From bbolker at gmail.com  Tue Sep  2 03:38:05 2014
From: bbolker at gmail.com (Ben Bolker)
Date: Mon, 1 Sep 2014 21:38:05 -0400
Subject: [Rd] ggplot2/plyr interaction with latest R-devel?
In-Reply-To: <CABghstQQdS1zgEBjW_cSYAY2M-M3cAQ_oUoUQRY6X80yPWLZQg@mail.gmail.com>
References: <5404BE1D.2020609@mcmaster.ca>
	<CAN_1p9ygzA+Kbb45QKqgASWE9vg11DV0=tLruSsMxWHULfYoCA@mail.gmail.com>
	<CABghstQyz36aboSegmTbKbETGnncK4oc8rc68d6uVcMbpkKOQw@mail.gmail.com>
	<CABghstQQdS1zgEBjW_cSYAY2M-M3cAQ_oUoUQRY6X80yPWLZQg@mail.gmail.com>
Message-ID: <CABghstSPevfEjBmBZTeSuCRcu2eX4ZMO+NdegQTGWFAhUyrd2w@mail.gmail.com>

PS this is on i686-pc-linux-gnu (32-bit).  On x86_64-apple-darwin10.8.0,
log(8,base=8)==1 is TRUE, so I'm guessing the problem wouldn't come up.

(At this point I believe the problem occurs if (and only?) if
log(8,base==8)==1 is FALSE, *and* you try to make a comparison that
involves a package version with an 8 in it ...)



On Mon, Sep 1, 2014 at 9:27 PM, Ben Bolker <bbolker at gmail.com> wrote:

> Further losing my marbles.  I *think* this is a subtle bug in the
> comparison operator for package_version objects that will be dependent on
> small (platform-dependent) numerical computation differences, possibly
> (???) introduced in r66259.
>
> If I have not completely lost it (which is entirely possible), the problem
> stems from the fact that floor(log(8,base=8L)) is 0 rather than 1 on my
> machine, since log(8,base=8L) is slightly less than 1 rather than equal to
> 1.  All of the following possibly entertaining code comes from excavating
> the guts of src/library/base/R/version.R : this file was changed on July 27
> <
> https://github.com/wch/r-source/commit/ce6732242c0757e07ebc4a5efb7d210cba6a0cfa>
> , which makes me suspicious, but I don't see directly how the modifications
> would have broken this.
>
> ## basic sanity-test of package version comparison
> as.package_version("1.0.0")>=as.package_version("0.9.9")  ## TRUE
>
> ## the specific comparison I'm trying to make:
> (e1 <- as.package_version("1.8.1"))>=(e2 <- as.package_version("1.7.1"))
> ## FALSE (!!!)
> unclass(e1)  ## 1 8 1
> unclass(e2)  ## 1 7 1
>
> ## part of the internal function operation .encode_numeric_version
> intwid <- log(max(unlist(e1), unlist(e2), 1L, na.rm = TRUE), base = 8L)
> ## (why base 8? Tom Lehrer: "base eight is just like base ten really if
> you're missing two fingers")
> ## I can see that we're sprintf()ing the results in octal a few lines
> later ...)
> ## 1  -- looks OK, but:
>
> intwid-1 ## [1] -1.110223e-16
> width <- floor(intwid) + 1L  ## this is the calculation that actually gets
> done:
> ##
> ## 1 ## should be 2
>
> log(8, base=8L)-1
> log(8, base=8)-1
> logvals <- setNames(log(2:25,base=2:25)-1,2:25)
> logvals[logvals!=0]  ## 5,8,14,18,19,25 all == .Machine$double.eps/2
>
>
> w1 <- .encode_numeric_version(e1, width = width, maxlen = maxlen) ## "1101"
> w2 <- .encode_numeric_version(e2, width = width, maxlen = maxlen) ## "171"
> w1>w2  ## FALSE
>
> w1A <- .encode_numeric_version(e1, width = 2, maxlen = maxlen) ## "011001"
> w2A <- .encode_numeric_version(e2, width = 2, maxlen = maxlen) ## "010701"
> w1A>w2A  ## TRUE
>
>
> If I had the patience I would revert to before this SVN change and see
> what happened:
>
> =================
> r66259 | hornik | 2014-07-27 15:45:29 -0400 (Sun, 27 Jul 2014) | 2 lines
>
> Have .encode_numeric_version() pad to common length with trailing zeros.
> Add [<-.numeric_version().
>
>
>
>
> On Mon, Sep 1, 2014 at 4:16 PM, Ben Bolker <bbolker at gmail.com> wrote:
>
>> thanks -- although I think `dplyr` is a red herring; my issue is with
>> `plyr` (which is imported by `ggplot2` so should get installed
>> automatically anyway ...)
>>
>>
>> On Mon, Sep 1, 2014 at 4:08 PM, Carl Boettiger <cboettig at gmail.com>
>> wrote:
>>
>>> Hi Ben,
>>>
>>> Just tested this on a fresh ubuntu 14:04 sandbox by using Dirk's docker
>>> image (
>>> https://github.com/eddelbuettel/docker-ubuntu-r/tree/master/add-r-devel-san)
>>> for Rdevel.
>>>
>>> > install.packages(c("dplyr", "ggplot2"))
>>> > library("dplyr")
>>> > library("ggplot2")
>>>
>>> runs fine for me (though takes a few minutes to compile everything). So
>>> it seems you must have done something to your local environment, but not
>>> sure what.
>>>
>>>
>>>
>>>
>>> On Mon, Sep 1, 2014 at 11:42 AM, Ben Bolker <bbolker at gmail.com> wrote:
>>>
>>>>
>>>>   I apologize in advance for not having done more homework in advance,
>>>> but thought I would send this along to see if anyone else was seeing
>>>> this.
>>>>
>>>>   I am having some sort of ggplot2/plyr/very-recent-R-devel dependency
>>>> issues.
>>>>
>>>>   Just installed
>>>>
>>>> R Under development (unstable) (2014-09-01 r66509) -- "Unsuffered
>>>> Consequences"
>>>>
>>>>  from source.
>>>>
>>>> > packageVersion("ggplot2")
>>>> [1] ?1.0.0?
>>>> > packageVersion("plyr")
>>>> [1] ?1.8.1?
>>>>
>>>> library(plyr) works
>>>>
>>>>   but then I get:
>>>>
>>>> library(ggplot2)
>>>> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
>>>> vI[[i]]) :
>>>>   namespace ?plyr? 1.8.1 is being loaded, but >= 1.7.1 is required
>>>> Error: package or namespace load failed for ?ggplot2?
>>>>
>>>>   I don't remember when I most recently updated my r-devel (it was
>>>> probably a few months old); nothing in recent commits rings a bell.
>>>>
>>>>   Works fine on R version 3.1.1 (except for a "ggplot2 built under
>>>> 3.2.0 warning").
>>>>
>>>>   Does anyone else see this or is it just something weird about my
>>>> setup?
>>>>
>>>>   Ben Bolker
>>>>
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>>>
>>>
>>> --
>>> Carl Boettiger
>>> UC Santa Cruz
>>> http://carlboettiger.info/
>>>
>>
>>
>

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[Rd] ggplot2/plyr interaction with latest R-devel?
Ben Bolker