Closed amber4mint closed 2 years ago
Please provide a session info
Hi,
Thanks for the quick response!
The session info was showed below:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Traditional)_Taiwan.950 LC_CTYPE=Chinese (Traditional)_Taiwan.950
[3] LC_MONETARY=Chinese (Traditional)_Taiwan.950 LC_NUMERIC=C
[5] LC_TIME=Chinese (Traditional)_Taiwan.950
attached base packages:
[1] splines parallel stats4 stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] sceasy_0.0.5 reticulate_1.20 gprofiler2_0.2.1
[4] readr_2.1.2 circlize_0.4.15 monocle_2.16.0
[7] DDRTree_0.1.5 irlba_2.3.3 VGAM_1.1-7
[10] Matrix_1.3-4 usethis_2.1.6 RColorBrewer_1.1-3
[13] openair_2.8-3 stringr_1.4.0 SingleCellExperiment_1.10.1
[16] SingleR_1.2.4 SummarizedExperiment_1.18.2 DelayedArray_0.14.1
[19] matrixStats_0.60.0 Biobase_2.50.0 GenomicRanges_1.40.0
[22] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
[25] BiocGenerics_0.36.1 ggplot2_3.3.5 cowplot_1.1.1
[28] patchwork_1.1.1 dplyr_1.0.7 Seurat_3.1.4
loaded via a namespace (and not attached):
[1] utf8_1.2.1 tidyselect_1.1.2 RSQLite_2.2.15
[4] AnnotationDbi_1.50.3 htmlwidgets_1.5.4 docopt_0.7.1
[7] combinat_0.0-8 grid_4.0.2 BiocParallel_1.22.0
[10] Rtsne_0.15 munsell_0.5.0 codetools_0.2-16
[13] mutoss_0.1-12 ica_1.0-3 interp_1.1-3
[16] future_1.27.0 withr_2.5.0 fastICA_1.2-3
[19] colorspace_2.0-2 ROCR_1.0-11 listenv_0.8.0
[22] Rdpack_2.4 slam_0.1-50 GenomeInfoDbData_1.2.3
[25] mnormt_2.0.2 pheatmap_1.0.12 bit64_4.0.5
[28] rprojroot_2.0.3 parallelly_1.32.1 vctrs_0.3.8
[31] generics_0.1.3 TH.data_1.1-1 BiocFileCache_1.12.1
[34] randomForest_4.6-10 R6_2.5.1 rsvd_1.0.5
[37] bitops_1.0-7 cachem_1.0.6 assertthat_0.2.1
[40] promises_1.2.0.1 scales_1.2.0 multcomp_1.4-19
[43] gtable_0.3.0 beachmat_2.4.0 globals_0.15.1
[46] processx_3.7.0 sandwich_3.0-2 rlang_1.0.2
[49] GlobalOptions_0.1.2 lazyeval_0.2.2 hexbin_1.28.2
[52] BiocManager_1.30.18 yaml_2.3.5 reshape2_1.4.4
[55] httpuv_1.6.2 tools_4.0.2 ellipsis_0.3.2
[58] ggridges_0.5.3 TFisher_0.2.0 Rcpp_1.0.7
[61] plyr_1.8.6 zlibbioc_1.34.0 densityClust_0.3.2
[64] purrr_0.3.4 RCurl_1.98-1.3 ps_1.7.1
[67] prettyunits_1.1.1 deldir_1.0-6 viridis_0.6.2
[70] pbapply_1.5-0 zoo_1.8-9 ggrepel_0.9.1
[73] cluster_2.1.0 fs_1.5.2 magrittr_2.0.1
[76] data.table_1.14.0 lmtest_0.9-38 RANN_2.6.1
[79] tmvnsim_1.0-2 mvtnorm_1.1-2 fitdistrplus_1.1-8
[82] pkgload_1.2.4 hms_1.1.1 mime_0.12
[85] xtable_1.8-4 jpeg_0.1-9 sparsesvd_0.2
[88] shape_1.4.6 gridExtra_2.3 HSMMSingleCell_1.8.0
[91] testthat_3.1.4 compiler_4.0.2 tibble_3.1.2
[94] maps_3.4.0 KernSmooth_2.23-17 crayon_1.5.1
[97] htmltools_0.5.1.1 mgcv_1.8-31 later_1.3.0
[100] tzdb_0.3.0 tidyr_1.1.3 lubridate_1.8.0
[103] DBI_1.1.3 ExperimentHub_1.14.2 dbplyr_2.1.1
[106] MASS_7.3-51.6 rappdirs_0.3.3 brio_1.1.3
[109] cli_3.0.1 rbibutils_2.2.3 metap_1.8
[112] qqconf_1.2.3 igraph_1.2.6 pkgconfig_2.0.3
[115] sn_2.0.2 numDeriv_2016.8-1.1 plotly_4.10.0
[118] multtest_2.46.0 XVector_0.28.0 callr_3.7.1
[121] digest_0.6.27 sctransform_0.3.2 RcppAnnoy_0.0.19
[124] tsne_0.1-3.1 leiden_0.3.9 uwot_0.1.10
[127] DelayedMatrixStats_1.10.1 curl_4.3.2 shiny_1.6.0
[130] lifecycle_1.0.1 nlme_3.1-148 jsonlite_1.7.2
[133] BiocNeighbors_1.6.0 mapproj_1.2.8 limma_3.44.3
[136] desc_1.4.1 viridisLite_0.4.0 fansi_0.5.0
[139] pillar_1.8.0 lattice_0.20-41 fastmap_1.1.0
[142] httr_1.4.3 plotrix_3.8-2 pkgbuild_1.3.1
[145] survival_3.1-12 remotes_2.4.2 interactiveDisplayBase_1.26.3
[148] glue_1.4.2 qlcMatrix_0.9.7 FNN_1.1.3.1
[151] png_0.1-7 BiocVersion_3.11.1 bit_4.0.4
[154] stringi_1.7.3 blob_1.2.3 BiocSingular_1.4.0
[157] AnnotationHub_2.20.2 latticeExtra_0.6-30 memoise_2.0.1
[160] mathjaxr_1.6-0 future.apply_1.9.0 ape_5.5
What is your Bioconductor version? (run BiocManager::version()
)
It seems your beachmat
version is from 3 years ago, which suggests an old bioconductor installation (bioconductor will always install the package version of the bioc release you have to avoid conflicts). This will be hard to debug if we can't reproduce it with recent versions. At any rate I'd strongly advise to update if it's indeed that old, as in the single-cell world 2-3y is a lot...
Will close this unless you can reproduce on newer versions.
Hi,
Sorry for the late reply. I've solved this error by updating the latest version of biocondutor. Thank you for all your helping!
Hi,
I installed scDblFinder by
BiocManager::install("scDblFinder")
. When I ranlibrary(scDblFinder)
, I got this error message:I tried to updated the package beachmat, but this error still remain unsolved.
Could you provide any suggestion for this? Thank you for your helping!