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as.Seurat fails in 4.0.2 #4549

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JTpath opened this issue May 29, 2021 · 1 comment
Closed

as.Seurat fails in 4.0.2 #4549

JTpath opened this issue May 29, 2021 · 1 comment
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bug Something isn't working

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@JTpath
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JTpath commented May 29, 2021 •
edited

Converting from SCE to Seurat fails with some datasets.

library(Seurat)
#> Registered S3 method overwritten by 'spatstat.geom':
#>   method     from
#>   print.boxx cli
#> Attaching SeuratObject
library(hdf5r)
url <-
  "https://cf.10xgenomics.com/samples/cell-exp/6.0.0/Brain_3p_LT/Brain_3p_LT_filtered_feature_bc_matrix.h5"
tmp_filename <- tempfile()
download.file(url, tmp_filename)
seu <- Read10X_h5(tmp_filename, use.names = TRUE)
#> Warning in sparseMatrix(i = indices[] + 1, p = indptr[], x = as.numeric(x =
#> counts[]), : 'giveCsparse' has been deprecated; setting 'repr = "T"' for you
seu <- CreateSeuratObject(seu)
sce <- as.SingleCellExperiment(seu)
seu2 <- as.Seurat(sce)
#> Error in .subset2(x, i, exact = exact): subscript out of bounds
Session info 
sessioninfo::session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.5 (2021-03-31)
 os       macOS Big Sur 10.16         
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_GB.UTF-8                 
 ctype    en_GB.UTF-8                 
 tz       Europe/London               
 date     2021-05-29                  

─ Packages ─────────────────────────────────────────────────────────────────────────────────
 package              * version    date       lib source                                 
 abind                  1.4-5      2016-07-21 [1] CRAN (R 4.0.2)                         
 assertthat             0.2.1      2019-03-21 [1] CRAN (R 4.0.2)                         
 backports              1.2.1      2020-12-09 [1] CRAN (R 4.0.2)                         
 Biobase                2.50.0     2020-10-27 [1] Bioconductor                           
 BiocGenerics           0.36.1     2021-04-16 [1] Bioconductor                           
 bit                    4.0.4      2020-08-04 [1] CRAN (R 4.0.2)                         
 bit64                  4.0.5      2020-08-30 [1] CRAN (R 4.0.2)                         
 bitops                 1.0-7      2021-04-24 [1] CRAN (R 4.0.2)                         
 bslib                  0.2.5.1    2021-05-18 [1] CRAN (R 4.0.2)                         
 cachem                 1.0.5      2021-05-15 [1] CRAN (R 4.0.2)                         
 callr                  3.7.0      2021-04-20 [1] CRAN (R 4.0.2)                         
 cli                    2.5.0      2021-04-26 [1] CRAN (R 4.0.2)                         
 clipr                  0.7.1      2020-10-08 [1] CRAN (R 4.0.2)                         
 cluster                2.1.2      2021-04-17 [1] CRAN (R 4.0.2)                         
 codetools              0.2-18     2020-11-04 [1] CRAN (R 4.0.5)                         
 colorspace             2.0-1      2021-05-04 [1] CRAN (R 4.0.2)                         
 cowplot                1.1.1      2020-12-30 [1] CRAN (R 4.0.2)                         
 crayon                 1.4.1      2021-02-08 [1] CRAN (R 4.0.2)                         
 data.table             1.14.0     2021-02-21 [1] CRAN (R 4.0.2)                         
 DBI                    1.1.1      2021-01-15 [1] CRAN (R 4.0.3)                         
 DelayedArray           0.16.3     2021-03-24 [1] Bioconductor                           
 deldir                 0.2-10     2021-02-16 [1] CRAN (R 4.0.2)                         
 digest                 0.6.27     2020-10-24 [1] CRAN (R 4.0.2)                         
 dplyr                  1.0.6      2021-05-05 [1] CRAN (R 4.0.2)                         
 ellipsis               0.3.2      2021-04-29 [1] CRAN (R 4.0.2)                         
 evaluate               0.14       2019-05-28 [1] CRAN (R 4.0.1)                         
 fansi                  0.4.2      2021-01-15 [1] CRAN (R 4.0.2)                         
 fastmap                1.1.0      2021-01-25 [1] CRAN (R 4.0.2)                         
 fitdistrplus           1.1-5      2021-05-28 [1] CRAN (R 4.0.5)                         
 fs                     1.5.0      2020-07-31 [1] CRAN (R 4.0.2)                         
 future                 1.21.0     2020-12-10 [1] CRAN (R 4.0.3)                         
 future.apply           1.7.0      2021-01-04 [1] CRAN (R 4.0.2)                         
 generics               0.1.0      2020-10-31 [1] CRAN (R 4.0.2)                         
 GenomeInfoDb           1.26.7     2021-04-08 [1] Bioconductor                           
 GenomeInfoDbData       1.2.4      2021-01-17 [1] Bioconductor                           
 GenomicRanges          1.42.0     2020-10-27 [1] Bioconductor                           
 ggplot2                3.3.3      2020-12-30 [1] CRAN (R 4.0.2)                         
 ggrepel                0.9.1      2021-01-15 [1] CRAN (R 4.0.2)                         
 ggridges               0.5.3      2021-01-08 [1] CRAN (R 4.0.2)                         
 globals                0.14.0     2020-11-22 [1] CRAN (R 4.0.2)                         
 glue                   1.4.2      2020-08-27 [1] CRAN (R 4.0.2)                         
 goftest                1.2-2      2019-12-02 [1] CRAN (R 4.0.2)                         
 gridExtra              2.3        2017-09-09 [1] CRAN (R 4.0.2)                         
 gtable                 0.3.0      2019-03-25 [1] CRAN (R 4.0.2)                         
 hdf5r                * 1.3.2      2020-03-25 [1] CRAN (R 4.0.1)                         
 highr                  0.9        2021-04-16 [1] CRAN (R 4.0.5)                         
 htmltools              0.5.1.1    2021-01-22 [1] CRAN (R 4.0.2)                         
 htmlwidgets            1.5.3      2020-12-10 [1] CRAN (R 4.0.3)                         
 httpuv                 1.6.1      2021-05-07 [1] CRAN (R 4.0.2)                         
 httr                   1.4.2      2020-07-20 [1] CRAN (R 4.0.2)                         
 ica                    1.0-2      2018-05-24 [1] CRAN (R 4.0.2)                         
 igraph                 1.2.6      2020-10-06 [1] CRAN (R 4.0.2)                         
 IRanges                2.24.1     2020-12-12 [1] Bioconductor                           
 irlba                  2.3.3      2019-02-05 [1] CRAN (R 4.0.2)                         
 jquerylib              0.1.4      2021-04-26 [1] CRAN (R 4.0.2)                         
 jsonlite               1.7.2      2020-12-09 [1] CRAN (R 4.0.2)                         
 KernSmooth             2.23-20    2021-05-03 [1] CRAN (R 4.0.2)                         
 knitr                  1.33       2021-04-24 [1] CRAN (R 4.0.2)                         
 later                  1.2.0      2021-04-23 [1] CRAN (R 4.0.2)                         
 lattice                0.20-44    2021-05-02 [1] CRAN (R 4.0.2)                         
 lazyeval               0.2.2      2019-03-15 [1] CRAN (R 4.0.2)                         
 leiden                 0.3.8      2021-05-24 [1] CRAN (R 4.0.5)                         
 lifecycle              1.0.0      2021-02-15 [1] CRAN (R 4.0.2)                         
 listenv                0.8.0      2019-12-05 [1] CRAN (R 4.0.2)                         
 lmtest                 0.9-38     2020-09-09 [1] CRAN (R 4.0.2)                         
 magrittr               2.0.1      2020-11-17 [1] CRAN (R 4.0.2)                         
 MASS                   7.3-54     2021-05-03 [1] CRAN (R 4.0.2)                         
 Matrix                 1.3-3      2021-05-04 [1] CRAN (R 4.0.2)                         
 MatrixGenerics         1.2.1      2021-01-30 [1] Bioconductor                           
 matrixStats            0.58.0     2021-01-29 [1] CRAN (R 4.0.2)                         
 mgcv                   1.8-35     2021-04-18 [1] CRAN (R 4.0.2)                         
 mime                   0.10       2021-02-13 [1] CRAN (R 4.0.2)                         
 miniUI                 0.1.1.1    2018-05-18 [1] CRAN (R 4.0.2)                         
 munsell                0.5.0      2018-06-12 [1] CRAN (R 4.0.2)                         
 nlme                   3.1-152    2021-02-04 [1] CRAN (R 4.0.5)                         
 parallelly             1.25.0     2021-04-30 [1] CRAN (R 4.0.2)                         
 patchwork              1.1.1      2020-12-17 [1] CRAN (R 4.0.2)                         
 pbapply                1.4-3      2020-08-18 [1] CRAN (R 4.0.2)                         
 pillar                 1.6.1      2021-05-16 [1] CRAN (R 4.0.2)                         
 pkgconfig              2.0.3      2019-09-22 [1] CRAN (R 4.0.2)                         
 plotly                 4.9.3      2021-01-10 [1] CRAN (R 4.0.2)                         
 plyr                   1.8.6      2020-03-03 [1] CRAN (R 4.0.2)                         
 png                    0.1-7      2013-12-03 [1] CRAN (R 4.0.2)                         
 polyclip               1.10-0     2019-03-14 [1] CRAN (R 4.0.2)                         
 processx               3.5.2      2021-04-30 [1] CRAN (R 4.0.2)                         
 promises               1.2.0.1    2021-02-11 [1] CRAN (R 4.0.2)                         
 ps                     1.6.0      2021-02-28 [1] CRAN (R 4.0.3)                         
 purrr                  0.3.4      2020-04-17 [1] CRAN (R 4.0.2)                         
 R6                     2.5.0      2020-10-28 [1] CRAN (R 4.0.2)                         
 RANN                   2.6.1      2019-01-08 [1] CRAN (R 4.0.2)                         
 RColorBrewer           1.1-2      2014-12-07 [1] CRAN (R 4.0.2)                         
 Rcpp                   1.0.6      2021-01-15 [1] CRAN (R 4.0.2)                         
 RcppAnnoy              0.0.18     2020-12-15 [1] CRAN (R 4.0.2)                         
 RCurl                  1.98-1.3   2021-03-16 [1] CRAN (R 4.0.2)                         
 reprex                 2.0.0      2021-04-02 [1] CRAN (R 4.0.2)                         
 reshape2               1.4.4      2020-04-09 [1] CRAN (R 4.0.2)                         
 reticulate             1.20       2021-05-03 [1] CRAN (R 4.0.2)                         
 rlang                  0.4.11     2021-04-30 [1] CRAN (R 4.0.2)                         
 rmarkdown              2.8        2021-05-07 [1] CRAN (R 4.0.5)                         
 ROCR                   1.0-11     2020-05-02 [1] CRAN (R 4.0.2)                         
 rpart                  4.1-15     2019-04-12 [1] CRAN (R 4.0.5)                         
 rstudioapi             0.13       2020-11-12 [1] CRAN (R 4.0.2)                         
 Rtsne                  0.15       2018-11-10 [1] CRAN (R 4.0.2)                         
 S4Vectors              0.28.1     2020-12-09 [1] Bioconductor                           
 sass                   0.4.0      2021-05-12 [1] CRAN (R 4.0.2)                         
 scales                 1.1.1      2020-05-11 [1] CRAN (R 4.0.2)                         
 scattermore            0.7        2020-11-24 [1] CRAN (R 4.0.2)                         
 sctransform            0.3.2.9006 2021-05-21 [1] Github (ChristophH/sctransform@73e2e3e)
 sessioninfo            1.1.1      2018-11-05 [1] CRAN (R 4.0.2)                         
 Seurat               * 4.0.2.9002 2021-05-28 [1] Github (satijalab/seurat@ec9dbe2)      
 SeuratObject         * 4.0.1      2021-05-08 [1] CRAN (R 4.0.2)                         
 shiny                * 1.6.0      2021-01-25 [1] CRAN (R 4.0.3)                         
 SingleCellExperiment   1.12.0     2020-10-27 [1] Bioconductor                           
 spatstat.core          2.1-2      2021-04-18 [1] CRAN (R 4.0.2)                         
 spatstat.data          2.1-0      2021-03-21 [1] CRAN (R 4.0.3)                         
 spatstat.geom          2.1-0      2021-04-15 [1] CRAN (R 4.0.2)                         
 spatstat.sparse        2.0-0      2021-03-16 [1] CRAN (R 4.0.2)                         
 spatstat.utils         2.1-0      2021-03-15 [1] CRAN (R 4.0.2)                         
 stringi                1.6.2      2021-05-17 [1] CRAN (R 4.0.2)                         
 stringr                1.4.0      2019-02-10 [1] CRAN (R 4.0.2)                         
 styler                 1.4.1      2021-03-30 [1] CRAN (R 4.0.2)                         
 SummarizedExperiment   1.20.0     2020-10-27 [1] Bioconductor                           
 survival               3.2-11     2021-04-26 [1] CRAN (R 4.0.2)                         
 tensor                 1.5        2012-05-05 [1] CRAN (R 4.0.2)                         
 tibble                 3.1.2      2021-05-16 [1] CRAN (R 4.0.2)                         
 tidyr                  1.1.3      2021-03-03 [1] CRAN (R 4.0.3)                         
 tidyselect             1.1.1      2021-04-30 [1] CRAN (R 4.0.2)                         
 utf8                   1.2.1      2021-03-12 [1] CRAN (R 4.0.2)                         
 uwot                   0.1.10     2020-12-15 [1] CRAN (R 4.0.2)                         
 vctrs                  0.3.8      2021-04-29 [1] CRAN (R 4.0.2)                         
 viridisLite            0.4.0      2021-04-13 [1] CRAN (R 4.0.5)                         
 withr                  2.4.2      2021-04-18 [1] CRAN (R 4.0.5)                         
 xfun                   0.23       2021-05-15 [1] CRAN (R 4.0.2)                         
 xtable                 1.8-4      2019-04-21 [1] CRAN (R 4.0.2)                         
 XVector                0.30.0     2020-10-28 [1] Bioconductor                           
 yaml                   2.2.1      2020-02-01 [1] CRAN (R 4.0.2)                         
 zlibbioc               1.36.0     2020-10-28 [1] Bioconductor                           
 zoo                    1.8-9      2021-03-09 [1] CRAN (R 4.0.2)                         

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

Created on 2021-05-29 by the reprex package (v2.0.0)
@JTpath JTpath added the bug Something isn't working label May 29, 2021
@JTpath JTpath mentioned this issue Jun 2, 2021
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@JTpath
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JTpath commented Jun 2, 2021

Fixed! #4353

@JTpath JTpath closed this as completed Jun 2, 2021
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