Closed raygozag closed 4 months ago
has you installed sucessfully? I did not
Hi - can you try to set thebin.size
to a vector, like so?
object <- Load10X_Spatial(data.dir = localdir, bin.size = c(8, 16))
that's not the issue. the problem is that the updated installation has no such parameter in the function. something is not updating even after forcing the update.
Have you tried installing via install.packages
? (this is generally the preferred method)
remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE)
remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE, force=T)
Are both pointing to the pre-release seurat5
branch - it will not resolve to the correct version
remotes::install_github("satijalab/seurat")
Probably would've worked had you included force = TRUE
Closing this issue as there has been no activity, but feel free to reopen if further issues arise. Thanks!
Hi i'm trying to follow the visium hd tutorial but i keep trying to update my seurat installetion with
remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE) remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE, force=T) remotes::install_github("satijalab/seurat")
and reinstalled everything again too, but i still can't see the bin.size parameter. Even after restarting R or terminating the session.
object <- Load10X_Spatial(data.dir = localdir, bin.size =(8, 16))
Can anybody help me install the eversion for visium hd?
Thanks
`R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS
Matrix products: default BLAS/LAPACK: /opt/OpenBLAS/lib/libopenblas-r0.3.3.so; LAPACK version 3.8.0
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/Chicago tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] dplyr_1.1.4 patchwork_1.2.0 ggplot2_3.5.1 Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4
loaded via a namespace (and not attached): [1] deldir_2.0-4 pbapply_1.7-2 gridExtra_2.3 remotes_2.5.0 rlang_1.1.3 magrittr_2.0.3 RcppAnnoy_0.0.22 spatstat.geom_3.2-9
[9] matrixStats_1.3.0 ggridges_0.5.6 compiler_4.3.1 callr_3.7.6 png_0.1-8 vctrs_0.6.5 reshape2_1.4.4 hdf5r_1.3.10
[17] stringr_1.5.1 pkgconfig_2.0.3 fastmap_1.2.0 utf8_1.2.4 promises_1.3.0 rmarkdown_2.27 ps_1.7.6 bit_4.0.5
[25] purrr_1.0.2 xfun_0.44 jsonlite_1.8.8 goftest_1.2-3 later_1.3.2 spatstat.utils_3.0-4 irlba_2.3.5.1 parallel_4.3.1
[33] cluster_2.1.4 R6_2.5.1 ica_1.0-3 stringi_1.8.4 RColorBrewer_1.1-3 spatstat.data_3.0-4 reticulate_1.37.0 parallelly_1.37.1
[41] lmtest_0.9-40 scattermore_1.2 Rcpp_1.0.12 knitr_1.46 tensor_1.5 future.apply_1.11.2 zoo_1.8-12 sctransform_0.4.1
[49] httpuv_1.6.15 Matrix_1.6-4 splines_4.3.1 igraph_2.0.3 tidyselect_1.2.1 abind_1.4-5 rstudioapi_0.16.0 yaml_2.3.8
[57] spatstat.random_3.2-3 codetools_0.2-19 miniUI_0.1.1.1 spatstat.explore_3.2-7 processx_3.8.4 curl_5.2.1 pkgbuild_1.4.4 listenv_0.9.1
[65] lattice_0.21-8 tibble_3.2.1 plyr_1.8.9 withr_3.0.0 shiny_1.8.1.1 ROCR_1.0-11 evaluate_0.23 Rtsne_0.17
[73] desc_1.4.3 future_1.33.2 fastDummies_1.7.3 survival_3.5-5 polyclip_1.10-6 xml2_1.3.6 fitdistrplus_1.1-11 pillar_1.9.0
[81] KernSmooth_2.23-21 plotly_4.10.4 generics_0.1.3 RcppHNSW_0.6.0 munsell_0.5.1 scales_1.3.0 globals_0.16.3 xtable_1.8-4
[89] glue_1.7.0 lazyeval_0.2.2 tools_4.3.1 data.table_1.15.4 RSpectra_0.16-1 RANN_2.6.1 leiden_0.4.3.1 dotCall64_1.1-1
[97] cowplot_1.1.3 grid_4.3.1 tidyr_1.3.1 colorspace_2.1-0 nlme_3.1-162 cli_3.6.2 spatstat.sparse_3.0-3 spam_2.10-0
[105] fansi_1.0.6 viridisLite_0.4.2 gt_0.10.1 uwot_0.2.2 gtable_0.3.5 digest_0.6.35 progressr_0.14.0 ggrepel_0.9.5
[113] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7 mime_0.12 bit64_4.0.5 MASS_7.3-60 `