rcorces
commented
1 year ago Hi @tingxie2020! 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.
tingxie2020
Zepeng-Mu
This is an issue template made by the developers of ArchR. You MUST follow these instructions.
Questions related to how to use ArchR or requests for new features should be posted in the Discussions forum (https://github.com/GreenleafLab/ArchR/discussions).
Before you submit this Bug Report please update ArchR to the latest stable version and make sure that this issue has not already been fixed in the latest release. ArchR is still in active development and we will fix problems as they arise. To update ArchR:
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
Skipping install of 'ArchR' from a github remote, the SHA1 (c61b0645) has not changed since last install.
If your issue persists, then please submit this bug report.
PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE.
Attach your log file ArchR has a built-in logging functionality for all complex functions. You MUST attach your log file (indicated in the console output) to this issue. Just drag and drop it here.
Describe the bug A clear and concise description of what the bug is.
when running archR addGeneIntegrationMatrix Error in addGeneIntegrationMatrix(ArchRProj = proj_2, useMatrix = "GeneScoreMatrix", : formal argument "groupRNA" matched by multiple actual arguments
code: proj_2 <- addGeneIntegrationMatrix( ArchRProj = proj_2, useMatrix = "GeneScoreMatrix", matrixName = "GeneIntegrationMatrix", reducedDims = "IterativeLSI", seRNA = myscRNA, groupRNA = "celltype", groupList = groupList, addToArrow = FALSE, groupRNA = "BioClassification", nameCell = "predictedCell_Un", nameGroup = "predictedGroup_Un", nameScore = "predictedScore_Un" )
To Reproduce To help us optimally address your issue, please try to reproduce this issue using the tutorial hematopoiesis dataset and provide us the command(s) to reproduce your bug. Our first question to you will be "can you reproduce this with the tutorial dataset" so please do this.
The error didn't occur when I use the tutorial hematopoiesis dataset.
Expected behavior A clear and concise description of what you expected to happen.
Screenshots If applicable, add screenshots to help explain your problem. Do not screenshot code or text but embed this in markdown using triple-backticks.
Session Info If you do not have a log file because the function that caused the error does not produce one, please paste the output of "sessionInfo()" here. 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
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=zh_CN.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=en_US.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
time zone: America/Los_Angeles tzcode source: system (glibc)
attached base packages: [1] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base
other attached packages: [1] rhandsontable_0.3.8 shiny_1.7.4
[3] ggrepel_0.9.3 hexbin_1.28.3
[5] circlize_0.4.15 ComplexHeatmap_2.16.0
[7] igraph_1.4.2 scran_1.28.1
[9] scuttle_1.10.1 SingleCellExperiment_1.22.0
[11] pheatmap_1.0.12 uwot_0.1.14
[13] harmony_0.1.1 ggridges_0.5.4
[15] nabor_0.5.0 SeuratObject_4.1.3
[17] Seurat_4.3.0 BSgenome.Mmusculus.UCSC.mm10_1.4.3 [19] BSgenome_1.68.0 rtracklayer_1.60.0
[21] Biostrings_2.68.1 XVector_0.40.0
[23] rhdf5_2.44.0 SummarizedExperiment_1.30.2
[25] Biobase_2.60.0 MatrixGenerics_1.12.2
[27] Rcpp_1.0.10 Matrix_1.5-4.1
[29] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1
[31] IRanges_2.34.1 S4Vectors_0.38.1
[33] BiocGenerics_0.46.0 matrixStats_1.0.0
[35] data.table_1.14.8 stringr_1.5.0
[37] plyr_1.8.8 magrittr_2.0.3
[39] ggplot2_3.4.2 gtable_0.3.3
[41] gtools_3.9.4 gridExtra_2.3
[43] ArchR_1.0.2
loaded via a namespace (and not attached): [1] fs_1.6.2 spatstat.sparse_3.0-2
[3] bitops_1.0-7 fontawesome_0.5.1
[5] devtools_2.4.5 httr_1.4.6
[7] RColorBrewer_1.1-3 doParallel_1.0.17
[9] profvis_0.3.8 tools_4.3.0
[11] sctransform_0.3.5 utf8_1.2.3
[13] R6_2.5.1 lazyeval_0.2.2
[15] rhdf5filters_1.12.1 GetoptLong_1.0.5
[17] urlchecker_1.0.1 withr_2.5.0
[19] sp_1.6-0 prettyunits_1.1.1
[21] progressr_0.13.0 textshaping_0.3.6
[23] cli_3.6.1 spatstat.explore_3.2-1
[25] sass_0.4.6 labeling_0.4.2
[27] spatstat.data_3.0-1 pbapply_1.7-0
[29] systemfonts_1.0.4 Rsamtools_2.16.0
[31] parallelly_1.36.0 sessioninfo_1.2.2
[33] limma_3.56.2 rstudioapi_0.14
[35] generics_0.1.3 shape_1.4.6
[37] BiocIO_1.10.0 ica_1.0-3
[39] spatstat.random_3.1-5 dplyr_1.1.2
[41] fansi_1.0.4 abind_1.4-5
[43] lifecycle_1.0.3 yaml_2.3.7
[45] edgeR_3.42.4 Rtsne_0.16
[47] promises_1.2.0.1 dqrng_0.3.0
[49] crayon_1.5.2 miniUI_0.1.1.1
[51] lattice_0.21-8 beachmat_2.16.0
[53] cowplot_1.1.1 magick_2.7.3
[55] pillar_1.9.0 knitr_1.43
[57] metapod_1.8.0 rjson_0.2.21
[59] future.apply_1.10.0 codetools_0.2-19
[61] leiden_0.4.3 glue_1.6.2
[63] remotes_2.4.2 vctrs_0.6.3
[65] png_0.1-8 cachem_1.0.8
[67] xfun_0.39 S4Arrays_1.0.4
[69] mime_0.12 survival_3.5-5
[71] shinythemes_1.2.0 iterators_1.0.14
[73] statmod_1.5.0 bluster_1.10.0
[75] ellipsis_0.3.2 fitdistrplus_1.1-11
[77] ROCR_1.0-11 nlme_3.1-162
[79] usethis_2.1.6 RcppAnnoy_0.0.20
[81] bslib_0.5.0 irlba_2.3.5.1
[83] KernSmooth_2.23-21 colorspace_2.1-0
[85] tidyselect_1.2.0 processx_3.8.1
[87] curl_5.0.1 compiler_4.3.0
[89] BiocNeighbors_1.18.0 DelayedArray_0.26.3
[91] plotly_4.10.2 scales_1.2.1
[93] lmtest_0.9-40 callr_3.7.3
[95] digest_0.6.32 goftest_1.2-3
[97] spatstat.utils_3.0-3 rmarkdown_2.22
[99] htmltools_0.5.5 pkgconfig_2.0.3
[101] sparseMatrixStats_1.12.1 fastmap_1.1.1
[103] rlang_1.1.1 GlobalOptions_0.1.2
[105] htmlwidgets_1.6.2 DelayedMatrixStats_1.22.1 [107] jquerylib_0.1.4 farver_2.1.1
[109] zoo_1.8-12 jsonlite_1.8.5
[111] BiocParallel_1.34.2 BiocSingular_1.16.0
[113] RCurl_1.98-1.12 GenomeInfoDbData_1.2.10
[115] patchwork_1.1.2 Rhdf5lib_1.22.0
[117] munsell_0.5.0 reticulate_1.28
[119] stringi_1.7.12 zlibbioc_1.46.0
[121] MASS_7.3-60 pkgbuild_1.4.0
[123] listenv_0.9.0 deldir_1.0-6
[125] splines_4.3.0 tensor_1.5
[127] locfit_1.5-9.7 ps_1.7.5
[129] spatstat.geom_3.2-1 reshape2_1.4.4
[131] ScaledMatrix_1.8.1 pkgload_1.3.2
[133] XML_3.99-0.14 evaluate_0.21
[135] BiocManager_1.30.21 foreach_1.5.2
[137] httpuv_1.6.11 RANN_2.6.1
[139] tidyr_1.3.0 purrr_1.0.1
[141] polyclip_1.10-4 future_1.32.0
[143] clue_0.3-64 scattermore_1.0
[145] rsvd_1.0.5 xtable_1.8-4
[147] restfulr_0.0.15 later_1.3.1
[149] ragg_1.2.1 viridisLite_0.4.2
[151] tibble_3.2.1 memoise_2.0.1
[153] GenomicAlignments_1.36.0 cluster_2.1.4
[155] globals_0.16.2
Additional context Add any other context about the problem here.