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bicciatolab / popsicleR

popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.
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MakeAnnotation erro, Error in `collect()`: ! Failed to collect lazy table. #4

Closed luying616 closed 6 months ago

luying616 commented 7 months ago

Cell type annotation

sample.umi <- MakeAnnotation(UMI = sample.umi, organism = "human", marker.list = "none", cluster_res= 0.8, out_folder = main.dir)

Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name? Backtrace:

  1. popsicleR::MakeAnnotation(...)
    1. dbplyr:::collect.tbl_sql(., Inf)
    2. dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...) Error in collect(., Inf) : Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name?

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.2.2 (2022-10-31) os CentOS Linux 7 (Core) system x86_64, linux-gnu ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Asia/Shanghai date 2024-03-22 rstudio 2023.06.1+524 Mountain Hydrangea (server) pandoc 3.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)

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matteomarchionni commented 6 months ago

Thank you for your report. We have identified an issue with certain dependency versions and have consequently updated them in the installation procedure. It is important to note that due to various changes in dependencies, it is no longer feasible to install all packages in R. We advise following the updated instructions for configuring the anaconda environment to ensure correct installation of the libraries.