Failure to convert h5ad to Rds

[RookieA1]

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

[iaaka]

Hi @RookieA1, not exactly answer to your questions, but could you consider to use schard instead?

[RookieA1]

Hi @RookieA1, not exactly answer to your questions, but could you consider to use schard instead?

Hi @iaaka , I encountered another error when installing the schard you recommended，What caused the installation to fail?

[iaaka]

Hi @RookieA1, thank you for reporting this, it was weird typo, should be fixed now, could you please try again?

[iaaka]

Hi @RookieA1, just to note: there was one more bug discovered in schard. It is fixed now.