Re: [Rd] 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
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Re: [Rd] Rscript fails with some packages (for example, h5)
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 | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rscript fails with some packages (for example, h5)
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 于2017年12月27日 周三21:15写道： > > 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 | e...@debian.org > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Numerical stability in chisq.test
The chisq.test on line 57 contains following code: STATISTIC <- sum(sort((x - E)^2/E, decreasing = TRUE)) However, based on book "Accuracy and stability of numerical algorithms" available from: http://ftp.demec.ufpr.br/CFD/bibliografia/Higham_2002_Accuracy%20and%20Stability%20of%20Numerical%20Algorithms.pdf Table 4.1 on page 89, it is better to sort the data in increasing order than in decreasing order, when the data are non-negative. An example: x = matrix(c(rep(1.1, 1)), 10^16, nrow = 10001, ncol = 1)# We have a vector with 1*1.1 and 1*10^16 c(sum(sort(x, decreasing = TRUE)), sum(sort(x, decreasing = FALSE))) The result: 100010996 100011000 When we sort the data in the increasing order, we get the correct result. If we sort the data in the decreasing order, we get a result that is off by 4. Shouldn't the sort be in the increasing order rather than in the decreasing order? Best regards, Jan Motl PS: This post is based on discussion on https://stackoverflow.com/questions/47847295/why-does-chisq-test-sort-data-in-descending-order-before-summation and the response from the post to r-h...@r-project.org. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rscript fails with some packages (for example, h5)
On 27/12/2017 9:11 AM, Sun Yijiang wrote: 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. As Dirk said, the argument was that the methods package used to take a long time to load, and many uses of Rscript shouldn't have to pay that time cost. I don't know whether that's still true or not. Dirk and I agree that the inconsistency between R and Rscript is undesirable, but neither of us is in a position to change it, or thinks it's worth the effort to argue for a change. Duncan Steve Dirk Eddelbuettel 于2017年12月27日 周三21:15写道： 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 | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
