callr error on install

[akgold]

Installing using pak inside a docker container fails with error Error: callr subprocess failed: Failed to download abind from 'https://demo.rstudiopm.com/cran/__linux__/bionic/latest/src/contrib/abind_1.4-5.tar.gz'. The link is valid for the correct tarball.

Installing using utils::install.packages works fine.

Dockerfile below reproduces.

# Setup --------
FROM ubuntu:bionic

ARG R_VERSION=3.6.1
ARG R_REPO='https://demo.rstudiopm.com/cran/__linux__/bionic/latest'

# Install R -------------------------------------------------------------------#

RUN apt-get update -y && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
    curl \
    gdebi

RUN curl -O https://cdn.rstudio.com/r/ubuntu-1804/pkgs/r-${R_VERSION}_1_amd64.deb && \
    DEBIAN_FRONTEND=noninteractive gdebi --non-interactive r-${R_VERSION}_1_amd64.deb

RUN ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R && \
    ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript

RUN echo "options(\"repos\" = c(RSPM = \"${R_REPO}\"), \"HTTPUserAgent\" = \"R/${R_VERSION} R (${R_VERSION} x86_64-pc-linux-gnu x86_64-pc-linux-gnu x86_64-pc-linux-gnu)\");" >> \
	/opt/R/${R_VERSION}/lib/R/etc/Rprofile.site

# works
RUN /opt/R/${R_VERSION}/bin/R -e "utils::install.packages('pak')"
# fails
RUN /opt/R/${R_VERSION}/bin/R -e "pak::pkg_install('abind')"
# works
RUN /opt/R/${R_VERSION}/bin/R -e "utils::install.packages('abind')"

[nviraj]

Not sure if this helps but faced a similar issue.

System Info

Sys.info()
sysname release version
"Linux" "4.19.104-microsoft-standard" "#1 SMP Wed Feb 19 06:37:35 UTC 2020"
nodename machine login
"9fb82202b4d1" "x86_64" "unknown"
user effective_user
"rstudio" "rstudio"

Session Info

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-openmp/libopenblasp-r0.3.8.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices datasets utils methods base

other attached packages:
[1] dplyr_1.0.1 pak_0.1.2 pacman_0.5.1 renv_0.11.0

pak::pkg_install(pkg = "tidyverse", ask = F, lib = .libPaths()[[1]])

                                              cli message status_cleare

→ Will install 55 packages:
askpass, BH, blob, broom, cellranger, clipr, colorspace, cpp11, DBI, dbplyr, evaluate, farver, forcats, fs,
ggplot2, gtable, haven, highr, htmltools, httr, isoband, knitr, labeling, lattice, lubridate, markdown, MASS,
Matrix, mgcv, mime, modelr, munsell, openssl, pkgload, praise, RColorBrewer, Rcpp, readr, readxl, rematch, reprex,
rmarkdown, rstudioapi, rvest, scales, sys, testthat, tidyr, tidyverse, tinytex, viridisLite, whisker, xfun, yaml,
nlme

→ Will not update 38 packages.

→ Will download 55 CRAN packages (47.15 MB).

Error: callr subprocess failed: Failed to download askpass from https://cran.rstudio.com/src/contrib/askpass_1.1.tar.gz and https://cran.rstudio.com/src/contrib/Archive/askpass_1.1.tar.gz.
Failed to download BH from https://cran.rstudio.com/src/contrib/BH_1.72.0-3.tar.gz and https://cran.rstudio.com/src/contrib/Archive/BH_1.72.0-3.tar.gz.
Failed to download blob from https://cran.rstudio.com/src/contrib/blob_1.2.1.tar.gz and https://cran.rstudio.com/src/contrib/Archive/blob_1.2.1.tar.gz.
Failed to download broom from https://cran.rstudio.com/src/contrib/broom_0.7.0.tar.gz and https://cran.rstudio.com/src/contrib/Archive/broom_0.7.0.tar.gz.
Failed to download cellranger from https://cran.rstudio.com/src/contrib/cellranger_1.1.0.tar.gz and https://cran.rstudio.com/src/contrib/Archive/cellranger_1.1.0.tar.gz.
Failed to download clipr from https://cran.rstudio.com/src/contrib/clipr_0.7.0.tar.gz and https://cran.rstudio.com/src/contrib/Archive/clipr_0.7.0.tar.gz.

[jimhester]

Changing your docker file to use utils::install.packages('pak', repos = 'https://r-lib.github.io/p/pak/dev/') makes the installation work, so I believe this can be closed.

[alexpghayes]

Just came across this for local installs on Ubuntu. To be clear, this is a hack to install the dev version of pak from install.packages()? And using the dev version is the fix?

[gaborcsardi]

It is not a hack, it is the supported way: https://github.com/r-lib/pak#installation