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combiz / scFlow

Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
https://combiz.github.io/scFlow/
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Error in file(con, "r") : cannot open the connection #192

Open umranyaman opened 1 year ago

umranyaman commented 1 year ago

Hi @Al-Murphy,

I am re-running the scFlow.Rmd, however report_qc_sce function throws the error below, cannot read overview.Rmd from system.files. 

#Store results in same temp dir
report_qc_sce(sce, report_file = "qc_report_scflow_individual_1",
              report_folder_path = paste0(outputDir,"/tmp_Zeisel2015_scflow/"))

Quitting from lines 41-41 (/var/folders/v_/l9xwzh_564n055d8skd_2sm0000gn/T//Rtmp2J5a68/krdqc/overview.Rmd) Quitting from lines NA-137 (/var/folders/v/l9xwzh_564n055d8skd_2_sm0000gn/T//Rtmp2J5a68/krdqc/overview.Rmd) Error in file(con, "r") : cannot open the connection Calls: ... lapply -> FUN -> knit -> -> readLines -> file Execution halted

Thanks, Umran

eduff commented 1 year ago

Hi Umran - are you still seeing this issue?

umranyaman commented 1 year ago

Hi @eduff Yes, still creates the temp files in /var/folders... not to the directory where the other output files are. Only some markdown files are in that folder. When it is compiling markdown somehow does not work with the overview.Rmd in the output directory. I have moved the files to the output but does not work that way as well. Is that markdown issue?

eduff commented 1 year ago

Hi Umran - we have had issues with recent versions of rmarkdown and find we need to install appropriate versions with: devtools::install_version("knitr", version = "1.33", repos = "http://cran.us.r-project.org/") devtools::install_version("rmarkdown", version = "2.10", repos = "http://cran.us.r-project.org/") Similarly monocle - if you come across something related to this: devtools::install_github('cole-trapnell-lab/monocle3@1.0.0')