Package: r-base-core Version: 4.6.0-2.2404.0 Severity: normal X-Debbugs-Cc: [email protected], [email protected]
Kurt Hornik of the upstream R Core team (also CC'ed in the bug report) contacted me stating that the .libPaths() setting in the Debian package is not quite right. This actually goes back to a discussion he and I had (along with Fritz Leisch) more than 20 years ago. In an nutshell, 'base R' (and R Core status 'recommended') packages go to /usr/lib/R/library, packages in the distribution go to /usr/lib/R/site-library and locally-installed system-wide packages go to /usr/local/lib/R/site-library. (Users can also have the standard per-user library below $HOME, but that is outside of this discussion.) Now, over the 20+ year I accommodated that via environment values or settings in /etc/R and _currently_ set it twice in /etc/R/Renviron and /etc/R/Renviron.site leading to a double entry in the (internal but accessible) state variable .Library.site: R> .Library.site [1] "/usr/local/lib/R/site-library/" "/usr/local/lib/R/site-library" [3] "/usr/lib/R/site-library" "/usr/lib/R/library" The easiest and cleanest fix will be to no longer set this in Renviron.site but only in Renviron leading to a clean split between .Library and .Library.site and an unchanged setting in .libPaths() (which combines them): > .Library [1] "/usr/lib/R/library" > .Library.site [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" > .libPaths() [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" [3] "/usr/lib/R/library" > I am mostly filing this bug report so that I can refer to it in a common in Renviron.site stating why we will no longer set it there. -- System Information: Debian Release: forky/sid APT prefers questing-updates APT policy: (500, 'questing-updates'), (500, 'questing-security'), (500, 'questing'), (100, 'questing-backports') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.17.0-23-generic (SMP w/32 CPU threads; PREEMPT) Kernel taint flags: TAINT_WARN, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages r-base-core depends on: ii ca-certificates 20250419 ii libblas3 [libblas.so.3] 3.12.1-6build1 ii libbz2-1.0 1.0.8-6build1 ii libc6 2.42-0ubuntu3.1 ii libcairo2 1.18.4-1build1 ii libcurl4t64 8.14.1-2ubuntu1.3 ii libdeflate0 1.23-2 ii libglib2.0-0t64 2.86.0-2ubuntu0.3 ii libgomp1 15.2.0-4ubuntu4 ii libicu74 74.2-1ubuntu4 ii libjpeg8 8c-2ubuntu11 ii liblapack3 [liblapack.so.3] 3.12.1-6build1 ii liblzma5 5.8.1-1build2 ii libopenblas0-pthread [liblapack.so.3] 0.3.30+ds-3 ii libpango-1.0-0 1.56.3-1build1 ii libpangocairo-1.0-0 1.56.3-1build1 ii libpaper-utils 2.2.5-0.3 ii libpcre2-8-0 10.46-1 ii libpng16-16t64 1.6.50-1ubuntu0.4 ii libreadline8t64 8.3-3 ii libtcl8.6 8.6.17+dfsg-1 ii libtiff6 4.7.0-3ubuntu3.1 ii libtirpc3t64 1.3.6+ds-1 ii libtk8.6 8.6.17-1 ii libx11-6 2:1.8.12-1build1 ii libxt6t64 1:1.2.1-1.3 ii libzstd1 1.5.7+dfsg-1build2 ii ucf 3.0052 ii unzip 6.0-28ubuntu7 ii xdg-utils 1.2.1-2ubuntu1 ii zip 3.0-15ubuntu2 ii zlib1g 1:1.3.dfsg+really1.3.1-1ubuntu2 Versions of packages r-base-core recommends: ii r-base-dev 4.6.0-2.2404.0 ii r-doc-html 4.6.0-2.2404.0 ii r-recommended 4.6.0-2.2404.0 Versions of packages r-base-core suggests: pn elpa-ess <none> ii r-base-html 4.6.0-2.2404.0 ii r-doc-info 4.6.0-2.2404.0 ii r-mathlib 4.6.0-2.2404.0 -- no debconf information
