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r-lib/pak/Issues

critical: unable to install Pak on at least Debian bookworm and Ubuntu noble - Error: package or namespace load failed for 'cli' in dyn.load(...): unable to load shared object ... pak/library/cli/libs/cli.so ... undefined symbol: R_getVarEx

#860OpenN0rbert 创建于 2026-04-15
N
N0rbertcommented
Steps to reproduce: try to install Pak package on fresh Debian or Ubuntu Docker container `docker run -it --rm debian:bookworm bash -c "apt-get update && apt-get dist-upgrade -y && apt-get install -y r-base-dev build-essential && apt-cache policy r-base-dev && R --version && R -e \"install.packages('pak', repos='http://cran.r-project.org/')\""` or `docker run -it --rm ubuntu:noble bash -c "apt-get update && apt-get dist-upgrade -y && apt-get install -y r-base-dev build-essential && apt-cache policy r-base-dev && R --version && R -e \"install.packages('pak', repos='http://cran.r-project.org/')\""` Note: Ubuntu Jammy is also affected. Expected result: Pak is installed and can load its dynamic libraries or whatever it needs. Actual result for Debian bookworm: ``` ... r-base-dev: Installed: 4.2.2.20221110-2 Candidate: 4.2.2.20221110-2 Version table: *** 4.2.2.20221110-2 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 500 http://deb.debian.org/debian bookworm/main i386 Packages 100 /var/lib/dpkg/status ... R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/. R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > install.packages('pak', repos='http://cran.r-project.org/') Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) trying URL 'http://cran.r-project.org/src/contrib/Transit/pak_0.9.3-1.tar.gz' Content type 'application/x-gzip' length 3172341 bytes (3.0 MB) ================================================== downloaded 3.0 MB * installing *source* package 'pak' ... ** using staged installation ** Running ./configure ** libs Current platform: x86_64-pc-linux-gnu Build platform: Target platform: Compiling R6 Compiling cli ... make[1]: Leaving directory '/tmp/Rtmpni76Sf/R.INSTALL1fb640fd4b79/pak/src/library/cli/src' installing to /usr/local/lib/R/site-library/00LOCK-pak/00new/pak/library/cli/libs Error: package or namespace load failed for 'cli' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib/R/site-library/00LOCK-pak/00new/pak/library/cli/libs/cli.so': /usr/local/lib/R/site-library/00LOCK-pak/00new/pak/library/cli/libs/cli.so: undefined symbol: R_getVarEx Error: loading failed Execution halted ERROR: loading failed Error in install_one(pkg, lib = lib) : FAILED Calls: install_embedded_main -> install_all -> install_one Execution halted installing via 'install.libs.R' to /usr/local/lib/R/site-library/00LOCK-pak/00new/pak Error in eval(ei, envir) : Compilation failed. * removing '/usr/local/lib/R/site-library/pak' The downloaded source packages are in '/tmp/Rtmp1pQJn1/downloaded_packages' Warning message: In install.packages("pak", repos = "http://cran.r-project.org/") : installation of package 'pak' had non-zero exit status > ``` You should respect the users of stable and supported Linux distros with LTS support! Also please note that Pak is now a dependency of *devtools* [since 2.5.0 release](https://github.com/r-lib/devtools/releases/tag/v2.5.0), so you should be really careful with `R_getVarEx` and other modern symbols.
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