Failure to convert h5ad to Rds
Closed this issue · 4 comments
Hi, I'm getting an error when I run the code to convert the h5ad file. I've checked my h5ad file and found no problems. What is causing the error and is there any way to fix it?
sceasy::convertFormat("select_sample_raw_after_remove_DupSymbol.h5ad", from="anndata", to="seurat",
outFile='select_sample_raw_after_remove_DupSymbol.rds')
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': invalid class “dgCMatrix” object: 'Dim' slot does not have length 2
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /home/zhout/miniconda3/lib/libblas.so.3.9.0
LAPACK: /home/zhout/miniconda3/lib/libmkl_rt.so.2; LAPACK version 3.10.1
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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sceasy_0.0.7 reticulate_1.30
loaded via a namespace (and not attached):
[1] deldir_1.0-9 pbapply_1.7-2 gridExtra_2.3 rlang_1.1.1.9000 magrittr_2.0.3 RcppAnnoy_0.0.21 matrixStats_1.0.0
[8] ggridges_0.5.4 compiler_4.3.1 spatstat.geom_3.2-4 png_0.1-8 vctrs_0.6.3 reshape2_1.4.4 stringr_1.5.0
[15] pkgconfig_2.0.3 fastmap_1.1.1 ellipsis_0.3.2 utf8_1.2.3 promises_1.2.0.1 purrr_1.0.1 jsonlite_1.8.7
[22] goftest_1.2-3 later_1.3.1 spatstat.utils_3.0-3 irlba_2.3.5.1 parallel_4.3.1 cluster_2.1.4 R6_2.5.1
[29] ica_1.0-3 stringi_1.7.12 RColorBrewer_1.1-3 spatstat.data_3.0-1 parallelly_1.36.0 lmtest_0.9-40 scattermore_1.2
[36] Rcpp_1.0.11 tensor_1.5 future.apply_1.11.0 zoo_1.8-12 sctransform_0.3.5 httpuv_1.6.11 Matrix_1.5-4.1
[43] splines_4.3.1 igraph_1.5.0.1 tidyselect_1.2.0 abind_1.4-5 codetools_0.2-19 spatstat.random_3.1-5 miniUI_0.1.1.1
[50] spatstat.explore_3.2-1 listenv_0.9.0 lattice_0.21-8 tibble_3.2.1 plyr_1.8.8 withr_2.5.0 shiny_1.7.4.1
[57] ROCR_1.0-11 Rtsne_0.16 future_1.33.0 survival_3.5-5 polyclip_1.10-4 fitdistrplus_1.1-11 pillar_1.9.0
[64] Seurat_4.3.0.1 KernSmooth_2.23-22 plotly_4.10.2 generics_0.1.3 sp_2.0-0 ggplot2_3.4.2 munsell_0.5.0
[71] scales_1.2.1 globals_0.16.2 xtable_1.8-4 glue_1.6.2 lazyeval_0.2.2 tools_4.3.1 data.table_1.14.8
[78] RANN_2.6.1 leiden_0.4.3 cowplot_1.1.1 grid_4.3.1 tidyr_1.3.0 colorspace_2.1-0 nlme_3.1-162
[85] patchwork_1.1.2 cli_3.6.1 spatstat.sparse_3.0-2 fansi_1.0.4 viridisLite_0.4.2 dplyr_1.1.1 uwot_0.1.16
[92] gtable_0.3.3 digest_0.6.33 progressr_0.13.0 ggrepel_0.9.3 htmlwidgets_1.6.2 SeuratObject_4.1.3 htmltools_0.5.5
[99] lifecycle_1.0.3 httr_1.4.6 mime_0.12 MASS_7.3-60
