From dtenenba at fhcrc.org  Thu Mar 21 18:30:10 2013
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Thu, 21 Mar 2013 10:30:10 -0700
Subject: [Rd] missing space in R version specifier makes PACKAGES file
 unreadable by install.packages()
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Message-ID: <CAF42j21viRX0QhfbCMTGpven+XfGkJZNLDtKth4AU3RtKYQuGQ@mail.gmail.com>

On Thu, Mar 21, 2013 at 10:28 AM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> On 21/03/2013 12:59 PM, Dan Tenenbaum wrote:
>>
>> On Thu, Mar 21, 2013 at 9:52 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> > Hi,
>> >
>> > After updating to R-3.0 beta r62328, I get the following:
>> >
>> >> install.packages("Biobase", type="source",
>> >> repos="http://george2/BBS/2.12/bioc")
>> > Error in do.call(op, list(v_c, v_t[[op]])) :
>> >   could not find function "R (>=2.15.1)"
>> >
>> > The problem can be fixed by adding a space after >= in the offending
>> > package's DESCRIPTION file and re-generating the PACKAGES file with
>> > tools:::write_PACKAGES().
>> >
>> > However, this worked OK in r62077.
>>
>> Beg pardon, this did not work in r62077 either.
>>
>> However I still think it's worth reporting.
>
>
> I don't think this has changed recently.  The manual currently says "The
> comment should contain a comparison operator, whitespace and a valid version
> number."  In 2.15.0 it was less explicit, but the example contained a space.
> It may be that some code path worked before more or less by accident,
> because in December changes were made to the parsing to avoid a tricky
> reentrancy problem, but I don't think it has ever been documented to work
> without whitespace.
>
> I can't think of the reason white space was required, but the code does
> explicitly look for it, so I'd be reluctant to change it.
>

You're right. It was not R that changed, but something on our side. R
CMD build will not build a package with such a malformed version
specifier, so it normally would not be an issue. Please disregard and
sorry for the noise.

Dan


> Duncan Murdoch
>
>> Dan
>>
>>
>> > I'm not sure if >=2.15.1 (without
>> > the space) is valid syntax, but I wonder if R can be a bit more
>> > forgiving, as this issue derailed our daily builds.
>> >
>> >> sessionInfo()
>> > R version 3.0.0 alpha (2013-03-18 r62312)
>> > Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> >
>> > locale:
>> > [1] C
>> >
>> > attached base packages:
>> > [1] stats     graphics  grDevices utils     datasets  methods   base
>> >
>> > loaded via a namespace (and not attached):
>> > [1] tools_3.0.0
>> >
>> >
>> > Thanks,
>> > Dan
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



[Rd] missing space in R version specifier makes PACKAGES file unreadable by install.packages()
Dan Tenenbaum