Error in function "open_loom"

[Beyondvisible]

Hi, I converted a seurat object to a loom file, and tried to open the loom file in R. But, I just faced an error with "open_loom" function.

loom <- open_loom(loomPath, mode="r") Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : HDF5-API Errors: error #000: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5F.c in H5Fopen(): line 591: invalid file name class: HDF5 major: Invalid arguments to routine minor: Bad value

I tried this command after removing the loom file in my global environment, but I got the same error messages again. All the packages in my R are updated.

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale: [1] LC_COLLATE=Korean_Korea.949 LC_CTYPE=Korean_Korea.949 LC_MONETARY=Korean_Korea.949 LC_NUMERIC=C
[5] LC_TIME=Korean_Korea.949

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] loomR_0.2.1.9000 hdf5r_1.3.2 R6_2.4.1 scater_1.16.2
[5] SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.2 DelayedArray_0.14.1 matrixStats_0.56.0
[9] Biobase_2.48.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 IRanges_2.22.2
[13] S4Vectors_0.26.1 BiocGenerics_0.34.0 SCopeLoomR_0.9.3 RColorBrewer_1.1-2
[17] cowplot_1.0.0 ggplot2_3.3.2 survival_3.2-3 SCENIC_1.1.3
[21] patchwork_1.0.1 Seurat_3.2.0 dplyr_1.0.1 clusterProfiler_3.16.0
[25] DOSE_3.14.0

loaded via a namespace (and not attached): [1] reticulate_1.16 R.utils_2.9.2 tidyselect_1.1.0 RSQLite_2.2.0
[5] AnnotationDbi_1.50.3 htmlwidgets_1.5.1 grid_4.0.2 BiocParallel_1.22.0
[9] Rtsne_0.15 devtools_2.3.1 scatterpie_0.1.4 munsell_0.5.0
[13] codetools_0.2-16 ica_1.0-2 future_1.18.0 miniUI_0.1.1.1
[17] withr_2.2.0 colorspace_1.4-1 GOSemSim_2.14.1 rstudioapi_0.11
[21] ROCR_1.0-11 tensor_1.5 listenv_0.8.0 labeling_0.3
[25] urltools_1.7.3 GenomeInfoDbData_1.2.3 polyclip_1.10-0 bit64_4.0.2
[29] farver_2.0.3 rprojroot_1.3-2 downloader_0.4 vctrs_0.3.2
[33] generics_0.0.2 ggbeeswarm_0.6.0 graphlayouts_0.7.0 rsvd_1.0.3
[37] bitops_1.0-6 spatstat.utils_1.17-0 fgsea_1.14.0 gridGraphics_0.5-0
[41] assertthat_0.2.1 promises_1.1.1 scales_1.1.1 ggraph_2.0.3
[45] enrichplot_1.8.1 beeswarm_0.2.3 gtable_0.3.0 globals_0.12.5
[49] processx_3.4.3 goftest_1.2-2 tidygraph_1.2.0 rlang_0.4.7
[53] splines_4.0.2 lazyeval_0.2.2 europepmc_0.4 BiocManager_1.30.10
[57] reshape2_1.4.4 abind_1.4-5 backports_1.1.8 httpuv_1.5.4
[61] qvalue_2.20.0 usethis_1.6.1 tools_4.0.2 ggplotify_0.0.5
[65] ellipsis_0.3.1 sessioninfo_1.1.1 ggridges_0.5.2 Rcpp_1.0.5
[69] plyr_1.8.6 progress_1.2.2 zlibbioc_1.34.0 purrr_0.3.4
[73] RCurl_1.98-1.2 ps_1.3.3 prettyunits_1.1.1 rpart_4.1-15
[77] deldir_0.1-28 pbapply_1.4-2 viridis_0.5.1 zoo_1.8-8
[81] ggrepel_0.8.2 cluster_2.1.0 fs_1.5.0 magrittr_1.5
[85] data.table_1.13.0 DO.db_2.9 lmtest_0.9-37 triebeard_0.3.0
[89] RANN_2.6.1 fitdistrplus_1.1-1 pkgload_1.1.0 hms_0.5.3
[93] mime_0.9 xtable_1.8-4 XML_3.99-0.5 AUCell_1.10.0
[97] gridExtra_2.3 testthat_2.3.2 compiler_4.0.2 tibble_3.0.3
[101] KernSmooth_2.23-17 crayon_1.3.4 R.oo_1.23.0 htmltools_0.5.0
[105] mgcv_1.8-31 later_1.1.0.1 tidyr_1.1.1 DBI_1.1.0
[109] tweenr_1.0.1 MASS_7.3-51.6 rappdirs_0.3.1 Matrix_1.2-18
[113] cli_2.0.2 R.methodsS3_1.8.0 igraph_1.2.5 pkgconfig_2.0.3
[117] rvcheck_0.1.8 plotly_4.9.2.1 xml2_1.3.2 annotate_1.66.0
[121] vipor_0.4.5 XVector_0.28.0 callr_3.4.3 stringr_1.4.0
[125] digest_0.6.25 sctransform_0.2.1 RcppAnnoy_0.0.16 graph_1.66.0
[129] spatstat.data_1.4-3 leiden_0.3.3 fastmatch_1.1-0 uwot_0.1.8
[133] DelayedMatrixStats_1.10.1 GSEABase_1.50.1 curl_4.3 shiny_1.5.0
[137] lifecycle_0.2.0 nlme_3.1-148 jsonlite_1.7.0 BiocNeighbors_1.6.0
[141] desc_1.2.0 fansi_0.4.1 viridisLite_0.3.0 pillar_1.4.6
[145] lattice_0.20-41 pkgbuild_1.1.0 fastmap_1.0.1 httr_1.4.2
[149] GO.db_3.11.4 remotes_2.2.0 glue_1.4.1 spatstat_1.64-1
[153] png_0.1-7 bit_4.0.4 ggforce_0.3.2 stringi_1.4.6
[157] blob_1.2.1 BiocSingular_1.4.0 memoise_1.1.0 irlba_2.3.3
[161] future.apply_1.6.0 ape_5.4

Thanks for your help! Jeong

[dweemx]

Hi @Two-J , It seems you are using HDF5 library version 1.8 while version 1.10.1 is at least required. I would recommend you to update your HDF5 library and then do a fresh reinstall of SCopeLoomR

[Beyondvisible]

@dweemx Oh, thank you for your quick reply! Btw, do I need to install new version of HDF5 binary code package to update HDF5 library version? Sorry, since I am very new here, step-by-step instructions would save my life..! Thanks for your time.

[dweemx]

You can install a new HDF5 library like this:

wget https://support.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.10.1.tar
cd hdf5-1.10.1
./configure
make -j4
make check
make install

And then check you have the new version installed:

h5stat --version

[Beyondvisible]

@dweemx I am currently trying to use SCENIC in R environment. But, in order to update HDF5, then do I need to install python and enter the commands you described above?

Thanks for your generous help.

[dweemx]

Why would you need to install python ? These bash commands should be run in a terminal

[dweemx]

Closing issue since no activity Please reopen issue if still encountering this issue