I tried to install SingleCellExperiment on a Linux server with
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SingleCellExperiment")
However, I got such error information, It seems the error is about the unmatched slot classes. I'm new to single-cell analyses and don't know how to fix this problem.
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
My session information is as follows:
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
More information from the console while installation:
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, 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
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
