenerics::dims’ by ‘Biobase::dims’ when loading ‘SummarizedExperiment’ 
9: replacing prevIoUs import ‘Biocgenerics::type’ by ‘DelayedArray::type’ when loading ‘SummarizedExperiment’ 
10: no function found corresponding to methods exports from ‘SummarizedExperiment’ for: ‘acbind’,‘arbind’ 
Warning: undefined slot classes in deFinition of "SingleCellExperiment": rowRanges(class "genomicrangesORGRangesList")
Error in makePrototypeFromClassDef(properties,where) : 
  in making the prototype for class “SingleCellExperiment” elements of the prototype Failed to match the corresponding slot class: rowRanges (class "genomicrangesORGRangesList" )
Error: unable to load R code in package ‘SingleCellExperiment’
Execution halted
ERROR: lazy loading Failed for package ‘SingleCellExperiment’
* removing ‘/mnt/sas0/AD/jli2274/R/x86_64-redhat-linux-gnu-library/3.6/SingleCellExperiment’

The downloaded source packages are in
    ‘/tmp/Rtmp2EIKEa/downloaded_packages’
Installation path not writeable,unable to update packages: ade4,annotate,AnnotationDbi,ape,assertthat,backports,BH,Biobase,Biocgenerics,BiocParallel,bit,bit64,blob,boot,checkmate,class,cli,cluster,coda,codetools,colorspace,data.table,DBI,DelayedArray,deldir,DESeq2,digest,doParallel,dplyr,e1071,evaluate,expm,fit.models,foreach,formatR,Formula,genefilter,geneplotter,generics,GenomeInfoDb,GenomeInfoDbData,genomicranges,ggplot2,glue,GO.db,gtable,hierfstat,highr,Hmisc,htmlTable,htmltools,htmlwidgets,igraph,impute,IRanges,iterators,jsonlite,KernSmooth,knitr,labeling,lambda.r,lattice,latticeExtra,lazyeval,locfit,magrittr,markdown,MASS,Matrix,matrixStats,mgcv,mime,mvtnorm,nlme,nnet,pheatmap,pillar,pkgconfig,pls,plyr,preprocesscore,prettyunits,R6,raster,Rcpp,RcppArmadillo,RCurl,reshape2,rlang,robust,robustbase,rrBLUP,rrcov,Rsqlite,rstudioapi,S4Vectors,scales,segmented,seqinr,sf,shiny,sp,spatial,spData,spdep,stringi,stringr,SummarizedExperiment,survival,tibble,units,vctrs,vegan,WGCNA,withr,XML,xtable,XVector,yaml,zlibbioc
Warning message:
In install.packages(...) :
  installation of package ‘SingleCellExperiment’ had non-zero exit status