rcorces
commented
1 year ago Hi @schnappi-wkl! Thanks for using ArchR! I am currently on vacation and will not be responding to any issues or discussion threads until 5/5.
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, how will we 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.
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example.
3. Did you post your log file? If not, add it now.
4. 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.
Hi, guys, i have tried to add the GeneIntegrationMatrix using the "addGeneIntegrationMatrix", unfortunately, it‘s erroring. the error is following: Error Found Iteration 1 : [1] "Error in .initializeMat(ArrowFile = ArrowFiles[sample], Group = matrixName, : \n Matrix Group Already Exists! Set force = TRUE to overwrite!\n" <simpleError in .initializeMat(ArrowFile = ArrowFiles[sample], Group = matrixName, Class = "double", Units = "NormCounts", cellNames = colnames(sampleMat), params = dfParams, featureDF = featureDF, force = force): Matrix Group Already Exists! Error Found Iteration 2 : [1] "Error in .initializeMat(ArrowFile = ArrowFiles[sample], Group = matrixName, : \n Matrix Group Already Exists! Set force = TRUE to overwrite!\n" <simpleError in .initializeMat(ArrowFile = ArrowFiles[sample], Group = matrixName, Class = "double", Units = "NormCounts", cellNames = colnames(sampleMat), params = dfParams, featureDF = featureDF, force = force): Matrix Group Already Exists! Error Found Iteration 3 : [1] "Error in .initializeMat(ArrowFile = ArrowFiles[sample], Group = matrixName, : \n Matrix Group
sessionInfo("ArchR") R version 4.2.2 (2022-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection
locale: [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C
[3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages: character(0)
other attached packages: [1] ArchR_1.0.2
loaded via a namespace (and not attached): [1] Seurat_4.3.0 Rtsne_0.16
[3] colorspace_2.1-0 deldir_1.0-6
[5] ellipsis_0.3.2 ggridges_0.5.4
[7] XVector_0.38.0 GenomicRanges_1.50.2
[9] spatstat.data_3.0-0 farver_2.1.1
[11] leiden_0.4.3 listenv_0.9.0
[13] stats_4.2.2 ggrepel_0.9.3
[15] fansi_1.0.4 codetools_0.2-18
[17] splines_4.2.2 polyclip_1.10-4
[19] jsonlite_1.8.4 Cairo_1.6-0
[21] ica_1.0-3 base_4.2.2
[23] cluster_2.1.4 png_0.1-7
[25] uwot_0.1.14 shiny_1.7.4
[27] sctransform_0.3.5 spatstat.sparse_3.0-0
[29] compiler_4.2.2 httr_1.4.5
[31] assertthat_0.2.1 SeuratObject_4.1.3
[33] Matrix_1.5-3 fastmap_1.1.1
[35] lazyeval_0.2.2 cli_3.6.0
[37] later_1.3.0 htmltools_0.5.4
[39] tools_4.2.2 igraph_1.3.5
[41] gtable_0.3.1 glue_1.6.2
[43] GenomeInfoDbData_1.2.9 RANN_2.6.1
[45] reshape2_1.4.4 dplyr_1.0.10
[47] grDevices_4.2.2 Rcpp_1.0.10
[49] Biobase_2.58.0 scattermore_0.8
[51] rhdf5filters_1.10.0 vctrs_0.5.2
[53] spatstat.explore_3.0-5 nlme_3.1-160
[55] progressr_0.12.0 lmtest_0.9-40
[57] spatstat.random_3.0-1 stringr_1.5.0
[59] globals_0.16.2 mime_0.12
[61] miniUI_0.1.1.1 lifecycle_1.0.3
[63] irlba_2.3.5.1 gtools_3.9.4
[65] goftest_1.2-3 future_1.30.0
[67] zlibbioc_1.44.0 MASS_7.3-58.1
[69] zoo_1.8-11 scales_1.2.1
[71] MatrixGenerics_1.10.0 graphics_4.2.2
[73] promises_1.2.0.1 spatstat.utils_3.0-1
[75] SummarizedExperiment_1.28.0 parallel_4.2.2
[77] rhdf5_2.42.1 RColorBrewer_1.1-3
[79] utils_4.2.2 reticulate_1.26
[81] pbapply_1.6-0 gridExtra_2.3
[83] ggplot2_3.4.1 datasets_4.2.2
[85] stringi_1.7.12 S4Vectors_0.36.2
[87] BiocGenerics_0.44.0 GenomeInfoDb_1.34.9
[89] rlang_1.0.6 pkgconfig_2.0.3
[91] matrixStats_0.63.0 bitops_1.0-7
[93] lattice_0.20-45 Rhdf5lib_1.20.0
[95] ROCR_1.0-11 purrr_1.0.1
[97] tensor_1.5 labeling_0.4.2
[99] patchwork_1.1.2 htmlwidgets_1.6.1
[101] cowplot_1.1.1 tidyselect_1.2.0
[103] parallelly_1.33.0 RcppAnnoy_0.0.20
[105] plyr_1.8.8 magrittr_2.0.3
[107] R6_2.5.1 IRanges_2.32.0
[109] generics_0.1.3 DelayedArray_0.24.0
[111] DBI_1.1.3 withr_2.5.0
[113] pillar_1.8.1 fitdistrplus_1.1-8
[115] survival_3.4-0 abind_1.4-5
[117] RCurl_1.98-1.12 sp_1.5-1
[119] tibble_3.1.8 future.apply_1.10.0
[121] KernSmooth_2.23-20 utf8_1.2.3
[123] spatstat.geom_3.0-3 plotly_4.10.1
[125] grid_4.2.2 data.table_1.14.8
[127] methods_4.2.2 digest_0.6.31
[129] xtable_1.8-4 tidyr_1.2.1
[131] httpuv_1.6.9 stats4_4.2.2
[133] munsell_0.5.0 viridisLite_0.4.1