Hi Robert,
I was able to load the dataset in the development version of R (which is higher than 4.0):
********
> library(Seurat)
> d <- readRDS("blish_covid.seu.rds")
> d
An object of class Seurat
52722 features across 44721 samples within 2 assays
Active assay: SCT (26361 features, 3000 variable features)
1 other assay present: RNA
2 dimensional reductions calculated: pca, umap
> sessionInfo()
R Under development (unstable) (2020-09-24 r79253)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Seurat_3.2.2
loaded via a namespace (and not attached):
[1] nlme_3.1-149 matrixStats_0.56.0 RcppAnnoy_0.0.16
[4] RColorBrewer_1.1-2 httr_1.4.2 sctransform_0.3.1
[7] tools_4.1.0 R6_2.4.1 irlba_2.3.3
[10] rpart_4.1-15 KernSmooth_2.23-17 uwot_0.1.8
[13] lazyeval_0.2.2 mgcv_1.8-33 colorspace_1.4-1
[16] tidyselect_1.1.0 gridExtra_2.3 compiler_4.1.0
[19] plotly_4.9.2.1 scales_1.1.1 lmtest_0.9-38
[22] spatstat.data_1.4-3 ggridges_0.5.2 pbapply_1.4-3
[25] spatstat_1.64-1 goftest_1.2-2 stringr_1.4.0
[28] digest_0.6.25 spatstat.utils_1.17-0 pkgconfig_2.0.3
[31] htmltools_0.5.0 fastmap_1.0.1 htmlwidgets_1.5.2
[34] rlang_0.4.7 shiny_1.5.0 generics_0.0.2
[37] zoo_1.8-8 jsonlite_1.7.1 ica_1.0-2
[40] dplyr_1.0.2 magrittr_1.5 patchwork_1.0.1
[43] Matrix_1.2-18 Rcpp_1.0.5 munsell_0.5.0
[46] abind_1.4-5 reticulate_1.18 lifecycle_0.2.0
[49] stringi_1.5.3 MASS_7.3-53 Rtsne_0.15
[52] plyr_1.8.6 grid_4.1.0 parallel_4.1.0
[55] listenv_0.8.0 promises_1.1.1 ggrepel_0.8.2
[58] crayon_1.3.4 miniUI_0.1.1.1 deldir_0.1-29
[61] lattice_0.20-41 cowplot_1.1.0 splines_4.1.0
[64] tensor_1.5 pillar_1.4.6 tcltk_4.1.0
[67] igraph_1.2.6 future.apply_1.6.0 reshape2_1.4.4
[70] codetools_0.2-16 leiden_0.3.3 glue_1.4.2
[73] data.table_1.13.2 png_0.1-7 vctrs_0.3.4
[76] httpuv_1.5.4 gtable_0.3.0 RANN_2.6.1
[79] purrr_0.3.4 polyclip_1.10-0 tidyr_1.1.2
[82] future_1.19.1 ggplot2_3.3.2 rsvd_1.0.3
[85] mime_0.9 xtable_1.8-4 later_1.1.0.1
[88] survival_3.2-3 viridisLite_0.3.0 tibble_3.0.3
[91] cluster_2.1.0 globals_0.13.1 fitdistrplus_1.1-1
[94] ellipsis_0.3.1 ROCR_1.0-11
********
Could you check again on your side?
We will also add md5sums to the website later today.
Hope this helps,
Cheers,
Vlad
--
Vladimir Kiselev
CellGen Informatics Team Leader
Wellcome Sanger Institute
Wellcome Genome Campus
Hinxton, Cambridge, CB10 1SA
Phone: +44 (0) 1223 496850
Message:
Mattermost or
Slack
From: "Gentleman, Robert C." <Robert_Gentleman@hms.harvard.edu>
Date: Monday, 26 October 2020 at 17:05
To: "cv19caingest@sanger.ac.uk" <cv19caingest@sanger.ac.uk>
Subject: [Cv19caingest] want to report a problem [EXT]
Hi
Sorry to send to this address but I could not find out where to report problems. I wanted to download and use this file
Which is supposed to be an R data set, unfortunately it is not and is corrupted or otherwise not valid (could be they used a very old version of R, but no information is provided on your website).
It would be helpful to provide md5 checksums or other tools to help
validate downloads etc.
Robert