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GreenleafLab
Error in addDoubletScores
Hi! When I use the tutorial data to run the sample code, I keep encountering this error. I also try to set threads=1, but it still appear same error. I also used diferent version, like ArchR v1.0.2 and ArchR 1.0.2, but the result is same. Could you please help me? Thanks!
doubScores <- addDoubletScores(
+ input = ArrowFiles,
+ k = 10,
+ knnMethod = "UMAP",
+ LSIMethod = 1
+ )
ArchR logging to : ArchRLogs/ArchR-addDoubletScores-fad5818efe33b-Date-2023-08-23_Time-08-58-48.log
If there is an issue, please report to github with logFile!
2023-08-23 08:58:48 : Batch Execution w/ safelapply!, 0 mins elapsed.
2023-08-23 08:58:48 : scATAC_BMMC_R1 (1 of 3) : Computing Doublet Statistics, 0 mins elapsed.
************************************************************
2023-08-23 08:59:04 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addDoubletScores-fad5818efe33b-Date-2023-08-23_Time-08-58-48.log
<simpleError in validityMethod(as(object, superClass)): object 'Csparse_validate' not found>
************************************************************
************************************************************
2023-08-23 08:59:04 : ERROR Found in addIterativeLSI for scATAC_BMMC_R1 (1 of 3) :
LogFile = ArchRLogs/ArchR-addDoubletScores-fad5818efe33b-Date-2023-08-23_Time-08-58-48.log
<simpleError in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
************************************************************
Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), :
Exiting See Error Above
> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] markdown_1.4 ArchR_1.0.2
[3] SeuratObject_4.1.3 Seurat_4.3.0
[5] BSgenome.Hsapiens.UCSC.hg38_1.4.5 Rsamtools_2.14.0
[7] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.66.3
[9] rtracklayer_1.58.0 Biostrings_2.66.0
[11] XVector_0.38.0 rhdf5_2.42.1
[13] SummarizedExperiment_1.28.0 Biobase_2.58.0
[15] MatrixGenerics_1.10.0 Rcpp_1.0.11
[17] Matrix_1.6-1 GenomicRanges_1.50.2
[19] GenomeInfoDb_1.34.9 IRanges_2.32.0
[21] S4Vectors_0.36.2 BiocGenerics_0.44.0
[23] matrixStats_1.0.0 data.table_1.14.8
[25] stringr_1.5.0 plyr_1.8.8
[27] magrittr_2.0.3 ggplot2_3.4.3
[29] gtable_0.3.4 gtools_3.9.4
[31] gridExtra_2.3
loaded via a namespace (and not attached):
[1] igraph_1.3.5 lazyeval_0.2.2 sp_1.5-1
[4] splines_4.2.2 BiocParallel_1.32.6 listenv_0.8.0
[7] scattermore_0.8 usethis_2.1.6 digest_0.6.33
[10] htmltools_0.5.6 fansi_1.0.4 memoise_2.0.1
[13] tensor_1.5 cluster_2.1.4 ROCR_1.0-11
[16] remotes_2.4.2 globals_0.16.1 spatstat.sparse_3.0-0
[19] prettyunits_1.1.1 colorspace_2.1-0 ggrepel_0.9.3
[22] xfun_0.40 dplyr_1.1.2 callr_3.7.3
[25] crayon_1.5.2 RCurl_1.98-1.12 jsonlite_1.8.7
[28] progressr_0.11.0 spatstat.data_3.0-0 survival_3.4-0
[31] zoo_1.8-11 glue_1.6.2 polyclip_1.10-4
[34] zlibbioc_1.44.0 leiden_0.4.3 DelayedArray_0.24.0
[37] pkgbuild_1.3.1 Rhdf5lib_1.20.0 future.apply_1.10.0
[40] abind_1.4-5 scales_1.2.1 DBI_1.1.3
[43] spatstat.random_3.0-1 miniUI_0.1.1.1 viridisLite_0.4.2
[46] xtable_1.8-4 reticulate_1.26 profvis_0.3.7
[49] htmlwidgets_1.6.2 httr_1.4.7 RColorBrewer_1.1-3
[52] ellipsis_0.3.2 ica_1.0-3 urlchecker_1.0.1
[55] pkgconfig_2.0.3 XML_3.99-0.14 uwot_0.1.16
[58] deldir_1.0-6 utf8_1.2.3 tidyselect_1.2.0
[61] rlang_1.1.1 reshape2_1.4.4 later_1.3.1
[64] cachem_1.0.8 munsell_0.5.0 tools_4.2.2
[67] cli_3.6.1 generics_0.1.3 devtools_2.4.5
[70] ggridges_0.5.4 fastmap_1.1.1 yaml_2.3.7
[73] goftest_1.2-3 processx_3.8.0 fs_1.6.3
[76] knitr_1.43 fitdistrplus_1.1-8 purrr_1.0.2
[79] RANN_2.6.1 nlme_3.1-160 pbapply_1.6-0
[82] future_1.29.0 mime_0.12 rhandsontable_0.3.8
[85] shinythemes_1.2.0 compiler_4.2.2 rstudioapi_0.14
[88] plotly_4.10.2 png_0.1-8 spatstat.utils_3.0-1
[91] tibble_3.2.1 stringi_1.7.12 ps_1.7.2
[94] lattice_0.20-45 vctrs_0.6.3 pillar_1.9.0
[97] lifecycle_1.0.3 rhdf5filters_1.10.1 BiocManager_1.30.22
[100] spatstat.geom_3.0-3 lmtest_0.9-40 RcppAnnoy_0.0.21
[103] cowplot_1.1.1 bitops_1.0-7 irlba_2.3.5.1
[106] httpuv_1.6.11 patchwork_1.1.2 R6_2.5.1
[109] BiocIO_1.8.0 promises_1.2.1 KernSmooth_2.23-20
[112] parallelly_1.32.1 sessioninfo_1.2.2 codetools_0.2-18
[115] pkgload_1.3.2 MASS_7.3-58.1 rjson_0.2.21
[118] withr_2.5.0 presto_1.0.0 GenomicAlignments_1.34.1
[121] sctransform_0.3.5 harmony_0.1.1 GenomeInfoDbData_1.2.9
[124] tidyr_1.3.0 Cairo_1.6-0 Rtsne_0.16
[127] spatstat.explore_3.0-5 shiny_1.7.5 restfulr_0.0.15
I run the following code
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
library(ArchR)
ArchR::installExtraPackages()
set.seed(1)
addArchRThreads(threads = 16)
addArchRGenome("hg19")
inputFiles <- getTutorialData("Hematopoiesis")
inputFiles
ArrowFiles <- createArrowFiles(
inputFiles = inputFiles,
sampleNames = names(inputFiles),
filterTSS = 4,
filterFrags = 1000,
addTileMat = TRUE,
addGeneScoreMat = TRUE
)
ArrowFiles
doubScores <- addDoubletScores(
input = ArrowFiles,
k = 10,
knnMethod = "UMAP",
LSIMethod = 1
)
Hi @zhangyina! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.
__In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.
When I use the tutorial data to run the sample code, I keep encountering this error. I also try to set threads=1, but it still appear same error. I also used diferent version, like ArchR v1.0.2 and ArchR 1.0.2, but the result is same. Could you please help me?
I met the same problem, anyone could help me? Error in .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), : Exiting See Error Above
