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Failure to convert h5ad to Rds #86

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RookieA1 opened this issue Feb 28, 2024 · 4 comments
Open

Failure to convert h5ad to Rds #86

RookieA1 opened this issue Feb 28, 2024 · 4 comments

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@RookieA1
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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
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@iaaka
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iaaka commented Feb 28, 2024

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

@RookieA1
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RookieA1 commented Mar 5, 2024

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?
image

@iaaka
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iaaka commented Mar 5, 2024

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

@iaaka
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iaaka commented Mar 6, 2024

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

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