[inlinedocs] inlinedocs generating spurious TRUE lines in examples

[Ponting, Keith (Keith)]

Thanks Thomas,

I have modified version 2013.9.3 with both your suggestion below and the exact match - the resulting modified versions work fine for me, passing R CMD check etc. 

Keith

> -----Original Message-----
> From: Thomas Wutzler [mailto:twutz at bgc-jena.mpg.de]
> Sent: 12 February 2014 07:58
> To: Ponting, Keith (Keith)
> Cc: inlinedocs-support at lists.r-forge.r-project.org
> Subject: Re: [inlinedocs] inlinedocs generating spurious TRUE lines in
> examples
> 
> Hello Keith,
> 
> requiring the package user to specify exact match of "ex" is ok.
> 
> If I am understanding correctly,  there is an additional problem: What
> happens if  there are several examples consisting of several lines for
> the same function?
> 
> Then the call to paste should be reformulated from
> paste(x, y, sep = "\n")
> to
> paste(c(x, y), collapse = "\n")
> 
> Would this break behaviour in other uses of  combine.character?
> 
> The several examples case may be prevented with requiring exact match of
> "ex". However, I vaguely remember that there were other ways to specify
> examples, making the several examples case possible.
> 
> Yours,
> Thomas
> 
> On 11.02.2014 15:54, Ponting, Keith (Keith) wrote:
> > Hello again,
> >
> >
> >
> > I have run across an interesting issue using the most recent
> inlinedocs
> > (2013.9.3) on one of my old libraries. The symptom is that running R
> CMD
> > check fails with:
> >
> >
> >
> > * checking examples ... ERROR
> >
> > Running examples in 'MinerHits-Ex.R' failed
> >
> > The error most likely occurred in:
> >
> >
> >
> >> ### Name: HitInfo
> >
> >> ### Title: HitInfo
> >
> >> ### Aliases: HitInfo
> >
> >>
> >
> >> ### ** Examples
> >
> >> library(MinerHits)
> >
> >> TRUE
> >
> > [1] TRUE
> >
> >> if ( file.exists("../MinerHits_testdata/SBC") ){ # text data too big
> > to package!
> >
> > + TRUE
> >
> > +   sbc.tiny.test <-
> > HitInfo("../MinerHits_testdata/SBC/PerformanceTester/%d/hits",
> >
> > + TRUE
> >
> > +                        ## select a very small subset of the hits for
> > testing
> >
> > + TRUE
> >
> > Error: unexpected numeric constant in:
> >
> > "                       ## select a very small subset of the hits for
> > testing
> >
> > TRUE"
> >
> > Execution halted
> >
> >
> >
> >
> >
> > The immediate cause of the problem is all those TRUE lines. Tracing
> the
> > process I find that in applying parsers, I get to the following state
> > after examples.in.attr parser:
> >
> >
> >
> > debug: docs <- combine(docs, L)
> >
> > Browse[2]> L$HitInfo
> >
> > $examples
> >
> > [1] TRUE
> >
> >
> >
> > Browse[2]> docs$HitInfo$examples
> >
> > [1]
> > "library(MinerHits)"
> >
> >
> >  [2] "if ( file.exists(\"../MinerHits_testdata/SBC\") ){ # text data
> too
> > big to package!"
> >
> >  [3] "  sbc.tiny.test <-
> > HitInfo(\"../MinerHits_testdata/SBC/PerformanceTester/%d/hits\","
> >
> > [4] "                       ## select a very small subset of the hits
> > for testing"
> >
> >  [5] "
> > term.ids=15:20,take.ids=(0:20),selector=HitThresh(2),"
> >
> >  [6] "
> > phrases=\"7-11\",dataset=\"SBC\")"
> >
> >  [7] "
> > sbc.tiny.test"
> >
> >
> >  [8] "
> > summary(sbc.tiny.test)"
> >
> >
> >  [9] "  ll(sbc.tiny.test)"
> >
> >
> > [10] "  ## normal use invokes R.oo
> > save.Object"
> >
> > [11] "
> > save(sbc.tiny.test,file=\"sbc.tiny.test.RData\")"
> >
> >
> > [12] "  ## But this code is saving for distribution with
> > package."
> >
> > [13] "  ## In order to be usable with data function, need to do normal
> > save:"
> >
> > [14] "
> > save(\"sbc.tiny.test\",file=\"sbc.tiny.test.RData\")"
> >
> >
> > [15] "}"
> >
> >
> >
> >
> > and after the combine call this becomes:
> >
> >
> >
> > Browse[2]> docs$HitInfo$examples
> >
> > [1]
> > "library(MinerHits)\nTRUE"
> >
> >
> >  [2] "if ( file.exists(\"../MinerHits_testdata/SBC\") ){ # text data
> too
> > big to package!\nTRUE"
> >
> >  [3] "  sbc.tiny.test <-
> >
> HitInfo(\"../MinerHits_testdata/SBC/PerformanceTester/%d/hits\",\nTRUE"
> >
> > [4] "                       ## select a very small subset of the hits
> > for testing\nTRUE"
> >
> >  [5] "
> > term.ids=15:20,take.ids=(0:20),selector=HitThresh(2),\nTRUE"
> >
> >  [6] "
> > phrases=\"7-11\",dataset=\"SBC\")\nTRUE"
> >
> >  [7] "  sbc.tiny.test\nTRUE"
> >
> >
> >  [8] "
> > summary(sbc.tiny.test)\nTRUE"
> >
> >
> >  [9] "
> > ll(sbc.tiny.test)\nTRUE"
> >
> >
> > [10] "  ## normal use invokes R.oo
> > save.Object\nTRUE"
> >
> > [11] "
> > save(sbc.tiny.test,file=\"sbc.tiny.test.RData\")\nTRUE"
> >
> >
> > [12] "  ## But this code is saving for distribution with
> > package.\nTRUE"
> >
> > [13] "  ## In order to be usable with data function, need to do normal
> > save:\nTRUE"
> >
> > [14] "
> > save(\"sbc.tiny.test\",file=\"sbc.tiny.test.RData\")\nTRUE"
> >
> >
> > [15] "}\nTRUE"
> >
> >
> >
> >
> > And all those TRUE lines subsequently break R CMD check. I note that
> the
> > definition of combine.character is:
> >
> > function (x, y)
> >
> > paste(x, y, sep = "\n")
> >
> > <environment: namespace:inlinedocs>
> >
> > which is where all the \nTRUE comes from.  Is that paste really what
> you
> > intended combine.character to do in the case where there are examples
> > both in the tests subdirectory and in attributes? I suspect that it
> > would work better as a simple concatenation of the two character
> vectors.
> >
> >
> >
> >
> >
> >
> >
> > The reason for the TRUE being found by examples.in.attr is that R.oo
> > (which I am using here), gives an "export" attribute, which is
> > discovered by the default behaviour of attr(o, "ex") in inlinedocs. We
> > cannot change that usage without breaking behaviour, but we could add
> > exact=TRUE to the attr call?
> >
> >
> >
> > Thanks,
> >
> >
> >
> > Keith
> >
> >
> >
> > Keith Ponting
> >
> > Avaya Speech Analytics, Malvern WR14 3SZ  UK
> >
> > Any opinions are those of the author not the company.
> >
> >
> >
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