`pkg_install()` fails on set of packages: `filelock` not found, then `install_extracted_binary` not found

[AdaemmerP]

Summary

With pak devel 0.10.0.9000, R 4.6.0 (manylinux_2_34) on ubuntu:24.04, and PPM's __linux__/manylinux_2_28 repo configured:

• pak::pkg_install('data.table') and
  pak::pkg_install(c('data.table', 'stringr', 'sf')) work fine. The same packages install fine with simple install.packages().
• But pak::pkg_install() on 80 packages (see list below) fails. The PPM binaries exist for these packages (confirmed via meta_list() and install.packages()).

Reproduction

options(repos = c(P3M_MANYLINUX = "https://packagemanager.posit.co/cran/__linux__/manylinux_2_28/2026-06-01"))

cran_packages <- c(
  'AER', 'AICcmodavg', 'arthistory', 'babynames', 'brms', 'caret', 'clue',
  'crayon', 'data.table', 'devtools', 'downlit', 'ellmer', 'friends',
  'GGally', 'gganimate', 'ggdist', 'gghighlight', 'gifski', 'ggpubr',
  'ggrepel', 'ggridges', 'ggthemes', 'glmmTMB', 'gridExtra', 'gt',
  'janitor', 'knitr', 'languageserver', 'lmerTest', 'mclust',
  'microbenchmark', 'mlr', 'moderndive', 'MuMIn', 'nycflights23',
  'openintro', 'ordinal', 'polycor', 'quanteda', 'quanteda.textmodels',
  'quanteda.textplots', 'quanteda.textstats', 'randomForest', 'Rcpp',
  'RCurl', 'readtext', 'renv', 'reticulate', 'rmarkdown', 'RODBC',
  'rvest', 'sandwich', 'scales', 'sf', 'showtext', 'stm', 'tidygam',
  'tidymodels', 'tidytext', 'tidyverse', 'udpipe', 'xml2',
  'corrplot', 'effects', 'Epi', 'epitools', 'EValue', 'ggeffects',
  'ggfortify', 'gmodels', 'gtsummary', 'Hmisc', 'marginaleffects',
  'mice', 'naniar', 'performance', 'pROC', 'psych', 'ResourceSelection',
  'rms', 'summarytools'
)

pak::pkg_install(cran_packages)

Error 1 (filelock missing)

The call above fails with:

! in callr subprocess.
Caused by error in `loadNamespace(x)`:
! there is no package called 'filelock'
---
Subprocess backtrace:
1. options$post_process()
2. pkgdepends:::install_extracted_binary(filename, lib_cache, pkg_cache, lib, ...
3. pkgdepends:::lock_cache(lib_cache, pkg_name, getOption("install.lock"))
4. base::loadNamespace(x)

This looks like a recurrence of #197, where filelock was likewise reported missing.

Error 2 (after installing filelock)

install.packages('filelock', repos = 'https://cloud.r-project.org')
pak::pkg_install(cran_packages)  # same list as above

New internal error:

! in callr subprocess.
Caused by error in `install_extracted_binary(filename, lib_cache, pkg_cache, lib, ...`:
! could not find function "install_extracted_binary"

[gaborcsardi]

I can't reproduce this with the Dockerfile below. Can you try to create a reproducible example?

FROM ghcr.io/r-lib/rig/ubuntu

WORKDIR /root

# https://pak.r-lib.org/reference/install.html#nightly-builds
RUN <<'EOF' Rscript -
  install.packages("pak", repos = sprintf(
    "https://r-lib.github.io/p/pak/devel/%s/%s/%s",
    .Platform$pkgType,
    R.Version()$os,
    R.Version()$arch
  ))
EOF

COPY <<'EOF' /root/.Rprofile
  options(repos = c(P3M_MANYLINUX =
    "https://packagemanager.posit.co/cran/__linux__/manylinux_2_28/2026-06-01"
  ))
EOF

# Ideally, but some packages do not have binaries
# ENV PKG_SYSREQS=false

RUN <<'EOF' Rscript -
  cran_packages <- c(
    'AER', 'AICcmodavg', 'arthistory', 'babynames', 'brms', 'caret', 'clue',
    'crayon', 'data.table', 'devtools', 'downlit', 'ellmer', 'friends',
    'GGally', 'gganimate', 'ggdist', 'gghighlight', 'gifski', 'ggpubr',
    'ggrepel', 'ggridges', 'ggthemes', 'glmmTMB', 'gridExtra', 'gt',
    'janitor', 'knitr', 'languageserver', 'lmerTest', 'mclust',
    'microbenchmark', 'mlr', 'moderndive', 'MuMIn', 'nycflights23',
    'openintro', 'ordinal', 'polycor', 'quanteda', 'quanteda.textmodels',
    'quanteda.textplots', 'quanteda.textstats', 'randomForest', 'Rcpp',
    'RCurl', 'readtext', 'renv', 'reticulate', 'rmarkdown', 'RODBC',
    'rvest', 'sandwich', 'scales', 'sf', 'showtext', 'stm', 'tidygam',
    'tidymodels', 'tidytext', 'tidyverse', 'udpipe', 'xml2',
    'corrplot', 'effects', 'Epi', 'epitools', 'EValue', 'ggeffects',
    'ggfortify', 'gmodels', 'gtsummary', 'Hmisc', 'marginaleffects',
    'mice', 'naniar', 'performance', 'pROC', 'psych', 'ResourceSelection',
    'rms', 'summarytools'
  )
  pak::pkg_install(cran_packages)
EOF

[AdaemmerP]

FROM ubuntu:24.04

RUN apt-get update && apt-get install -y --no-install-recommends \
    ca-certificates curl tar \
    build-essential gfortran zlib1g-dev \
    && rm -rf /var/lib/apt/lists/*

ARG R_VERSION=4.6.0
RUN curl -fsSL https://cdn.posit.co/r/manylinux_2_34/R-${R_VERSION}-manylinux_2_34.tar.gz -o /tmp/R.tar.gz \
    && mkdir -p /opt/R && tar --strip-components=1 -C /opt/R -xf /tmp/R.tar.gz \
    && rm /tmp/R.tar.gz

# Deliberately false: we only want binary installs and do not want pak
# to fall back to compiling from source for packages without binaries.
ENV PATH="/opt/R/bin:${PATH}" \
    PKG_SYSREQS=false

RUN <<'EOF' Rscript -
  install.packages("pak", repos = sprintf(
    "https://r-lib.github.io/p/pak/devel/%s/%s/%s",
    .Platform$pkgType,
    R.Version()$os,
    R.Version()$arch
  ))
EOF

COPY <<'EOF' /opt/R/lib/R/etc/Rprofile.site
  options(repos = c(P3M_MANYLINUX =
    "https://packagemanager.posit.co/cran/__linux__/manylinux_2_28/2026-06-01"
  ))
EOF

RUN <<'EOF' Rscript -
  cran_packages <- c(
    'AER', 'AICcmodavg', 'arthistory', 'babynames', 'brms', 'caret', 'clue',
    'crayon', 'data.table', 'devtools', 'downlit', 'ellmer', 'friends',
    'GGally', 'gganimate', 'ggdist', 'gghighlight', 'gifski', 'ggpubr',
    'ggrepel', 'ggridges', 'ggthemes', 'glmmTMB', 'gridExtra', 'gt',
    'janitor', 'knitr', 'languageserver', 'lmerTest', 'mclust',
    'microbenchmark', 'mlr', 'moderndive', 'MuMIn', 'nycflights23',
    'openintro', 'ordinal', 'polycor', 'quanteda', 'quanteda.textmodels',
    'quanteda.textplots', 'quanteda.textstats', 'randomForest', 'Rcpp',
    'RCurl', 'readtext', 'renv', 'reticulate', 'rmarkdown', 'RODBC',
    'rvest', 'sandwich', 'scales', 'sf', 'showtext', 'stm', 'tidygam',
    'tidymodels', 'tidytext', 'tidyverse', 'udpipe', 'xml2',
    'corrplot', 'effects', 'Epi', 'epitools', 'EValue', 'ggeffects',
    'ggfortify', 'gmodels', 'gtsummary', 'Hmisc', 'marginaleffects',
    'mice', 'naniar', 'performance', 'pROC', 'psych', 'ResourceSelection',
    'rms', 'summarytools'
  )
  pak::pkg_install(cran_packages)
EOF

Ths build also fails when PKG_SYSREQS=false is removed.

[gaborcsardi]

# Deliberately false: we only want binary installs and do not want pak
# to fall back to compiling from source for packages without binaries.

Except that some packages that have system requirements do not have binaries in this repository, so indeed then the installation will fail.

529.1 v Installed pak 0.9.5  (5.2s)
533.9 Error:
533.9 ! error in pak subprocess
533.9 Caused by error:
533.9 ! in callr subprocess.
533.9 Caused by error in `install_extracted_binary(filename, lib_cache, pkg_cache, lib, ...`:
533.9 ! could not find function "install_extracted_binary"

This is overwriting pak itself, with a different version, so that's indeed not going to work. Install pak into a different library than the one you are installing the packages into. E.g. install pak into the system library and the packages into the user library.

[AdaemmerP]

Great, thank you so much, also for explaining how PKG_SYSREQS works! Installing pak into the system library fixes the image.