r-lib
Error in `res_one_row_df(entries)`: ! `nrow(out)` must equal `1`
Problem
pak::pkg_install(dependencies = TRUE) errors when trying to install the following 189 R packages at once:
pkgs_cran <- c(
"anesrake",
"anytime",
"archive",
"arrow",
"asciicast",
"assertr",
"available",
"bench",
"BFS",
"blastula",
"blogdown",
"bookdown",
"brio",
"broom",
"checkmate",
"cli",
"clipr",
"clock",
"commonmark",
"constructive",
"covr",
"crayon",
"crosstalk",
"crul",
"curl",
"daff",
"datapasta",
"DBI",
"deeplr",
"desc",
"DescTools",
"devtools",
"DiagrammeR",
"DiagrammeRsvg",
"dials",
"diffobj",
"diffviewer",
"digest",
"dm",
"dplyr",
"dqrng",
"DT",
"duckdb",
"forcats",
"fs",
"gargle",
"gert",
"ggeffects",
"ggforce",
"ggiraph",
"ggplot2",
"ggstream",
"gh",
"gitlabr",
"glue",
"googledrive",
"googlesheets4",
"graphql",
"gt",
"gtsummary",
"haven",
"heck",
"hexSticker",
"hms",
"htmltools",
"htmlwidgets",
"httr2",
"imager",
"infer",
"ISOcodes",
"janitor",
"jsonlite",
"kableExtra",
"katex",
"keyring",
"knitr",
"komaletter",
"labelled",
"languageserver",
"learnr",
"lifecycle",
"listviewer",
"lobstr",
"lubridate",
"magick",
"magrittr",
"miniUI",
"mirt",
"modeldata",
"modelr",
"mongolite",
"oai",
"openssl",
"pak",
"paletteer",
"pander",
"parsedate",
"parsnip",
"pins",
"pkgbuild",
"pkgcache",
"pkgdepends",
"pkgdown",
"pkgload",
"pkgsearch",
"plumber",
"prettycode",
"prettyunits",
"purrr",
"qpdf",
"qs",
"R6",
"ragg",
"rcmdcheck",
"RColorBrewer",
"Rcpp",
"RcppTOML",
"RCurl",
"readODS",
"readr",
"readxl",
"recipes",
"remotes",
"renv",
"reprex",
"reticulate",
"revealjs",
"rex",
"rio",
"rJava",
"rlang",
"rmarkdown",
"RPostgres",
"rsample",
"rsconnect",
"RSelenium",
"rstudioapi",
"rsvg",
"rvest",
"s2",
"s3fs",
"servr",
"sessioninfo",
"sf",
"shiny",
"showtext",
"skimr",
"staplr",
"stringdist",
"stringi",
"stringr",
"styler",
"swissparl",
"testthat",
"tibble",
"tidyr",
"tidyRSS",
"tidyselect",
"tidytext",
"tidyverse",
"tiff",
"tinkr",
"tokenizers",
"tune",
"tweenr",
"uaparserjs",
"units",
"urltools",
"usethis",
"uuid",
"V8",
"vctrs",
"viridis",
"visdat",
"vroom",
"webshot2",
"whoami",
"widyr",
"withr",
"workflows",
"writexl",
"xfun",
"xml2",
"xopen",
"xslt",
"yaml",
"yardstick",
"yesno",
"zip"
)
pak::pkg_install(pkg = pkgs_cran,
ask = FALSE,
dependencies = TRUE)
#> ℹ Loading metadata database
#> ✔ Loading metadata database ... done
#>
#> Error: ! error in pak subprocess
#> Caused by error in `res_one_row_df(entries)`:
#> ! `nrow(out)` must equal `1`.
Created on 2025-07-27 with reprex v2.1.1
.Last.error then gives:
<callr_error/rlib_error_3_0/rlib_error/error>
Error:
! error in pak subprocess
Caused by error in `res_one_row_df(entries)`:
! `nrow(out)` must equal `1`.
---
Backtrace:
1. pak::pkg_install(pkg = pkgs_cran, ask = FALSE, dependencies = TRUE)
2. pak:::remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...), …
3. err$throw(res$error)
---
Subprocess backtrace:
1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("pkg_install_make_plan", asNamespace("pak"))(...)
3. prop$solve()
4. private$plan$solve(policy = private$policy)
5. pkgdepends:::pkgplan_solve(self, private, match.arg(policy))
6. self$resolve()
7. pkgdepends:::pkgplan_resolve(self, private)
8. pkgdepends:::synchronise(self$async_resolve())
9. asNamespace("pkgcache")$synchronise(...)
10. base::stop(priv$value)
11. global (function (e) …
And additionally warns (because I set options(warnPartialMatchDollar = TRUE)):
Warning message:
In cond$parent : partial match of 'parent' to 'parents'
System info
sessioninfo::session_info(info = "all") is:
─ Session info ────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.5.1 (2025-06-13)
os Ubuntu 24.04.2 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2025-07-27
rstudio 2025.05.1+513 Mariposa Orchid (desktop)
pandoc 3.7.0.2 @ /var/home/salim/.local/state/pixi/bin/ (via rmarkdown)
quarto 1.7.32 @ /usr/local/bin/quarto
─ Packages ────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
brio 1.1.5 2024-04-24 [1] RSPM
callr 3.7.6 2024-03-25 [1] RSPM (R 4.5.0)
cli 3.6.5 2025-04-23 [1] RSPM
clipr 0.8.0 2022-02-22 [1] RSPM
crayon 1.5.3 2024-06-20 [1] RSPM
debugme 1.2.0 2024-04-25 [1] RSPM (R 4.5.0)
digest 0.6.37 2024-08-19 [1] RSPM
evaluate 1.0.4 2025-06-18 [1] RSPM
fastmap 1.2.0 2024-05-15 [1] RSPM (R 4.5.0)
fs 1.6.6 2025-04-12 [1] RSPM
glue 1.8.0 2024-09-30 [1] RSPM
htmltools 0.5.8.1 2024-04-04 [1] RSPM
knitr 1.50 2025-03-16 [1] RSPM
lifecycle 1.0.4 2023-11-07 [1] RSPM
magrittr * 2.0.3 2022-03-30 [1] RSPM
pak 0.9.0 2025-05-27 [1] RSPM
pillar 1.11.0 2025-07-04 [1] RSPM
pkgcache 2.2.4 2025-05-26 [1] RSPM
pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.5.0)
pkgdepends 0.9.0 2025-05-27 [1] RSPM
processx 3.8.6 2025-02-21 [1] RSPM (R 4.5.0)
ps 1.9.1 2025-04-12 [1] RSPM (R 4.5.0)
R6 2.6.1 2025-02-15 [1] RSPM
reprex 2.1.1 2024-07-06 [1] RSPM
rlang * 1.1.6 2025-04-11 [1] RSPM
rmarkdown 2.29 2024-11-04 [1] RSPM
rprojroot 2.0.4.9005 2025-07-27 [1] Github (salim-b/rprojroot@152bfee)
rstudioapi 0.17.1 2024-10-22 [1] RSPM
sessioninfo 1.2.3 2025-02-05 [1] RSPM
testthat 3.2.3 2025-01-13 [1] RSPM
tibble 3.3.0 2025-06-08 [1] RSPM
vctrs 0.6.5 2023-12-01 [1] RSPM
withr 3.0.2 2024-10-28 [1] RSPM
xfun 0.52 2025-04-02 [1] RSPM
yaml 2.3.10 2024-07-26 [1] RSPM
[1] /var/home/salim/.local/share/distrobox/ubuntu-toolbox-salim/.local/lib/r/x86_64-pc-linux-gnu-library/4.5
[2] /opt/R/4.5.1/lib/R/library
* ── Packages attached to the search path.
─ External software ───────────────────────────────────────────────────────────────────────────────
setting value
cairo 1.18.0
cairoFT
pango 1.52.1
png 1.6.43
jpeg 8.0
tiff LIBTIFF, Version 4.5.1
tcl 8.6.14
curl 8.5.0
zlib 1.3
bzlib 1.0.8, 13-Jul-2019
xz 5.4.5
deflate 1.19
PCRE 10.42 2022-12-11
ICU 74.2
TRE TRE 0.8.0 R_fixes (BSD)
iconv glibc 2.39
readline 8.2
BLAS /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
lapack /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so
lapack_version 3.12.0
─ Python configuration ────────────────────────────────────────────────────────────────────────────
Python is not available
───────────────────────────────────────────────────────────────────────────────────────────────────
getOption("repos") is:
CRAN
"https://p3m.dev/cran/__linux__/noble/latest"
Further observations
-
When splitting
pkgs_cranin half (pkgs_cran[1:95]andpkgs_cran[95:189]), installing each half works fine, i.e. doesn't trigger the error. -
Setting
dependencies = FALSEalso avoids triggering the error.
I can't reproduce this.
When splitting pkgs_cran in half (
pkgs_cran[1:95]andpkgs_cran[95:189]), installing each half works fine, i.e. doesn't trigger the error.
That's weird, because some suggested dependencies of your package list are not CRAN packages, e.g. RDCOMClient, so you can't install that from CRAN.
Setting
dependencies = FALSEalso avoids triggering the error.
dependencies = TRUE is a bad idea in general, because it installs development dependencies of packages, which might not be available on CRAN.
If you want to install the subset that is available, then this might work, assuming the original bug does not happen:
pak::pkg_install(pkg = c(pkgs_cran, "*=?ignore-unavailable"),
ask = FALSE,
dependencies = TRUE)
I can't reproduce this.
On what system? Did you also test Ubuntu 24.04 x86_64?
dependencies = TRUEis a bad idea in general, because it installs development dependencies of packages, which might not be available on CRAN.
I understand that. But I wanted to report the bug nevertheless.
Thanks for the hint about "*=?ignore-unavailable".
I can't reproduce this.
On what system? Did you also test Ubuntu 24.04 x86_64?
Yes.
FROM ubuntu:24.04
RUN apt update
RUN apt install -y curl
RUN curl -L https://rig.r-pkg.org/deb/rig.gpg -o /etc/apt/trusted.gpg.d/rig.gpg
RUN echo "deb http://rig.r-pkg.org/deb rig main" > /etc/apt/sources.list.d/rig.list
RUN apt update
RUN apt install r-rig
RUN rig add release
We are having a similar issue, but only when using our internal Posit Package Manager. The reproducible example goes like this:
FROM rocker/tidyverse:4.5
# certificates
ADD <...> /usr/local/share/ca-certificates/
RUN update-ca-certificates
ENV SSL_CERT_FILE=/etc/ssl/certs/ca-certificates.crt
RUN install2.r pak
ENV PPM=<url>
RUN echo "options(repos = c(ppm = '$PPM'))" >>"$R_HOME"/etc/Rprofile.site
RUN git clone https://github.com/bedapub/ribiosIO.git /src
RUN cd /src && Rscript -e 'pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)'
RUN rm -rf /src
RUN git clone https://github.com/bedapub/ribiosArg.git /src
RUN cd /src && Rscript -e 'pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)'
The error looks like this:
error message
STEP 15/15: RUN Rscript -e 'pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)'
! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
✔ Updated metadata database: 3.27 MB in 9 files.
ℹ Updating metadata database
✖ Updating metadata database ... failed
Error:
! error in pak subprocess
Caused by error in `res_one_row_df(entries)`:
! `nrow(out)` must equal `1`.
---
Backtrace:
1. pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)
2. pak:::remote(function(...) { …
3. err$throw(res$error)
---
Subprocess backtrace:
1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("local_install_dev_deps_make_plan", asNamespace("pak"))(...)
3. prop$solve()
4. private$plan$solve(policy = private$policy)
5. pkgdepends:::pkgplan_solve(self, private, match.arg(policy))
6. self$resolve()
7. pkgdepends:::pkgplan_resolve(self, private)
8. pkgdepends:::synchronise(self$async_resolve())
9. asNamespace("pkgcache")$synchronise(...)
10. base::stop(priv$value)
11. global (function (e) …
Execution halted
Error: building at STEP "RUN Rscript -e 'pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)'": while running runtime: exit status 1
Necessary conditions to reproduce the error:
- internal PPM enabled
- it will always fail on the second package upon building, if I remove the first installation statement the error disappears.
It only started failing a few days ago, and I do not understand why. Using an older PPM snapshot will still trigger an error; so it's not the package versions it seems. The PPM software version is also from April.
I understand that this is very difficult to debug like this. Are there any debug options you could suggest?
In our case there is an offending entry which looks something like this:
Package: pkg
Version: 0.8.1
Depends: R (>= 3.5.0)
NeedsCompilation: no
License: BSD_3_clause + file LICENSE
SystemRequirements: XXX
(https://xxx.org/)
There's a whitespace on the last line. So it's "SystemRequirements: XXX\n (https://xxx.org/)\n \n". I am not sure if this violates how the PACKAGES file should look like or not.
Now I should be able to make a reproducible example. Would you need it or this is a malformed PACKAGES file?
Thanks, then here's a reproducible example:
Dockerfile:
FROM rocker/tidyverse:4.5
RUN install2.r pak
RUN git clone https://github.com/bedapub/ribiosIO.git /src
RUN cd /src && Rscript -e 'pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)'
RUN rm -rf /src
RUN git clone https://github.com/bedapub/ribiosArg.git /src
RUN echo "options(repos = c(repo = 'file:///repo'))" >>"$R_HOME"/etc/Rprofile.site
ADD https://gist.githubusercontent.com/idavydov/0bfcdd07a0cba786ea08b83dcd84cf27/raw/05c6ea718e89c696e5177632a0b9419b90ecf83e/PACKAGES \
/repo/src/contrib/PACKAGES
RUN cd /src && Rscript -e 'pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)'
See PACKAGES.
Output of build:
STEP X/X: RUN cd /src && Rscript -e 'pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)'
! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
✔ Updated metadata database: 3.25 MB in 9 files.
ℹ Updating metadata database
✖ Updating metadata database ... failed
Error:
! error in pak subprocess
Caused by error in `res_one_row_df(entries)`:
! `nrow(out)` must equal `1`.
---
Backtrace:
1. pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)
2. pak:::remote(function(...) { …
3. err$throw(res$error)
---
Subprocess backtrace:
1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("local_install_dev_deps_make_plan", asNamespace("pak"))(...)
3. prop$solve()
4. private$plan$solve(policy = private$policy)
5. pkgdepends:::pkgplan_solve(self, private, match.arg(policy))
6. self$resolve()
7. pkgdepends:::pkgplan_resolve(self, private)
8. pkgdepends:::synchronise(self$async_resolve())
9. asNamespace("pkgcache")$synchronise(...)
10. base::stop(priv$value)
11. global (function (e) …
Execution halted
Error: building at STEP "RUN cd /src && Rscript -e 'pak::local_install_dev_deps(upgrade = FALSE, dependencies = NA)'": while running runtime: exit status 1
It appears that ‘pkgcache’ fails to parse PACKAGE DCF files that contain empty lines with whitespace. read.dcf can read the same file, so there’s an inconsistency between the native R installation mechanism and the package resolution mechanism used by ‘pak’. From our investigation this seems to be related to (/ might cause) the above issue, because the PACKAGE file of our private PPM instance has such a whitespace line in it:
pkgs = list(
c(Package = 'foo', Version = '1.0.0', Depends = 'R (>= 3.5.0)', Imports = 'utils', NeedsCompilation = 'no', License = 'GPL'),
c(Package = 'bar', Version = '1.0.0', Depends = 'R (>= 3.5.0)', Imports = 'foo', NeedsCompilation = 'no', License = 'GPL')
)
tmp = tempfile()
write.dcf(do.call(rbind, pkgs), file = tmp)
pkgcache::parse_packages(tmp)
# # A data frame: 2 × 6
# Package Version Depends Imports NeedsCompilation License
# <chr> <chr> <chr> <chr> <chr> <chr>
# 1 foo 1.0.0 R (>= 3.5.0) utils no GPL
# 2 bar 1.0.0 R (>= 3.5.0) foo no GPL
# Insert a line with a space after the ‘foo’ entry
lines = readLines(tmp)
writeLines(c(lines[1 : 6], ' ', lines[7 : 13]), tmp)
pkgcache::parse_packages(tmp)
# # A data frame: 2 × 6
# Package Version Depends Imports NeedsCompilation License
# <chr> <chr> <chr> <chr> <chr> <chr>
# 1 bar 1.0.0 R (>= 3.5.0) foo no GPL
# 2 NA NA NA NA NA NA
# But it works with read.dcf:
read.dcf(tmp)
# Package Version Depends Imports NeedsCompilation License
# [1,] "foo" "1.0.0" "R (>= 3.5.0)" "utils" "no" "GPL"
# [2,] "bar" "1.0.0" "R (>= 3.5.0)" "foo" "no" "GPL"
Seems to be fixed in dev pkgcache:
❯ readLines(tmp)
[1] "Package: foo" "Version: 1.0.0" "Depends: R (>= 3.5.0)"
[4] "Imports: utils" "NeedsCompilation: no" "License: GPL"
[7] " " "" "Package: bar"
[10] "Version: 1.0.0" "Depends: R (>= 3.5.0)" "Imports: foo"
[13] "NeedsCompilation: no" "License: GPL"
❯ pkgcache::parse_packages(tmp)
# A data frame: 2 × 6
Package Version Depends Imports NeedsCompilation License
<chr> <chr> <chr> <chr> <chr> <chr>
1 foo 1.0.0 R (>= 3.5.0) utils no GPL
2 bar 1.0.0 R (>= 3.5.0) foo no GPL
I can confirm that adding this line seem to fix the issue.
RUN Rscript -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/%s/%s/%s/%s", "devel", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
Does it build on top of dev pkgcache?
I am still confused why it doesn't break right away, but only on the second package dependencies installation.
No, dev pak does not have the latest dev pkgcache. I just updated it, so it should work from tomorrow: https://github.com/r-lib/pak/commit/ab497a7ae5228963bfd2d87f95ccc488340e7729
After building pak from ab497a7ae5228963bfd2d87f95ccc488340e7729 I wasn't able to reproduce the error in production. Thanks!
From my perspective this is resolved now and I can reopen it if the error reappears.
Hey @gaborcsardi, is it possible to release that fix forpkgcache to CRAN? This bug is currently impacting our pipelines.
