Error in loadNamespace(name): there is no package called `BiocInstaller`
moldach opened this issue · 0 comments
moldach commented
I'm getting an error when trying to look up some functions from the scater Bioconductor package. It's giving me an error about BiocInstaller which shouldn't be an issue since that's been replaced with BiocManager:
lookup::lookup(scater::calculateQCMetrics)
Error in loadNamespace(name) : there is no package called ‘BiocInstaller’
sessionInfo():
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /home/tsundoku/anaconda3/lib/libmkl_rt.so
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8
[6] LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] scater_1.12.2 SingleCellExperiment_1.6.0 SummarizedExperiment_1.14.1 DelayedArray_0.10.0 BiocParallel_1.18.1
[6] matrixStats_0.55.0 Biobase_2.44.0 GenomicRanges_1.36.1 GenomeInfoDb_1.20.0 IRanges_2.18.3
[11] S4Vectors_0.22.1 BiocGenerics_0.30.0 ggplot2_3.2.1 rlang_0.4.1 lookup_0.0.0.9000
[16] Seurat_3.1.1 dplyr_0.8.3
loaded via a namespace (and not attached):
[1] ggbeeswarm_0.6.0 Rtsne_0.15 colorspace_1.4-1 ggridges_0.5.1 XVector_0.24.0 BiocNeighbors_1.2.0
[7] rstudioapi_0.10 leiden_0.3.1 listenv_0.7.0 npsurv_0.4-0 ggrepel_0.8.1 codetools_0.2-16
[13] splines_3.6.1 R.methodsS3_1.7.1 lsei_1.2-0 zeallot_0.1.0 jsonlite_1.6 ica_1.0-2
[19] cluster_2.1.0 png_0.1-7 R.oo_1.22.0 uwot_0.1.4 sctransform_0.2.0 BiocManager_1.30.9
[25] compiler_3.6.1 httr_1.4.1 backports_1.1.5 assertthat_0.2.1 Matrix_1.2-17 lazyeval_0.2.2
[31] BiocSingular_1.0.0 htmltools_0.4.0 tools_3.6.1 rsvd_1.0.2 igraph_1.2.4.1 gtable_0.3.0
[37] glue_1.3.1 GenomeInfoDbData_1.2.1 RANN_2.6.1 reshape2_1.4.3 Rcpp_1.0.2 vctrs_0.2.0
[43] gdata_2.18.0 ape_5.3 nlme_3.1-141 DelayedMatrixStats_1.6.1 gbRd_0.4-11 lmtest_0.9-37
[49] stringr_1.4.0 globals_0.12.4 lifecycle_0.1.0 irlba_2.3.3 gtools_3.8.1 future_1.14.0
[55] MASS_7.3-51.4 zlibbioc_1.30.0 zoo_1.8-6 scales_1.0.0 RColorBrewer_1.1-2 memoise_1.1.0.9000
[61] reticulate_1.13 pbapply_1.4-2 gridExtra_2.3 stringi_1.4.3 highlite_0.0.0.9000 caTools_1.17.1.2
[67] bibtex_0.4.2 Rdpack_0.11-0 SDMTools_1.1-221.1 pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-38
[73] ROCR_1.0-7 purrr_0.3.3 htmlwidgets_1.5.1 labeling_0.3 cowplot_1.0.0 tidyselect_0.2.5
[79] RcppAnnoy_0.0.13 plyr_1.8.4 magrittr_1.5 R6_2.4.0 gplots_3.0.1.1 pillar_1.4.2
[85] withr_2.1.2 fitdistrplus_1.0-14 survival_2.44-1.1 RCurl_1.95-4.12 tibble_2.1.3 future.apply_1.3.0
[91] tsne_0.1-3 crayon_1.3.4 KernSmooth_2.23-16 plotly_4.9.0 viridis_0.5.1 grid_3.6.1
[97] data.table_1.12.6 metap_1.1 digest_0.6.22 tidyr_1.0.0 R.utils_2.9.0 RcppParallel_4.4.4
[103] munsell_0.5.0 beeswarm_0.2.3 viridisLite_0.3.0 vipor_0.4.5