Your message dated Thu, 07 May 2026 18:33:34 +0000
with message-id <[email protected]>
and subject line Bug#1135944: fixed in r-base 4.6.0-3
has caused the Debian Bug report #1135944,
regarding r-base-core: Refine setting of user and system libraries
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1135944: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1135944
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: r-base
Source-Version: 4.6.0-3
Done: Dirk Eddelbuettel <[email protected]>
We believe that the bug you reported is fixed in the latest version of
r-base, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Dirk Eddelbuettel <[email protected]> (supplier of updated r-base package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 07 May 2026 12:57:51 -0500
Source: r-base
Architecture: source
Version: 4.6.0-3
Distribution: unstable
Urgency: medium
Maintainer: Dirk Eddelbuettel <[email protected]>
Changed-By: Dirk Eddelbuettel <[email protected]>
Closes: 1126018 1135944
Changes:
r-base (4.6.0-3) unstable; urgency=medium
.
* debian/rules: Ensure LIBR_LDFLAGS is empty when calling 'make install'
which prevent extra spillage into libR.pc (Closes: #1126018)
* debian/Renviron.site: No longer set R_LIBS_SITE here as Renviron already
sets it via the regularly applied patch (Closes: #1135944)
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