Impute weights - Githubissues

Hi,

I am able to run the ShinyArchRUiO just fine on my local development server. However when I copy the entire ArchR project directory onto my production server and run the initialization, I get the following error. Can you please help in resolving this?

[susrinivasan@sc-bcwgweb ShinyArchRUiO]$ more /var/log/shiny-server/ShinyArchRUiO-shiny-20230518-152337-38651.log su: ignoring --preserve-environment, it's mutually exclusive with --login Loading required package: Seurat Attaching SeuratObject Loading required package: shinycssloaders Loading required package: hexbin Loading required package: magick Linking to ImageMagick 6.9.12.86 Enabled features: cairo, fontconfig, freetype, ghostscript, lcms, pango, raw, rsvg, webp, x11 Disabled features: fftw, heic Using 16 threads Loading required package: gridExtra Loading required package: grid Loading required package: patchwork Loading required package: shinybusy Loading required package: ArchR

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/ ____ \ | |\ \ | ----.| | | | | |\ \\___. /__/ \__\ | _|.| _||| || | | `.____| ArchR : Version 1.0.2 For more information see our website : www.ArchRProject.com If you encounter a bug please report : https://github.com/GreenleafLab/ArchR/issues Loading Required Packages... Loading Package : grid v4.3.0 Loading Package : gridExtra v2.3 Loading Package : gtools v3.9.4 Loading Package : gtable v0.3.3 Loading Package : ggplot2 v3.4.2 Loading Package : magrittr v2.0.3 Loading Package : plyr v1.8.8 Loading Package : stringr v1.5.0 Loading Package : data.table v1.14.8 Loading Package : matrixStats v0.63.0 Loading Package : S4Vectors v0.38.1 Loading Package : GenomicRanges v1.52.0 Loading Package : BiocGenerics v0.46.0 Loading Package : Matrix v1.5.4 Loading Package : Rcpp v1.0.10 Loading Package : SummarizedExperiment v1.30.1 Loading Package : rhdf5 v2.44.0 Loading required package: ggseqlogo Loading required package: monocle3 Loading required package: SingleCellExperiment

Attaching package: ‘monocle3’

The following objects are masked from ‘package:Biobase’:

exprs, fData, fData<-, pData, pData<- Input threads is equal to or greater than ncores minus 1 (15) Setting cores to ncores minus 2. Set force = TRUE to set above this number! Setting default number of Parallel threads to 14. Setting default genome to Mm10. Successfully loaded ArchRProject!

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\ ' ##__ ,--,,=##, /// , == ,-,,--'#' ===' `-' | ##,-/ -,,---' \####\____,--\##,/ .____ __ .__
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/ ____ \ | |\ \ | ----.| | | | | |\ \\___. /__/ \__\ | _|.| _||| || | | `.____| ArchR logging to : ArchRLogs/ArchR-addImputeWeights-289505d13f07f-Date-2023-05-18_Time-15-24-01.970172.log If there is an issue, please report to github with logFile! 2023-05-18 15:24:02.039044 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed. ArchR logging to : ArchRLogs/ArchR-addImputeWeights-2895047537686-Date-2023-05-18_Time-15-24-09.261349.log If there is an issue, please report to github with logFile! 2023-05-18 15:24:09.290386 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed. ArchR logging to : ArchRLogs/ArchR-addImputeWeights-289502bc0556c-Date-2023-05-18_Time-15-24-17.415933.log If there is an issue, please report to github with logFile! 2023-05-18 15:24:17.444849 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed. Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-289504545676b-Date-2023-05-18_Time-15-24-26.491546.log If there is an issue, please report to github with logFile! Imputing Matrix Warning in mclapply(..., mc.cores = threads, mc.preschedule = preschedule) : 4 function calls resulted in an error Error in .safelapply(seq_along(blocks), function(y) { : Error Found Iteration 1 : [1] "Error in h(simpleError(msg, call)) : \n error in evaluating the argument 'x' in selecting a method for function 't': requires nu meric/complex matrix/vector arguments\n" <simpleError in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 't': requires numer ic/complex matrix/vector arguments> Error Found Iteration 2 : [1] "Error in h(simpleError(msg, call)) : \n error in evaluating the argument 'x' in selecting a method for function 't': requires nu meric/complex matrix/vector arguments\n" <simpleError in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 't': requires numer ic/complex matrix/vector arguments> Error Found Iteration 3 : [1] "Error in h(simpleError(msg, call)) : \n error in evaluating the argument 'x' in selecting a method for function 't': requires nu meric/complex matrix/vector arguments\n" <simpleError in h(simpleError(msg, cal Calls: runApp ... Reduce -> lapply -> FUN -> %>% -> Reduce -> .safelapply Execution halted

EskelandLab / ShinyArchRUiO

Impute weights #7