[Rd] Library lib.loc Option Ignored for Dependencies

[Uwe Ligges]

On 24.07.2018 23:37, Benjamin Tyner wrote:
> 
> 
> On 07/24/2018 07:50 AM, Martin Maechler wrote:
>>>>>>> Benjamin Tyner
>>>>>>>      on Sat, 21 Jul 2018 13:42:43 -0400 writes:
>>      > Not sure whether it is the same issue as was raised here:
>>      > https://stat.ethz.ch/pipermail/r-devel/2010-October/058729.html
>>
>>      > but in any case perhaps the problem could partially be remedied 
>> on line
>>      > 245 of src/library/base/R/library.R by passing the lib.loc to
>>      > .getRequiredPackages2() ...here is a patch (untested)
>>
>>      > Index: src/library/base/R/library.R
>>      > 
>> ===================================================================
>>      > --- src/library/base/R/library.R    (revision 74997)
>>      > +++ src/library/base/R/library.R    (working copy)
>>      > @@ -242,7 +242,7 @@
>>      >                      pos <- 2
>>      >                  } else pos <- npos
>>      >              }
>>      > -            .getRequiredPackages2(pkgInfo, quietly = quietly)
>>      > +            .getRequiredPackages2(pkgInfo, lib.loc = lib.loc, 
>> quietly = quietly)
>>      >              deps <- unique(names(pkgInfo$Depends))
>>
>>      >              ## If the namespace mechanism is available and the 
>> package
>>
>> This - directly - fails even more miserably e.g. in my own setup
>> when I have dependency to my package.
>>
>> But it seems a good idea to use 'lib.loc', and safer and
>> probably better than the current code maybe to use
>>
>>    .getRequiredPackages2(pkgInfo,
>>             lib.loc = c(lib.loc, .libPaths()),
>>             quietly = quietly)
>>
>> instead of the current code which uses lib.loc = NULL
>> equivalently to   lib.loc = .libPaths()
> Seems reasonable to me.
>>
>> Others / ideas?
>> Reproducible examples with small fake packages?
> Or how about an example with a "real" CRAN package with just one 
> dependency:
> 
>      > dir.create("~/lib")
>      > list.files("~/lib")
>      character(0)
>      > install.packages("spam", lib = "~/lib", dependencies = TRUE)
>      > list.files("~/lib")
>      [1] "dotCall64" "spam"
>      > library(spam, lib.loc = "~/lib")
>      Error: package ‘dotCall64’ required by ‘spam’ could not be found


Not sure if this is a bug: where is it documented that this works not as 
above (which is what I would expect)?

For development puposes, you may want to try some devekopment version of 
one package agaiunst release versions of the others.
This is the purpose of the above: take spam from ~lib and the other from 
.libPath().

Best,
Uwe Ligges


>>
>> Martin
>>
>>      > On 07/21/2018 12:34 PM, Martin Maechler wrote:
>>      >>>>>>> Benjamin Tyner
>>      >>>>>>> on Fri, 20 Jul 2018 19:42:09 -0400 writes:
>>      >> > Here's a trick/workaround; if lib.loc is the path to your
>>      >> > library, then prior to calling library(),
>>      >>
>>      >> >> environment(.libPaths)$.lib.loc <- lib.loc
>>      >>
>>      >> Well, that is quite a "trick"  -- and potentially a pretty
>>      >> dangerous one, not intended when making .libPaths a closure ....
>>      >>
>>      >>
>>      >> I do think that there is a problem with R's dealing of R_LIBS
>>      >> and other libPaths settings, notably when checking packages and
>>      >> within that recompiling vignettes etc, where the R process
>>      >> starts new versions of R via system() / system2() and then gets
>>      >> to wrong .libPaths() settings,
>>      >> and I personally would be very happy if we got reprex'es with
>>      >> small fake packages -- possibly only easily reproducible on
>>      >> unix-alikes ... so we could address this as a bug (or more than
>>      >> one) to be fixed.
>>      >>
>>      >> Notably with the 3.4.x --> 3.5.0 transition and my/our tendency
>>      >> of having quite a few paths in R_LIBS / lib.loc / ... I've been
>>      >> bitten by problems when the wrong version of package was taken
>>      >> from the wrong library path ....
>>      >>
>>      >> Martin
>>      >>
>>      >>
>>      >> >> 
>> ------------------------------------------------------------------------
>>      >> >> Good day,
>>      >> >>
>>      >> >> If there's a library folder of the latest R packages and
>>      >> >> a particular package from it is loaded using the lib.loc
>>      >> >> option, the dependencies of that package are still
>>      >> >> attempted to be loaded from another folder of older
>>      >> >> packages specified by R_LIBS, which may cause errors
>>      >> >> about version requirements not being met. The
>>      >> >> documentation of the library function doesn't explain
>>      >> >> what the intended result is in such a case, but it could
>>      >> >> reasonably be expected that R would also load the
>>      >> >> dependencies from the user-specified lib.loc folder.
>>      >> >>
>>      >> >> --------------------------------------
>>      >> >> Dario Strbenac University of Sydney Camperdown NSW 2050
>>      >> >> Australia
> 
> ______________________________________________
> R-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel