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satijalab / azimuth

A Shiny web app for mapping datasets using Seurat v4
https://satijalab.org/azimuth
GNU General Public License v3.0
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Error about RunAzimuth #166

Closed Junedays closed 1 year ago

Junedays commented 1 year ago

I have the following error:

pbmcsca <- LoadData("pbmcsca") pbmcsca <- RunAzimuth(pbmcsca, reference = "pbmcref")

An AzimuthData object - reference version: 1.0.0 Contains 3 meta.data field(s) to transfer.Error in validObject(object = object) : invalid class “Assay5” object: Layers must be two-dimensional objects

I cannot understand the reason . The first time that i have install azimuth, it is ok for these two lines and no error. But i re-installed it later and this error came out.

sessionInfo() R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.2 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0

locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8
[6] LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

time zone: Asia/Shanghai tzcode source: system (glibc)

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

other attached packages: [1] GSEABase_1.62.0 graph_1.78.0 annotate_1.78.0 XML_3.99-0.14
[5] AnnotationDbi_1.62.2 SCINA_1.2.0 gplots_3.1.3 MASS_7.3-60
[9] readxl_1.4.3 SingleR_2.2.0 scater_1.28.0 scuttle_1.10.1
[13] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2 GenomicRanges_1.52.0 GenomeInfoDb_1.36.1
[17] IRanges_2.34.1 S4Vectors_0.38.1 MatrixGenerics_1.12.2 matrixStats_1.0.0
[21] sceasy_0.0.7 reticulate_1.30 glmGamPoi_1.12.2 sctransform_0.3.5
[25] harmony_0.1.1 monocle_2.28.0 DDRTree_0.1.5 irlba_2.3.5.1
[29] VGAM_1.1-8 Biobase_2.60.0 BiocGenerics_0.46.0 Matrix_1.6-0
[33] Rcpp_1.0.11 R.utils_2.12.2 R.oo_1.25.0 R.methodsS3_1.8.2
[37] cowplot_1.1.1 patchwork_1.1.2 lubridate_1.9.2 forcats_1.0.0
[41] stringr_1.5.0 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0
[45] tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0 dplyr_1.1.2
[49] Seurat_4.9.9.9049 SeuratObject_4.9.9.9086 sp_2.0-0 SeuratWrappers_0.3.1
[53] pbmcsca.SeuratData_3.0.0 pbmcref.SeuratData_1.0.0 adiposeref.SeuratData_1.0.0 SeuratData_0.2.2
[57] Azimuth_0.4.6 shinyBS_0.61.1

loaded via a namespace (and not attached): [1] fs_1.6.3 spatstat.sparse_3.0-2 bitops_1.0-7 httr_1.4.6 RColorBrewer_1.1-3
[6] docopt_0.7.1 tools_4.3.0 utf8_1.2.3 R6_2.5.1 DT_0.28.1
[11] lazyeval_0.2.2 uwot_0.1.16 withr_2.5.0 gridExtra_2.3 progressr_0.13.0
[16] cli_3.6.1 spatstat.explore_3.2-1 fastDummies_1.7.3 shinyjs_2.1.0 slam_0.1-50
[21] spatstat.data_3.0-1 ggridges_0.5.4 pbapply_1.7-2 parallelly_1.36.0 limma_3.56.2
[26] RSQLite_2.3.1 rstudioapi_0.15.0 generics_0.1.3 combinat_0.0-8 gtools_3.9.4
[31] ica_1.0-3 spatstat.random_3.1-5.001 googlesheets4_1.1.1 ggbeeswarm_0.7.2 fansi_1.0.4
[36] abind_1.4-5 lifecycle_1.0.3 Rtsne_0.16 blob_1.2.4 grid_4.3.0
[41] promises_1.2.0.1 crayon_1.5.2 shinydashboard_0.7.2 miniUI_0.1.1.1 lattice_0.21-8
[46] beachmat_2.16.0 KEGGREST_1.40.0 pillar_1.9.0 future.apply_1.11.0 codetools_0.2-19
[51] leiden_0.4.3 glue_1.6.2 leidenbase_0.1.25 data.table_1.14.8 remotes_2.4.2.1
[56] vctrs_0.6.3 png_0.1-8 spam_2.9-1 cellranger_1.1.0 gtable_0.3.3
[61] cachem_1.0.8 S4Arrays_1.0.4 mime_0.12 qlcMatrix_0.9.7 HSMMSingleCell_1.20.0
[66] survival_3.5-5 gargle_1.5.2 pheatmap_1.0.12 fastICA_1.2-3 ellipsis_0.3.2
[71] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-162 bit64_4.0.5 RcppAnnoy_0.0.21
[76] vipor_0.4.5 KernSmooth_2.23-22 DBI_1.1.3 SeuratDisk_0.0.0.9020 colorspace_2.1-0
[81] tidyselect_1.2.0 bit_4.0.5 compiler_4.3.0 BiocNeighbors_1.18.0 hdf5r_1.3.8
[86] DelayedArray_0.26.6 plotly_4.10.2 caTools_1.18.2 scales_1.2.1 lmtest_0.9-40
[91] rappdirs_0.3.3 digest_0.6.33 goftest_1.2-3 spatstat.utils_3.0-3 presto_1.0.0
[96] sparsesvd_0.2-2 XVector_0.40.0 htmltools_0.5.5 pkgconfig_2.0.3 sparseMatrixStats_1.12.2 [101] fastmap_1.1.1 rlang_1.1.1 htmlwidgets_1.6.2 shiny_1.7.4.1 DelayedMatrixStats_1.22.1 [106] zoo_1.8-12 jsonlite_1.8.7 BiocParallel_1.34.2 BiocSingular_1.16.0 RCurl_1.98-1.12
[111] magrittr_2.0.3 GenomeInfoDbData_1.2.10 dotCall64_1.0-2 munsell_0.5.0 viridis_0.6.3
[116] stringi_1.7.12 zlibbioc_1.46.0 plyr_1.8.8 parallel_4.3.0 listenv_0.9.0
[121] ggrepel_0.9.3 deldir_1.0-9 Biostrings_2.68.1 tensor_1.5 hms_1.1.3
[126] igraph_1.5.0 spatstat.geom_3.2-4 RcppHNSW_0.4.1 reshape2_1.4.4 ScaledMatrix_1.8.1
[131] BiocManager_1.30.21.1 tzdb_0.4.0 httpuv_1.6.11 RANN_2.6.1 polyclip_1.10-4
[136] future_1.33.0 scattermore_1.2 rsvd_1.0.5 xtable_1.8-4 RSpectra_0.16-1
[141] later_1.3.1 viridisLite_0.4.2 googledrive_2.1.1 memoise_2.0.1 beeswarm_0.4.0
[146] cluster_2.1.4 timechange_0.2.0 globals_0.16.2

liangyu02 commented 1 year ago

me too

Gesmira commented 1 year ago

Hi, Installing the v5 version of Azimuth should fix these issues. remotes::install_github("satijalab/azimuth", "seurat5", quiet = TRUE)

hernandezvargash commented 11 months ago

same issue here, re-installing did not work for me.

`> sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=fr_FR.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Paris tzcode source: system (glibc)

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

other attached packages: [1] patchwork_1.1.3 Seurat_5.0.0 SeuratObject_5.0.0 sp_2.1-1 pbmcsca.SeuratData_3.0.0 pbmcref.SeuratData_1.0.0 [7] SeuratData_0.2.2 Azimuth_0.5.0 shinyBS_0.61.1

loaded via a namespace (and not attached): [1] fs_1.6.3 ProtGenerics_1.32.0 matrixStats_1.0.0 spatstat.sparse_3.0-2
[5] bitops_1.0-7 DirichletMultinomial_1.42.0 TFBSTools_1.40.0 httr_1.4.7
[9] RColorBrewer_1.1-3 tools_4.3.1 sctransform_0.4.1 utf8_1.2.3
[13] R6_2.5.1 DT_0.17 lazyeval_0.2.2 uwot_0.1.16
[17] rhdf5filters_1.12.1 withr_2.5.2 prettyunits_1.2.0 gridExtra_2.3
[21] progressr_0.14.0 cli_3.6.1 Biobase_2.60.0 spatstat.explore_3.2-3
[25] fastDummies_1.7.3 EnsDb.Hsapiens.v86_2.99.0 shinyjs_2.1.0 spatstat.data_3.0-1
[29] readr_2.1.4 ggridges_0.5.4 pbapply_1.7-2 Rsamtools_2.16.0
[33] R.utils_2.12.2 parallelly_1.36.0 BSgenome_1.70.1 rstudioapi_0.15.0
[37] RSQLite_2.2.9 generics_0.1.3 BiocIO_1.10.0 gtools_3.9.4
[41] ica_1.0-3 spatstat.random_3.1-6 googlesheets4_1.1.1 dplyr_1.1.3
[45] GO.db_3.17.0 Matrix_1.6-1.1 fansi_1.0.5 S4Vectors_0.38.2
[49] abind_1.4-5 R.methodsS3_1.8.2 lifecycle_1.0.3 yaml_2.3.7
[53] SummarizedExperiment_1.30.2 rhdf5_2.44.0 BiocFileCache_2.8.0 Rtsne_0.16
[57] grid_4.3.1 blob_1.2.2 promises_1.2.1 shinydashboard_0.7.2
[61] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.22-5 cowplot_1.1.1
[65] GenomicFeatures_1.52.2 annotate_1.78.0 KEGGREST_1.40.1 pillar_1.9.0
[69] GenomicRanges_1.52.1 rjson_0.2.21 future.apply_1.11.0 codetools_0.2-19
[73] fastmatch_1.1-3 leiden_0.4.3 glue_1.6.2 data.table_1.14.8
[77] remotes_2.4.2.1 vctrs_0.6.4 png_0.1-8 spam_2.10-0
[81] cellranger_1.1.0 gtable_0.3.4 poweRlaw_0.70.6 cachem_1.0.8
[85] Signac_1.12.9000 S4Arrays_1.2.0 mime_0.12 pracma_2.4.2
[89] survival_3.5-7 gargle_1.5.2 RcppRoll_0.3.0 ellipsis_0.3.2
[93] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-163 bit64_4.0.5
[97] progress_1.2.2 filelock_1.0.2 RcppAnnoy_0.0.21 GenomeInfoDb_1.36.4
[101] rprojroot_2.0.3 irlba_2.3.5.1 KernSmooth_2.23-22 SeuratDisk_0.0.0.9020
[105] colorspace_2.1-0 seqLogo_1.68.0 BiocGenerics_0.46.0 DBI_1.1.2
[109] tidyselect_1.2.0 processx_3.8.2 bit_4.0.5 compiler_4.3.1
[113] curl_5.1.0 hdf5r_1.3.8 xml2_1.3.3 desc_1.4.2
[117] DelayedArray_0.26.7 plotly_4.10.2 rtracklayer_1.60.1 scales_1.2.1
[121] caTools_1.18.2 lmtest_0.9-40 callr_3.7.3 rappdirs_0.3.3
[125] stringr_1.5.0 digest_0.6.33 goftest_1.2-3 presto_1.0.0
[129] spatstat.utils_3.0-3 XVector_0.40.0 htmltools_0.5.6.1 pkgconfig_2.0.3
[133] MatrixGenerics_1.12.3 dbplyr_2.3.4 fastmap_1.1.1 ensembldb_2.24.1
[137] rlang_1.1.2 htmlwidgets_1.6.2 shiny_1.7.5.1 zoo_1.8-12
[141] jsonlite_1.8.7 BiocParallel_1.34.2 R.oo_1.25.0 RCurl_1.98-1.12
[145] magrittr_2.0.3 GenomeInfoDbData_1.2.10 dotCall64_1.1-0 Rhdf5lib_1.22.1
[149] munsell_0.5.0 Rcpp_1.0.11 reticulate_1.34.0 stringi_1.7.12
[153] zlibbioc_1.46.0 MASS_7.3-60 plyr_1.8.9 pkgbuild_1.4.2
[157] parallel_4.3.1 listenv_0.9.0 ggrepel_0.9.4 deldir_1.0-9
[161] CNEr_1.38.0 Biostrings_2.68.1 splines_4.3.1 tensor_1.5
[165] hms_1.1.3 BSgenome.Hsapiens.UCSC.hg38_1.4.5 ps_1.7.5 igraph_1.5.1
[169] spatstat.geom_3.2-7 RcppHNSW_0.5.0 reshape2_1.4.4 biomaRt_2.56.1
[173] stats4_4.3.1 TFMPvalue_0.0.9 XML_3.99-0.9 JASPAR2020_0.99.10
[177] tzdb_0.4.0 httpuv_1.6.11 RANN_2.6.1 tidyr_1.3.0
[181] purrr_1.0.2 polyclip_1.10-6 future_1.33.0 scattermore_1.2
[185] ggplot2_3.4.4 xtable_1.8-4 restfulr_0.0.15 AnnotationFilter_1.24.0
[189] RSpectra_0.16-1 later_1.3.1 googledrive_2.1.1 viridisLite_0.4.2
[193] tibble_3.2.1 memoise_2.0.1 AnnotationDbi_1.62.2 GenomicAlignments_1.36.0
[197] IRanges_2.34.1 cluster_2.1.4 globals_0.16.2

`

Gesmira commented 11 months ago

Hi, Can you see if installing the newest version of SeuratData fixes this issue for you? devtools::install_github('satijalab/seurat-data')

hernandezvargash commented 11 months ago

Thanks a lot @Gesmira , the example data works perfectly after reinstalling SeuratData!. I do have an error when testing with my own data: Error inobject[[assay]]: ! 'SCT' not found in this Seurat object Did you mean "SCT_snn_res.0.5"? I tried UpdateSeuratObject thinking that this was a version problem, but I still get this error. Should I open a separate issue for this?

Gesmira commented 11 months ago

Hi @hernandezvargash, glad to hear! It would be great if you could open a new issue documenting the problem that you're having and how the object was made. Thanks!

hernandezvargash commented 11 months ago

actually no need for new issue, I was using the wrong reference (human for a mouse query object), the error is gone after changing my reference. Thanks again for your help @Gesmira !

Gesmira commented 11 months ago

Great, no problem!

qwang178 commented 9 months ago

Same problem, but the fix doesn't work:

remotes::install_github("satijalab/azimuth", "seurat5") Downloading GitHub repo satijalab/azimuth@seurat5 Error: Failed to install 'Azimuth' from GitHub: HTTP error 404. No commit found for the ref seurat5

Did you spell the repo owner (stuart-lab) and repo name (signac) correctly?