R devel - Dec 2017 - Rscript fails with some packages (for example, h5)

On 26/12/2017 9:40 AM, Dirk Eddelbuettel wrote:
> 
> On 26 December 2017 at 22:14, Sun Yijiang wrote:
> | Thanks for the solution.  Now I know the work-arounds, but still
don't
> | quite get it. Why does R_DEFAULT_PACKAGES has anything to do with
> | library(methods)?
> 
> Because it governs which packages are loaded by default.  And while R also
> loads 'methods', Rscript does not. Source of endless confusion.
Mostly irrelevant correction of the jargon:  that setting controls which 
packages are "attached" by default.  library(h5) would be enough to
load
methods, because h5 imports things from methods.  But loading doesn't 
put a package on the search list.  library(methods) both loads methods 
(if it hasn't already been loaded), and attaches it.
> 
> | If library(h5) works, it should just work, not depend on an environment
variable.
> 
> Every package using S4 will fail under Rscript unless 'methods'
explicitly.
That's not quite true (or quite English, as per fortune(112)).  The 
"gmp" package imports methods, and it works in Rscript.  What
doesn't
work is to expect library(h5) or library(gmp) to cause methods functions 
like show() to be available to the user.

There is a way to do that, but it is discouraged nowadays. My ancient 
package "orientlib" depends on methods, and that forces methods to be 
attached so show() works in Rscript.  ("Depends" is used in the 
DESCRIPTION file sense.)  h5 doesn't "depend" on methods, it
"imports"
methods.

> 
> | Rscript is not consistent with R, that's my confusion.
> 
> Indeed. And you are not the first person confused by it.
And that's still true, and less irrelevant than my corrections.

Duncan Murdoch

Duncan,

Very nice tutorial. However it does NOT take away from the fact that _very_
simple_ scripts (like the one posted by Sun at the beginning of this thread)
simply _fail_ in error under Rscript.

Whereas they don't under R or r.

The R environment ships an interpreter meant for command-line and scripting
use which fails on simple scripts that happen to use S4. But I am tired of
arguing for reversing this as I have gotten nowhere in all those years.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

Thanks for the details. I?m new to R, and I?m not blaming anything here,
just that I?m still not clear what good it makes to keep this inconsistency
between R and Rscript. To me (and probably to many others from Perl/Python
etc.), this is shockingly weird. I can live with that, and I also want to
know why.

Steve
Dirk Eddelbuettel <edd at debian.org>?2017?12?27? ??21:15???
>
> Duncan,
>
> Very nice tutorial. However it does NOT take away from the fact that _very_
> simple_ scripts (like the one posted by Sun at the beginning of this
> thread)
> simply _fail_ in error under Rscript.
>
> Whereas they don't under R or r.
>
> The R environment ships an interpreter meant for command-line and scripting
> use which fails on simple scripts that happen to use S4. But I am tired of
> arguing for reversing this as I have gotten nowhere in all those years.
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>
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>>>>> Duncan Murdoch <murdoch.duncan at gmail.com>
>>>>>     on Wed, 27 Dec 2017 06:13:12 -0500 writes:
    > On 26/12/2017 9:40 AM, Dirk Eddelbuettel wrote:
    >> 
    >> On 26 December 2017 at 22:14, Sun Yijiang wrote: | Thanks
    >> for the solution.  Now I know the work-arounds, but still
    >> don't | quite get it. Why does R_DEFAULT_PACKAGES has
    >> anything to do with | library(methods)?
    >> 
    >> Because it governs which packages are loaded by default.
    >> And while R also loads 'methods', Rscript does
    >> not. Source of endless confusion.

    > Mostly irrelevant correction of the jargon: that setting
    > controls which packages are "attached" by default.
    > library(h5) would be enough to load methods, because h5
    > imports things from methods.  But loading doesn't put a
    > package on the search list.  library(methods) both loads
    > methods (if it hasn't already been loaded), and attaches
    > it.

    >> 
    >> | If library(h5) works, it should just work, not depend
    >> on an environment variable.
    >> 
    >> Every package using S4 will fail under Rscript unless
    >> 'methods' explicitly.

    > That's not quite true (or quite English, as per
    > fortune(112)).  The "gmp" package imports methods, and
    > it works in Rscript.  What doesn't work is to expect
    > library(h5) or library(gmp) to cause methods functions
    > like show() to be available to the user.

But indeed, in this case Sun's  test.R  script did not use any
such user level functions, and it still did not work when
methods is not attached...
and indeed that's the case also with R if you run it without
loading methods e.g. by

  R_DEFAULT_PACKAGES=NULL R CMD BATCH test.R

shows the same error...

===> There is really a bug in  h5 :  It does not import enough
from methods or it would all work fine, even with Rscript !!

===> So we have something relevant to R-devel , actually at
least one bug in R's  checking :

Why did
    	R   CMD check --as-cran h5

not see that h5 defines methods for initialize() but never
imports that from methods ?
and so "should not work" when methods is not attached....

--

After all, the fact that the default packages attached at the
beginning differ between R and Rscript  has contributed to
revealing a bug in both 'h5' and R's checking procedures.

Maybe we should keep Rscript's incompatibility therefore ;-)

Martin