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> (job.dir <- readLines("JOBDIR", n=1))
[1] "/scratch/th798/data.table-revdeps/2025-04-02"
> rmarkdown::render("analyze.Rmd")


processing file: analyze.Rmd

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output file: analyze.knit.md

/home/th798/.conda/envs/emacs1/bin/pandoc +RTS -K512m -RTS analyze.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output analyze.html --lua-filter /projects/genomic-ml/R/4.1/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /projects/genomic-ml/R/4.1/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /projects/genomic-ml/R/4.1/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/th798/16231403/RtmpKcdP6Q/rmarkdown-str1c7a9a72575557.html 

Output created: analyze.html
Warning messages:
1: In do_once((if (is_R_CMD_check()) stop else warning)("The function xfun::isFALSE() will be deprecated in the future. Please ",  :
  The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
2: In png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
> job.date <- basename(job.dir)
> index.html <- file.path("analyze", job.date, "index.html")
> unlink(index.html)
> file.copy("analyze.html", index.html)
[1] TRUE
> analyze.dirs <- sort(Sys.glob("analyze/*"), decreasing=TRUE)
> max.check.days <- 7
> keep.dirs <- analyze.dirs[1:min(max.check.days,length(analyze.dirs))]
> (rm.dirs <- setdiff(analyze.dirs, keep.dirs))
[1] "analyze/2025-03-25"
> unlink(rm.dirs, recursive=TRUE)
> system("cd /projects/genomic-ml && unpublish_data data.table-revdeps && publish_data data.table-revdeps")
public_data/data.table-revdeps unpublished
/usr/bin/cp -rdl ../data.table-revdeps .
data.table-revdeps has been published
Any published files are now accessible at https://rcdata.nau.edu/genomic-ml
> unlink("/scratch/th798/data.table-revdeps/*", recursive=TRUE)
> 
>