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[[ by group takes forever (24 hours +) with v1.13.0 vs 4 seconds with v1.12.8 #4646 #1

@DorisAmoakohene

Description

@DorisAmoakohene

@tdhock
I am running this performance test and I am encountering this error which is I am not able to install one of the commit ids, which is the (Before)

This is the link to the PR that fixes the issue (Rdatatable/data.table#4655) and the link to the issue (Rdatatable/data.table#4646)

Error in atime_versions_install(Package, pkg.path, new.Package.vec, SHA.vec,  : 
  R CMD INSTALL C:\Users\amoak\AppData\Local\Temp\Rtmp2fszsJ\file9d2c199c3f4d/file9d2c7a36b5e.e0140eafa07ad39a7ac9d67737cc43c4c95ca935 returned error status code 1

This is code I am running

atime.list.4646 <- atime::atime_versions(
  pkg.path=tdir,
  pkg.edit.fun=function(old.Package, new.Package, sha, new.pkg.path){
    pkg_find_replace <- function(glob, FIND, REPLACE){
      atime::glob_find_replace(file.path(new.pkg.path, glob), FIND, REPLACE)
    }
    Package_regex <- gsub(".", "_?", old.Package, fixed=TRUE)
    Package_ <- gsub(".", "_", old.Package, fixed=TRUE)
    new.Package_ <- paste0(Package_, "_", sha)
    pkg_find_replace(
      "DESCRIPTION", 
      paste0("Package:\\s+", old.Package),
      paste("Package:", new.Package))
    pkg_find_replace(
      file.path("src","Makevars.*in"),
      Package_regex,
      new.Package_)
    pkg_find_replace(
      file.path("R", "onLoad.R"),
      Package_regex,
      new.Package_)
    pkg_find_replace(
      file.path("R", "onLoad.R"),
      sprintf('packageVersion\\("%s"\\)', old.Package),
      sprintf('packageVersion\\("%s"\\)', new.Package))
    pkg_find_replace(
      file.path("src", "init.c"),
      paste0("R_init_", Package_regex),
      paste0("R_init_", gsub("[.]", "_", new.Package_)))
    pkg_find_replace(
      "NAMESPACE",
      sprintf('useDynLib\\("?%s"?', Package_regex),
      paste0('useDynLib(', new.Package_))
  },
  N=10^seq(1,7),
  setup={ 
    set.seed(123L)
    n_nested = 40L
    dt = data.table(id = seq_len(N),
                    value = replicate(N, data.table(val1 = sample(n_nested)), simplify = FALSE))
  },
  expr=data.table:::`[.data.table`(dt,, value[[1L]], by = id),
  "Before"="e0140eafa07ad39a7ac9d67737cc43c4c95ca935",#This is the commit tag 1.12.8(https://github.com/Rdatatable/data.table/tags)
  "Regression"="c041f78691f9f9495c0f25b78109cd3f5295f4f", #parent of the last commit (https://github.com/Rdatatable/data.table/commit/ec041f78691f9f9495c0f25b78109cd3f5295f4f)
  "Fixed"="ec041f78691f9f9495c0f25b78109cd3f5295f4f") #This is the last commit in the PR (https://github.com/Rdatatable/data.table/pull/4655)

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