Gabriel Becker
2022-Sep-16 04:51 UTC
[Rd] Respecting custom repositories files in interactive/batch R sessions
Hi Dirk, So there's a couple of things going on. First off you're correct that that works generally. There are a couple of reasons that made it not. The first is a bug/design error in Rstudio which is causing the R_PROFILE to not be adhered to when you build there. I will be filing a bug regarding that with them, as I know that is irrelevant to this list. There was some indication that even raw R CMD check running via an R studio server installation was missing the profile, but that ended up being spurious upon deeper testing. That said, I do think that there is a case to be made for the ability to modify what repositories R knows about at a more fundamental level than setting options in a site profile, and that is, ostensibly, what the repositories file machinery does. I understand it was intended initially and is currently only (?) used for the windows repository gui menu and related setRepositories function, but I still think there is some value in extending it in the ways I described. One major difference is that in this case, even when run with --vanilla, administrators would still be in control of which repositories users hit (by default only, of course, but there is still value in that). Best, ~G On Thu, Sep 15, 2022 at 11:31 AM Dirk Eddelbuettel <edd at debian.org> wrote:> > I may be missing something here but aren't you overcomplicating things? > One > can avoid the repetitive dialog by setting options(repos) accordingly, > and I have long done so. The Debian (and hence Ubuntu and other > derivatives) > package does so via the Rprofile.site I ship. See e.g. here > > https://sources.debian.org/src/r-base/4.2.1-2/debian/Rprofile.site/ > > I have used the same mechanism to point to intra-company repositories, > easily > a decade or so ago. I had no problems with R CMD check of in-house packages > using this. > > Dirk > > -- > dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >[[alternative HTML version deleted]]
Kurt Hornik
2022-Sep-16 07:57 UTC
[Rd] Respecting custom repositories files in interactive/batch R sessions
>>>>> Gabriel Becker writes:Friends, I always keep forgetting how these things currently/precisely work, but I guess the principle is that utils:::.onLoad() does options(repos = c(CRAN = "@CRAN@")) unless the repos option was already set (in the user or site profiles). As the latter are not used when checking, the check code in tools takes advantage of the repositories file mechanism, see ? setRepositories: The default list of known repositories is stored in the file ?R_HOME/etc/repositories?. That file can be edited for a site, or a user can have a personal copy in the file pointed to by the environment variable ?R_REPOSITORIES?, or if this is unset or does not exist, in ?HOME/.R/repositories?, which will take precedence. which also points to Startup etc). I guess one could teach utils:::.onLoad() to use the user/site repositories setting instead of the hard-wired CRAN = @CRAN@? Afaict, that would make no difference if the repositories file was not configured, and provide the configured setting in case repos was not set in the user/site profile ... Best -k> Hi Dirk, > So there's a couple of things going on. First off you're correct that that > works generally. There are a couple of reasons that made it not. The first > is a bug/design error in Rstudio which is causing the R_PROFILE to not be > adhered to when you build there. I will be filing a bug regarding that with > them, as I know that is irrelevant to this list. There was some indication > that even raw R CMD check running via an R studio server installation was > missing the profile, but that ended up being spurious upon deeper testing.> That said, I do think that there is a case to be made for the ability to > modify what repositories R knows about at a more fundamental level than > setting options in a site profile, and that is, ostensibly, what the > repositories file machinery does. I understand it was intended initially > and is currently only (?) used for the windows repository gui menu and > related setRepositories function, but I still think there is some value in > extending it in the ways I described.> One major difference is that in this case, even when run with --vanilla, > administrators would still be in control of which repositories users hit > (by default only, of course, but there is still value in that).> Best, > ~G> On Thu, Sep 15, 2022 at 11:31 AM Dirk Eddelbuettel <edd at debian.org> wrote:>> >> I may be missing something here but aren't you overcomplicating things? >> One >> can avoid the repetitive dialog by setting options(repos) accordingly, >> and I have long done so. The Debian (and hence Ubuntu and other >> derivatives) >> package does so via the Rprofile.site I ship. See e.g. here >> >> https://sources.debian.org/src/r-base/4.2.1-2/debian/Rprofile.site/ >> >> I have used the same mechanism to point to intra-company repositories, >> easily >> a decade or so ago. I had no problems with R CMD check of in-house packages >> using this. >> >> Dirk >> >> -- >> dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >>> [[alternative HTML version deleted]]> ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel