Encourage Imports not Depends

[mattdowle]

CRAN + BioC:

---

I've only recently realized how bad Depends: is, thanks to Jan's importing vignette. I just made its discouragement stronger : 51590bc

We could disallow Depends. This would also be beneficial to cedta()'s awkward implementation on its last line where it needs to do the tryCatch just for packages which Depend; that line could be removed.

But before we disallow Depends, we'd need to ask 69 CRAN packages to change from Depends to Imports. (Most revdeps already Import.) The longer we leave it, the greater the potential for new packages using Depends to be added to CRAN and the harder it will be to change.

	Package	Host	Last Upload	Issue?	PR?	Fixed in dev
1	DiSCos	CRAN	2026-07-12	✅
2	KMD	CRAN	2026-07-09
3	unvs.med	CRAN	2026-06-30
4	OmicFlow	CRAN	2026-05-19	✅		2026-06-25
5	poissonsuperlearner	CRAN	2026-05-18	✅
6	CoSMoS	CRAN	2026-05-07	✅
7	pep725	CRAN	2026-04-24	✅
8	RapidoPGS	CRAN	2026-04-03	✅
9	circhelp	CRAN	2026-04-02	✅		2024-09-04
10	rMIDAS	CRAN	2026-03-13	✅	✅
11	didimputation	CRAN	2026-03-09	✅		2026-08-18
12	partools	CRAN	2026-02-06	✅	✅
13	rTLS	CRAN	2026-01-19	✅
14	normfluodbf	CRAN	2025-10-10	✅
15	tma	CRAN	2025-09-19
16	colocPropTest	CRAN	2025-09-16	✅
17	FORD	CRAN	2025-05-30	✅	✅
18	damr	CRAN	2025-04-21	✅	✅
19	behavr	CRAN	2025-03-27	✅	✅
20	HospitalNetwork	CRAN	2024-12-22	✅		2025-07-08
21	ZIM4rv	CRAN	2024-12-19	✅	✅
22	lori	CRAN	2024-11-18		✅
23	SOMnmR	CRAN	2024-07-04	✅	✅
24	LKT	CRAN	2024-07-01	✅	✅
25	SeaVal	CRAN	2024-06-14	✅	✅
26	limexhub	CRAN	2024-05-06	✅	✅
27	rblt	CRAN	2024-02-19	✅	✅
28	nosoi	CRAN	2024-02-09	✅
29	tablecompare	CRAN	2023-11-14	✅
30	sqlHelpers	CRAN	2023-10-14
31	PreProcessRecordLinkage	CRAN	2023-09-13
32	fplyr	CRAN	2023-08-23	✅	✅
33	IBRtools	CRAN	2023-08-14	✅	✅
34	TrumpetPlots	CRAN	2023-06-13	✅	✅
35	DiDforBigData	CRAN	2023-04-03	✅	✅
36	pgTools	CRAN	2023-03-24	✅	✅
37	rasterDT	CRAN	2022-12-15	✅	✅
38	libbib	CRAN	2022-11-05	✅	✅
39	mind	CRAN	2022-10-27
40	acdcR	CRAN	2022-06-27	✅	✅
41	chicane	CRAN	2021-11-06
42	FeatureImpCluster	CRAN	2021-10-20	✅	✅
43	edl	CRAN	2021-09-20
44	ZIprop	CRAN	2021-06-09
45	FOCI	CRAN	2021-03-18
46	shinyML	CRAN	2021-02-24	✅	✅
47	textTools	CRAN	2021-02-05
48	dbWebForms	CRAN	2021-01-28
49	classifierplots	CRAN	2020-10-13		✅
50	intervalaverage	CRAN	2020-07-23	✅	✅
51	LSPFP	CRAN	2020-05-13
52	eyeTrackR	CRAN	2020-03-29
53	birankr	CRAN	2020-03-23	✅	✅
54	GenomicTools.fileHandler	CRAN	2020-03-05	✅	✅
55	gdxdt	CRAN	2019-11-30
56	cdparcoord	CRAN	2019-08-04
57	twl	CRAN	2018-08-24
58	RWildbook	CRAN	2018-04-06
59	miLineage	CRAN	2018-03-23
60	Ac3net	CRAN	2018-02-26
61	bea.R	CRAN	2018-02-23		✅
62	heims	CRAN	2018-01-25	✅	✅
63	slim	CRAN	2017-05-15
64	orgR	CRAN	2014-12-20	✅	✅
65	Chicago	Bioconductor	2026-04-28	✅	✅
66	GOTHiC	Bioconductor	2026-04-28
67	GladiaTOX	Bioconductor	2026-04-28	✅	✅
68	HMMcopy	Bioconductor	2026-04-28	✅	✅
69	ModCon	Bioconductor	2026-04-28	✅		2026-07-16
70	RCAS	Bioconductor	2026-04-28	✅
71	TIN	Bioconductor	2026-04-28
72	chimeraviz	Bioconductor	2026-04-28	✅		2026-08-18
73	deconvR	Bioconductor	2026-04-28			2025-07-13
74	methrix	Bioconductor	2026-04-28	✅		2025-12-01
75	rBiopaxParser	Bioconductor	2026-04-28	✅	✅
76	sangeranalyseR	Bioconductor	2026-04-28	✅		2026-05-05
77	SNPhood	Bioconductor	2025-11-04

Repro script to re-generate this table

library(tools)
library(data.table)

# 1. Fetch CRAN metadata and reverse dependencies (Depends: data.table)
cran_db = as.data.table(CRAN_package_db())
cran_deps = package_dependencies("data.table", db = as.matrix(cran_db), reverse = TRUE, which = "Depends")$data.table
cran_sub = cran_db[Package %in% cran_deps]

# 2. Fetch Bioconductor metadata and reverse dependencies (Depends: data.table)
bioc_views_url = "https://bioconductor.org/packages/release/bioc/VIEWS"
tf = tempfile()
download.file(bioc_views_url, tf, quiet = TRUE)
bioc_views = as.data.table(read.dcf(tf))
bioc_deps = package_dependencies("data.table", db = as.matrix(bioc_views), reverse = TRUE, which = "Depends")$data.table
bioc_sub = bioc_views[Package %in% bioc_deps]

# 3. Harvest existing tracked links dynamically from GitHub issue #3076 body
issue_body = tryCatch({
  res = httr::GET("https://api.github.com/repos/Rdatatable/data.table/issues/3076", httr::user_agent("Rdatatable"))
  httr::content(res, "parsed")$body
}, error = function(e) "")

known_links = list()
fixed_links = list()
lines = strsplit(issue_body, "\r?\n")[[1]]

for (l in lines) {
  # Parse table rows: | # | [pkg](repo) | [Host](host_url) | Last Upload | [✅](issue) | [✅](pr) | [date](fix) |
  if (grepl(r"{^\|.*\|.*\|.*\|}", l)) {
    parts = strsplit(l, "\\|")[[1]]
    if (length(parts) > 0 && parts[1] == "") parts = parts[-1]
    parts = trimws(parts)
    if (length(parts) >= 4 && !any(grepl("Last Upload|:---", parts))) {
      pkg_col = if (grepl("^[0-9]+$", parts[1])) 2 else 1
      pkg = sub(r"{^\[([^]]+)\].*}", "\\1", parts[pkg_col])
      
      issue_col = pkg_col + 3
      pr_col    = pkg_col + 4
      fix_col   = pkg_col + 5
      
      if (length(parts) >= issue_col && grepl(r"{https?://}", parts[issue_col])) {
        m_iss = regmatches(parts[issue_col], regexec(r"{\((https?://[^)]+)\)}", parts[issue_col]))[[1]]
        if (length(m_iss) > 1) {
          known_links[[length(known_links) + 1]] = data.table(Package = pkg, Type = "Issue", URL = m_iss[2])
        }
      }
      if (length(parts) >= pr_col && grepl(r"{https?://}", parts[pr_col])) {
        m_pr = regmatches(parts[pr_col], regexec(r"{\((https?://[^)]+)\)}", parts[pr_col]))[[1]]
        if (length(m_pr) > 1) {
          known_links[[length(known_links) + 1]] = data.table(Package = pkg, Type = "PR", URL = m_pr[2])
        }
      }
      if (length(parts) >= fix_col && grepl(r"{https?://}", parts[fix_col])) {
        fixed_links[[length(fixed_links) + 1]] = data.table(Package = pkg, Fixed_In_Dev = parts[fix_col])
      }
    }
  }
}

links_dt = if (length(known_links) > 0) {
  dcast(unique(rbindlist(known_links)), Package ~ Type, value.var = "URL", fun.aggregate = function(x) x[1])
} else {
  data.table(Package = character(), Issue = character(), PR = character())
}

fixed_dt = if (length(fixed_links) > 0) unique(rbindlist(fixed_links)) else data.table(Package = character(), Fixed_In_Dev = character())

# Helper: extract source forge repository (GitHub/GitLab) from package fields or links
extract_repo <- function(pkg, url_fields, issue_url, pr_url) {
  ref_url = na.omit(c(issue_url, pr_url))
  if (length(ref_url) > 0) {
    m = regmatches(ref_url[1], regexec(r"{(https?://[^/]+/[^/]+/[^/#?]+)}", ref_url[1]))[[1]]
    if (length(m) > 1) {
      repo = sub(r"{/(issues|pull|tree|blob|commit)/?.*$}", "", m[2])
      repo = sub(r"{/-/issues/?.*$}", "", repo)
      return(repo)
    }
  }
  urls = unlist(strsplit(url_fields[!is.na(url_fields)], "[,\n\t ]+"))
  urls = urls[urls != ""]
  repo_urls = grep("git(hub|lab)", urls, value = TRUE)
  repo_urls = repo_urls[!grepl("\\.github\\.io", repo_urls)]
  if (length(repo_urls) > 0) {
    m = regmatches(repo_urls[1], regexec(r"{(https?://[^/]+/[^/]+/[^/#?]+)}", repo_urls[1]))[[1]]
    if (length(m) > 1) {
      repo = sub(r"{\.git$}", "", m[2])
      repo = sub(r"{/(issues|pull)/?.*$}", "", repo)
      repo = sub(r"{/-/issues/?.*$}", "", repo)
      return(repo)
    }
  }
  NA_character_
}

# CRAN data
cran_dt = data.table(
  Package_Name = cran_sub$Package,
  Host_Name = "CRAN",
  Host_URL = sprintf("https://cran.r-project.org/package=%s", cran_sub$Package),
  Last_Upload = as.character(as.Date(as.POSIXct(cran_sub[["Date/Publication"]]))),
  URL_Fields = paste(cran_sub$URL, cran_sub$BugReports, sep = ", ")
)

# Bioconductor data
bioc_dt = data.table(
  Package_Name = bioc_sub$Package,
  Host_Name = "Bioconductor",
  Host_URL = sprintf("https://bioconductor.org/packages/%s", bioc_sub$Package),
  Last_Upload = bioc_sub[["Date/Publication"]],
  URL_Fields = paste(bioc_sub$URL, bioc_sub$BugReports, bioc_sub$git_url, sep = ", ")
)

all_pkgs = rbind(cran_dt, bioc_dt)
all_pkgs = merge(all_pkgs, links_dt, by.x = "Package_Name", by.y = "Package", all.x = TRUE)
all_pkgs = merge(all_pkgs, fixed_dt, by.x = "Package_Name", by.y = "Package", all.x = TRUE)

all_pkgs[, Repo := mapply(extract_repo, Package_Name, URL_Fields, Issue, PR)]
all_pkgs[, Package := ifelse(!is.na(Repo) & Repo != "", sprintf("[%s](%s)", Package_Name, Repo), Package_Name)]
all_pkgs[, Host := sprintf("[%s](%s)", Host_Name, Host_URL)]
all_pkgs[, `Issue?` := ifelse(!is.na(Issue) & Issue != "", sprintf("[✅](%s)", Issue), "")]
all_pkgs[, `PR?` := ifelse(!is.na(PR) & PR != "", sprintf("[✅](%s)", PR), "")]
all_pkgs[, `Fixed in dev` := ifelse(!is.na(Fixed_In_Dev), Fixed_In_Dev, "")]

# Sort by Host (CRAN then Bioconductor) and descending Last_Upload
all_pkgs[, Host_Order := factor(Host_Name, levels = c("CRAN", "Bioconductor"))]
setorder(all_pkgs, Host_Order, -Last_Upload)

# Leftmost column numbered 1...n with empty header
all_pkgs[, ` ` := .I]

out_dt = all_pkgs[, .(` `, Package, Host, `Last Upload` = Last_Upload, `Issue?`, `PR?`, `Fixed in dev`)]
writeLines(knitr::kable(out_dt, format = "markdown", align = c("r", "l", "l", "l", "c", "c", "l")))

[jangorecki]

It shouldn't be disallowed because there are valid use cases for Depends, for example my package dtq which is a logging mechanism for [.data.table. I recall other package too: dt.nuggets(?). We should definitely recommend to imports instead of depends, but IMO it should not be disallowed as there are valid use cases for Depends.

[mattdowle]

Fair enough. Why exactly is it that those packages need Depends and can't use Imports?

[jangorecki]

They are extensions of data.table, their existence without data.table is pointless. They not just "use" data.table.

[mattdowle]

I still don't follow. Importing is as strong as depending in that imports are required. No package importing data.table can install without it. What would fail if they changed to Imports? There is also Enhances:.
Does dtq mask [.data.table so it need to be attached in front of data.table on the search path?

[jangorecki]

It is as strong, except the fact that imported namespace doesn't need to be attached. It doesn't mask, but it expects data.table to be attached. There are definitely very few use cases like this so general rule should be to import.
In case of listed rev deps that depends on data.table we could propose to change that to imports. Change might need to update examples and unit tests (thus all dependent scripts too) to require data.table explicitly together with such rev dep package, which is potentially significant breaking change, still easy to fix.
Regarding change of depends to imports of Rbitcoin rev dep, I am not maintaining this package anymore. It might eventually be incompatible with later versions of data.table or exchange market APIs, I have no idea. Latest CRAN release is 4+ years old, dev version is 2+ years old. If someone is willing to take maintenance of it then it will be best, otherwise it will probably gets removed from CRAN once it will start breaking to many newly added rules.

[mattdowle]

75 maintainers emailed today (up from the 69 in Sep 2018) :

deps = tools::package_dependencies("data.table", which="Depends", reverse=TRUE)[[1]]
paste(sapply(deps, maintainer),collapse=";")

Dear maintainer,

Hello! Thanks for using data.table. Your package is one of 75 CRAN packages that Depend on data.table. Another 469 Import data.table. Importing is much preferred.

The data.table importing vignette now contains this text :

" Besides the Imports: field, you can also use Depends: data.table but we strongly discourage this approach (and may disallow it in future) because this loads data.table into your user’s workspace; i.e. it enables data.table functionality in your user’s scripts without them requesting that. Imports: is the proper way to use data.table within your package without inflicting data.table on your user. In fact, we hope the Depends: field is eventually deprecated in R since this is true for all packages. "

https://cran.r-project.org/web/packages/data.table/vignettes/datatable-importing.html

Another motivation is that it would be beneficial to cedta()'s awkward implementation on its last line where it needs to do the tryCatch just for packages which Depend. That line could be removed.

Eventually we'll add a message, then a warning, and after a few years possibly only allow Importing and not Depending on data.table. The next time you update your package on CRAN, are you ok to change from Depends to Imports please?

We're tracking this issue here : #3076

It's very early days on this issue and this is just a first email to let you know our thoughts and the plan. Feedback and comments are very welcome, ideally directly in the GitHub issue.

Best, Matt

[mbannert]

First of all thanks a ton for reaching out to the package maintainers.

I fully agree. I always use data.table for my backends and have imported on my more recent packages. In my case panelaggregation was a try to put a package on CRAN back when people wore pyjamas and lived life slow. Last time a data.table change caused issues I tried to get the package of CRAN but was discouraged to do so. I'd rather put my time into my newer packages than to fix a package which is more or less abandoned. On the other hand it would probably not be that much of deal to fix it though I haven't looked at the package in years.

Bottom line: from my point of view, disallowing would be a bit too much since it would get my old package of CRAN forcefully.

[tdhock]

hi I just updated my penaltyLearning package, tdhock/penaltyLearning@ef8e7fb. now it imports data.table instead of depends. basically I just had to add a bunch of library(data.table) lines in tests and examples.

[bozenne]

Hi thanks for the email and for data.table
I have also changed to imports in the Github version of the BuyseTest package.
Will be updated on CRAN at some point.

Best
brice