[R-SIG-Mac] CRAN installer for macOS - directory permissions

Henrik Bengtsson henr|k@bengt@@on @end|ng |rom gm@||@com
Fri Jun 3 18:45:21 CEST 2022

I see two fairly big problems with users installing R packages to
.Library by default.  One is related to package checking and CRAN, and
one is related to translation of expectations when moving between
operating systems (as Patrick already pointed out).  At the end, I'll
also argue that R_LIBS_SITE exists for those who wish to maintain
site-wide R package libraries to be shared among users, which is
better than using .Library for this.

# R CMD check

When you check a package with 'R CMD check --as-cran', or, with
environment variable `_R_CHECK_DEPENDS_ONLY_` set to true, the checks
are run in a sandbox where only declared package dependencies and any
packages in the system package library (= .Library) are on the library
path (= .libPaths()), e.g.

[1] "/tmp/alice/RtmpYDq3KF/RLIBS_2410b74eb16752"
[2] "/path/to/R-4.2.0/lib/R/library"

What's in the user's library (= R_LIBS_USER) or in the site library (=
.Library.site/R_LIBS_SITE) is not part of the testing.  This mechanism
is very valuable since it helps to identify undeclared package

**The default behavior on macOS discussed here, where R packages are
installed to .Library, breaks this.**  Developers with non-base R
packages in .Library will not benefit from the 'R CMD check --as-cran'
checks for undeclared packages. This increases the risk of them not
being aware of the problem of undeclared packages, which is a
discussion we see from time to time on R-devel and R-pkg-devel, e.g.
when it comes to what should be listed under Suggests: or not.

BTW, this makes me wonder how many macOS developers notice this
problem only as they submit to CRAN, and have to resubmit. Also, this
issue might add extra work to the CRAN Team, e.g. spending time
locking at and responding to possible false positives, handling more
emails, and handling more re-submissions.

# Social expectations

The second problem with the current default macOS behavior is when
people hop between systems and operating systems.  Particularly, a
macOS user coming to Unix or Windows does not immediately understand
how and where R packages are installed.  They get a prompt about a
"personal library" and might choose to decline because it's not what
they're used to seeing.  Then they might end up in the Stack Overflow
cut'n'paste rabbit hole, where they find some instructions on setting
'R_LIBS_USER=$HOME/R-lib' without version specifiers.  Works fine
until they upgrade R next year, when they start getting weird warnings
or errors of some packages not working that they slowly start to
accept as the normal behavior of R. I see this problem on large HPC
environments where I help out thousands of HPC users. Also, reading
various support forums out there, I think this is a real problem. It's
only recently, thanks to Patrick, I learned about this rather odd
macOS behavior, and I do think it is a cause for confusion and
miscommunication.  Another problem with different OS behaviors is that
it complicated documentation and instructions.  I strongly believe, it
would be beneficial to the R community if we all have the same
experience and expectations regardless of OS.

I believe the above problems are best addressed by changing the
*default* settings on macOS so that it is *not* possible to install to
.Library, and instead require a user to install to their personal
package library.  Advanced users who prefer to install to .Library,
can still configure R, or .Library, to do so.

As Patrick suggests, defaulting .Library to 755, instead of 775, or
avoid setting the "admin" group, seems like a simple solution that
would help harmonize the user experience of R.

# Maintaining a site-wide package library

> I would argue that the current setup tends to be a lot safer than the alternatives, because it allows commonly used packages to be installed at the system level and private packages to be installed at user level. This is also the design typically used on shared machines, where you separate local packages from user packages where local ones are installed by administrators - so exactly the same setup. Moreover R upgrades are a lot cleaner, since you can easily upgrade all system packages at once so you don't have to worry about individual users having stale packages - the biggest problem for admins.

I believe .Library.site/R_LIBS_SITE exists to address this purpose,
and I argue it is better suited for this than using .Library.  It also
has the benefit of *not* conflicting with the
_R_CHECK_DEPENDS_ONLY_=true checks (Problem #1 above).  It also allows
users to opt out from centrally installed packages (by setting
R_LIBS_SITE=""), which they cannot do if they're installed in the
system library.

All the best,


PS. FWIW, for all of the above reasons, I always set 755 on .Library,
even if I install R to my personal home folder; it simply lowers the
risk for side effects when developing and troubleshooting.

On Thu, Jun 2, 2022 at 11:50 PM Patrick Schratz
<patrick.schratz using gmail.com> wrote:
> I’d like to bump this thread again, especially since I am interested in a reply from Simon (or any other core member) on the arguments raised in the most recent messages of this thread.
> What would be the best way for this idea/proposal going forward?
> I’ve found https://contributor.r-project.org/, which links to a public Slack channel. Would this be a better place to discuss this matter?
> Or https://github.com/r-devel/rcontribution?
> Best,
> Patrick_______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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