PLEASE ADVISE:
While working on the scRNAseq using Seurat, I installed and had no problem with the code
BiocManager::install("SingleCellExperiment")
However when tried to load it using the code
library(SingleCellExperiment)
it failed and message showed in my console as:
Error: package ‘GenomeInfoDb’ could not be loaded
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stop(gettextf("package %s could not be loaded", sQuote(pkg)), call. = FALSE, domain = NA)
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.getRequiredPackages2(pkgInfo, quietly = quietly)
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library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
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.getRequiredPackages2(pkgInfo, quietly = quietly)
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library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
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.getRequiredPackages2(pkgInfo, quietly = quietly)
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library(SingleCellExperiment)
here is my sessionInfo
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.0 MatrixGenerics_1.2.0 matrixStats_0.57.0
[6] cowplot_1.1.0 scales_1.1.1 RCurl_1.98-1.2 Matrix_1.3-0 forcats_0.5.0
[11] stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[16] tibble_3.0.4 ggplot2_3.3.2 tidyverse_1.3.0 Seurat_3.2.3 BiocManager_1.30.10
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_2.0-0 deldir_0.2-3 ellipsis_0.3.1 ggridges_0.5.2
[6] fs_1.5.0 rstudioapi_0.13 spatstat.data_1.7-0 leiden_0.3.6 listenv_0.8.0
[11] ggrepel_0.9.0 fansi_0.4.1 lubridate_1.7.9.2 xml2_1.3.2 codetools_0.2-18
[16] splines_4.0.3 knitr_1.30 polyclip_1.10-0 jsonlite_1.7.2 broom_0.7.3
[21] ica_1.0-2 cluster_2.1.0 dbplyr_2.0.0 png_0.1-7 uwot_0.1.10
[26] shiny_1.5.0 sctransform_0.3.2 compiler_4.0.3 httr_1.4.2 backports_1.2.1
[31] assertthat_0.2.1 fastmap_1.0.1 lazyeval_0.2.2 cli_2.2.0 later_1.1.0.1
[36] htmltools_0.5.0 tools_4.0.3 rsvd_1.0.3 igraph_1.2.6 gtable_0.3.0
[41] glue_1.4.2 RANN_2.6.1 reshape2_1.4.4 tinytex_0.28 Rcpp_1.0.5
[46] spatstat_1.64-1 scattermore_0.7 cellranger_1.1.0 vctrs_0.3.6 nlme_3.1-151
[51] lmtest_0.9-38 xfun_0.19 globals_0.14.0 rvest_0.3.6 mime_0.9
[56] miniUI_0.1.1.1 lifecycle_0.2.0 irlba_2.3.3 renv_0.12.3 goftest_1.2-2
[61] future_1.21.0 MASS_7.3-53 zoo_1.8-8 hms_0.5.3 promises_1.1.1
[66] spatstat.utils_1.17-0 RColorBrewer_1.1-2 yaml_2.2.1 reticulate_1.18 pbapply_1.4-3
[71] gridExtra_2.3 rpart_4.1-15 stringi_1.5.3 bitops_1.0-6 rlang_0.4.9
[76] pkgconfig_2.0.3 evaluate_0.14 lattice_0.20-41 ROCR_1.0-11 tensor_1.5
[81] patchwork_1.1.1 htmlwidgets_1.5.3 tidyselect_1.1.0 parallelly_1.22.0 RcppAnnoy_0.0.18
[86] plyr_1.8.6 magrittr_2.0.1 R6_2.5.0 generics_0.1.0 DBI_1.1.0
[91] withr_2.3.0 pillar_1.4.7 haven_2.3.1 mgcv_1.8-33 fitdistrplus_1.1-3
[96] survival_3.2-7 abind_1.4-5 future.apply_1.6.0 modelr_0.1.8 crayon_1.3.4
[101] KernSmooth_2.23-18 plotly_4.9.2.2 rmarkdown_2.6 readxl_1.3.1 grid_4.0.3
[106] data.table_1.13.4 reprex_0.3.0 digest_0.6.27 xtable_1.8-4 httpuv_1.5.4
[111] munsell_0.5.0 viridisLite_0.3.0