Error in `res_one_row_df(entries)`: ! `nrow(out)` must equal `1`

[salim-b]

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_cran in half (pkgs_cran[1:95] and pkgs_cran[95:189]), installing each half works fine, i.e. doesn't trigger the error.

• Setting dependencies = FALSE also avoids triggering the error.

[gaborcsardi]

I can't reproduce this.

When splitting pkgs_cran in half (pkgs_cran[1:95] and pkgs_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 = FALSE also 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)

[salim-b]

I can't reproduce this.

On what system? Did you also test Ubuntu 24.04 x86_64?

dependencies = TRUE is 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".

[gaborcsardi]

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