why monocle invoke BiocGenerics package error ?
Hi @ctrapnell , I am very confused that the BiocGenerics pacakage had exists but the monocle can not be invoked it showing below error: 8 nodes produced errors; first error: there is no package called ‘BiocGenerics’ Calls: differentialGeneTest ... mcesApply -> clusterCall -> clusterCall -> checkForRemoteErrors I am runing the monocle on Rscript on the centos7 backgroup. The R info laid below, R version 3.6.0 (2019-04-26) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C
[3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] getopt_1.20.3 Seurat_3.2.0 dplyr_1.0.2
[4] stringr_1.4.0 monocle_2.14.0 DDRTree_0.1.5
[7] irlba_2.3.3 VGAM_1.1-2 ggplot2_3.3.2
[10] Biobase_2.46.0 BiocGenerics_0.34.0 Matrix_1.2-18
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_1.4-1 deldir_0.1-23
[4] ggridges_0.5.1 spatstat.data_1.4-3 leiden_0.3.1
[7] listenv_0.8.0 npsurv_0.4-0 ggrepel_0.8.1
[10] codetools_0.2-16 docopt_0.6.1 lsei_1.2-0
[13] polyclip_1.10-0 jsonlite_1.6 ica_1.0-2
[16] cluster_2.1.0 png_0.1-7 uwot_0.1.5
[19] pheatmap_1.0.12 shiny_1.4.0 sctransform_0.2.1
[22] compiler_3.6.0 httr_1.4.1 fastmap_1.0.1
[25] lazyeval_0.2.2 limma_3.42.0 later_1.0.0
[28] htmltools_0.4.0 tools_3.6.0 rsvd_1.0.2
[31] igraph_1.2.4.2 gtable_0.3.0 glue_1.4.1
[34] RANN_2.6.1 reshape2_1.4.3 rappdirs_0.3.1
[37] Rcpp_1.0.3 spatstat_1.63-3 slam_0.1-47
[40] vctrs_0.3.2 gdata_2.18.0 ape_5.3
[43] nlme_3.1-143 lmtest_0.9-37 globals_0.12.5
[46] mime_0.8 miniUI_0.1.1.1 lifecycle_0.2.0
[49] gtools_3.8.1 goftest_1.2-2 future_1.15.1
[52] MASS_7.3-51.5 zoo_1.8-6 scales_1.1.0
[55] promises_1.1.0 spatstat.utils_1.17-0 RColorBrewer_1.1-2
[58] reticulate_1.14 pbapply_1.4-2 gridExtra_2.3
[61] rpart_4.1-15 fastICA_1.2-2 stringi_1.4.3
[64] caTools_1.17.1.3 densityClust_0.3 rlang_0.4.7
[67] pkgconfig_2.0.3 matrixStats_0.55.0 bitops_1.0-6
[70] qlcMatrix_0.9.7 lattice_0.20-38 tensor_1.5
[73] ROCR_1.0-7 purrr_0.3.3 patchwork_1.0.0
[76] htmlwidgets_1.5.1 cowplot_1.0.0 tidyselect_1.1.0
[79] RcppAnnoy_0.0.14 plyr_1.8.5 magrittr_1.5
[82] R6_2.4.1 gplots_3.0.1.1 generics_0.0.2
[85] combinat_0.0-8 mgcv_1.8-31 pillar_1.4.3
[88] withr_2.1.2 fitdistrplus_1.0-14 abind_1.4-5
[91] survival_3.1-8 tibble_2.1.3 future.apply_1.3.0
[94] crayon_1.3.4 KernSmooth_2.23-16 plotly_4.9.1
[97] viridis_0.5.1 grid_3.6.0 data.table_1.12.8
[100] FNN_1.1.3 HSMMSingleCell_1.6.0 sparsesvd_0.2
[103] digest_0.6.23 xtable_1.8-4 tidyr_1.0.0
[106] httpuv_1.5.2 RcppParallel_4.4.4 munsell_0.5.0
[109] viridisLite_0.3.0
Any advice would be appreciated
Bests,
hanhuihong