README

genproc turns one-off iterative R procedures (for, lapply(), purrr::pmap(), …) into production-grade workflows by wrapping them with orthogonal, composable execution layers: Logged and Reproducibility are always active; Parallel, Non-blocking, and Monitoring compose on top. The goal is to make the transition from “a script that works on one case” to “a system that runs reliably on many cases” an architectural step, not an improvised rewrite.

genproc has zero Shiny dependency. A companion package (genprocShiny) will later build a UI on top of these functions.

Installation

# install.packages("remotes")
remotes::install_github("danielrak/genproc")

A minimal example

A toy file-conversion task: read a few CSVs from one directory, save them as RDS into another. One case per file.

library(genproc)

# Synthetic workspace
src_dir <- file.path(tempdir(), "src")
dst_dir <- file.path(tempdir(), "dst")
dir.create(src_dir, showWarnings = FALSE, recursive = TRUE)
dir.create(dst_dir, showWarnings = FALSE, recursive = TRUE)

write.csv(head(iris),       file.path(src_dir, "a.csv"), row.names = FALSE)
write.csv(head(mtcars),     file.path(src_dir, "b.csv"), row.names = FALSE)
write.csv(head(airquality), file.path(src_dir, "c.csv"), row.names = FALSE)

# Per-case function
convert <- function(src_dir, src_file, dst_dir, dst_file) {
  df <- read.csv(file.path(src_dir, src_file))
  saveRDS(df, file.path(dst_dir, dst_file))
}

# Iteration mask: one row per conversion
mask <- data.frame(
  src_dir  = src_dir,
  src_file = c("a.csv", "b.csv", "c.csv"),
  dst_dir  = dst_dir,
  dst_file = c("a.rds", "b.rds", "c.rds"),
  stringsAsFactors = FALSE
)

result <- genproc(convert, mask)

Every run returns a genproc_result — a structured list with a stable shape across runs:

result
#> genproc result
#>   Status   : done 
#>   Started  : 2026-05-07 21:05:36 CEST 
#>   Mode     : sequential 
#>   Cases    : 3 ( 3 ok, 0 error )
#>   Duration : 0.06 secs

The log data.frame holds one row per case, with case_id, the mask parameter values (src_dir, src_file, dst_dir, dst_file here), then success, error_message, traceback, and duration_secs. Below we display a subset of those columns for readability — error_message and traceback are NA on this happy path:

result$log[, c("case_id", "src_file", "dst_file",
               "success", "duration_secs")]
#>     case_id src_file dst_file success duration_secs
#> 1 case_0001    a.csv    a.rds    TRUE          0.02
#> 2 case_0002    b.csv    b.rds    TRUE          0.00
#> 3 case_0003    c.csv    c.rds    TRUE          0.00

If a case fails, the run continues — the error is captured, not thrown. Below we point one row of the mask to a file that does not exist; b.csv itself is left untouched on disk so subsequent sections of this README can still reference it:

mask_with_missing <- mask
mask_with_missing$src_file[2] <- "does_not_exist.csv"

result2 <- genproc(convert, mask_with_missing)
#> Warning in file(file, "rt"): cannot open file
#> 'C:\Users\rheri\AppData\Local\Temp\RtmpMjCXRi/src/does_not_exist.csv': No such
#> file or directory
errors(result2)[, c("case_id", "src_file", "error_message")]
#>     case_id           src_file              error_message
#> 2 case_0002 does_not_exist.csv cannot open the connection
result2$n_success
#> [1] 2
result2$n_error
#> [1] 1

The traceback column holds the real R call stack of the failing case (filtered for the tryCatch/withCallingHandlers machinery), so debugging a failed case reads like a normal R error.

Inspect and act on a result

errors(result2)        # data.frame of failed cases only
#>     case_id                                                src_dir
#> 2 case_0002 C:\\Users\\rheri\\AppData\\Local\\Temp\\RtmpMjCXRi/src
#>             src_file                                                dst_dir
#> 2 does_not_exist.csv C:\\Users\\rheri\\AppData\\Local\\Temp\\RtmpMjCXRi/dst
#>   dst_file success              error_message
#> 2    b.rds   FALSE cannot open the connection
#>                                                                                                                                                                                     traceback
#> 2 1. read.csv(file.path(src_dir, src_file))\n2. read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, comment.char = comment.ch ...\n3. file(file, "rt")
#>   duration_secs
#> 2             0
summary(result2)       # printable digest: status, success rate,
#> genproc result summary
#>   Status     : done
#>   Cases      : 3 (2 ok, 1 error)
#>   Success    : 67%
#>   Total time : 0.02s
#>   Per case   : mean 0.000s, max 0.000s (slowest: case_0001)
#> 
#> Top errors:
#>     1x  cannot open the connection
                       # duration stats, top recurring errors

rerun_failed(result2, convert)            # only failed cases
rerun_affected(result0, diff, convert)    # only cases referenced
                                          # by changed inputs (see
                                          # next section)

The reproducibility snapshot

result$reproducibility is a plain list recording the R version, OS, timezone, loaded package versions, the exact mask used, the specs of any optional layer, and a fingerprint of every input file referenced by the mask. This snapshot lives inside the result — no side file to keep in sync:

str(result$reproducibility, max.level = 1)
#> List of 11
#>  $ timestamp    : POSIXct[1:1], format: "2026-05-07 21:05:36"
#>  $ r_version    : chr "R version 4.5.1 (2025-06-13 ucrt)"
#>  $ platform     : chr "x86_64-w64-mingw32"
#>  $ os           : chr "Windows 10 x64"
#>  $ locale       : chr "LC_COLLATE=French_France.utf8;LC_CTYPE=French_France.utf8;LC_MONETARY=French_France.utf8;LC_NUMERIC=C;LC_TIME=F"| __truncated__
#>  $ timezone     : chr "Europe/Paris"
#>  $ packages     : Named chr [1:22] "0.2.0" "4.5.1" "1.2.0" "3.6.5" ...
#>   ..- attr(*, "names")= chr [1:22] "genproc" "compiler" "fastmap" "cli" ...
#>  $ mask_snapshot:'data.frame':   3 obs. of  4 variables:
#>  $ parallel     : NULL
#>  $ nonblocking  : NULL
#>  $ inputs       :List of 3

head(result$reproducibility$packages, 5)
#>  genproc compiler  fastmap      cli    tools 
#>  "0.2.0"  "4.5.1"  "1.2.0"  "3.6.5"  "4.5.1"

Detecting silent input drift

result$reproducibility$inputs records the size and mtime of every input file the mask refers to. The intent is to flag the most common reproducibility failure: re-running the same code on the same paths after an upstream file has been silently rewritten.

genproc detects input columns automatically: any character column of the mask whose values are existing files is treated as such. Pass track_inputs = FALSE to skip the capture, or override the heuristic with input_cols = c(...) (force) or skip_input_cols = c(...) (exclude).

mask_paths <- data.frame(
  csv_in = file.path(src_dir, c("a.csv", "b.csv", "c.csv")),
  stringsAsFactors = FALSE
)
do_one <- function(csv_in) nrow(read.csv(csv_in))

run0 <- genproc(do_one, mask_paths)
run0$reproducibility$inputs$files
#>                                                     path size
#> 1 C:/Users/rheri/AppData/Local/Temp/RtmpMjCXRi/src/a.csv  221
#> 2 C:/Users/rheri/AppData/Local/Temp/RtmpMjCXRi/src/b.csv  303
#> 3 C:/Users/rheri/AppData/Local/Temp/RtmpMjCXRi/src/c.csv  161
#>                 mtime
#> 1 2026-05-07 21:05:36
#> 2 2026-05-07 21:05:36
#> 3 2026-05-07 21:05:36

diff_inputs() compares two runs and tells you which referenced files have changed since the first one:

# Rewrite a.csv with strictly more content (size changes)
write.csv(iris, file.path(src_dir, "a.csv"), row.names = FALSE)

run1 <- genproc(do_one, mask_paths)
diff_inputs(run0, run1)
#> genproc input diff (method: stat)
#>   Changed:   1
#>   Unchanged: 2
#>   Removed:   0
#>   Added:     0
#>   Cases affected: 1
#> 
#> Changed files:
#>   C:/Users/rheri/AppData/Local/Temp/RtmpMjCXRi/src/a.csv
#>       size:  221 B -> 4.1 KB
#>       mtime: 2026-05-07 21:05:36 -> 2026-05-07 21:05:36
#> 
#> Cases affected (use rerun_affected() to re-run):
#>   case_0001

The default method is "stat" (size + mtime). It detects every legitimate modification at near-zero cost; a content-hash variant is on the roadmap for stronger guarantees on adversarial workloads.

Parallel execution

# Four workers, a temporary multisession plan, restored on exit
result <- genproc(
  convert, mask,
  parallel = parallel_spec(workers = 4)
)

The two mandatory layers remain active in parallel mode. Case order is preserved in the log regardless of the order in which workers return. Under the hood, parallel_spec() builds a configuration object consumed by future.apply::future_lapply().

If you manage future::plan() yourself (recommended across several calls to amortize worker startup), pass parallel_spec() without a strategy and your current plan is used unchanged.

Non-blocking execution

job <- genproc(
  convert, mask,
  nonblocking = nonblocking_spec()
)

status(job)        # "running", "done (not collected)", "done", or "error"
job <- await(job)  # blocks until resolution
job$log

nonblocking_spec() can be composed with parallel_spec() — the non-blocking wrapper envelops the parallel dispatch:

job <- genproc(
  convert, mask,
  parallel    = parallel_spec(workers = 4),
  nonblocking = nonblocking_spec()
)

Progress monitoring

Wrap a run in progressr::with_progress() to opt in to per-case progress reporting:

library(progressr)

with_progress({
  result <- genproc(convert, mask)
})

Pick a renderer once per session with progressr::handlers() (default "txtprogressbar", alternatives include "progress" and "cli"). Without with_progress(), or without progressr installed, the integration is a complete no-op. Live monitoring of non-blocking runs is on the roadmap.

Status

Lifecycle: experimental. The five execution layers (logged, reproducibility, parallel, non-blocking, monitoring) and the genproc_result contract are committed to forward compatibility across the 0.x series — existing fields are guaranteed not to be removed or renamed. New fields and new optional layers may be added.

The 0.2.0 release is the first public submission and is not yet on CRAN. Install from GitHub for now (see above).

Learn more

See vignette("genproc") for a deep dive: anatomy of the log and reproducibility snapshot, per-case error handling, composition patterns, and roadmap.

genproc