Warning: missing text for item ... in \describe?

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Warning: missing text for item ... in \describe?

Spencer Graves
Hello:

      What might be the problem generating messages like "Warning:
missing text for item ... in \describe" with "R CMD check" and "R CMD
install"?

      With the current version of "fda" on R-Forge, I get the following:


Warning: missing text for item 'fd' in \describe
Warning: missing text for item 'fdPar' in \describe


      I found a where someone else asked about essentially this warning
message, but I didn't find a reply.  I also found that
"https://svn.r-project.org/R/trunk/share/perl/R/Rdconv.pm" is coded to
issue such messages.  However, I still don't know what I'm doing to
generate it.

      Thanks in advance for any suggestions.

      Best Wishes,
      Spencer

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Re: Warning: missing text for item ... in \describe?

Berwin A Turlach
G'day Spencer,

On Sun, 30 Nov 2008 22:31:54 -0800
Spencer Graves <[hidden email]> wrote:

> Hello:
>
>       What might be the problem generating messages like "Warning:
> missing text for item ... in \describe" with "R CMD check" and "R CMD
> install"?
>
>       With the current version of "fda" on R-Forge, I get the
> following:
>
>
> Warning: missing text for item 'fd' in \describe
> Warning: missing text for item 'fdPar' in \describe

fRegress.Rd, which contains

\item{fd} { ...
\item{fdPar} {...

Apparently the space between the closing and the opening bracket leads
to some confusion; remove the space and the warning goes away.

I am not sure why an extra space here leads to problems, would be nicer
if it would not.  If it have to lead to a problem, then it would be
nice if the name of the .Rd files that produces the problem is actually
mentioned. :)

Don't ask me how I found this, let us just say that long live
find-grep-dired in emacs and perseverance (or should that be
stubbornness?)

HTH.

Cheers,

        Berwin

=========================== Full address =============================
Berwin A Turlach                            Tel.: +65 6516 4416 (secr)
Dept of Statistics and Applied Probability        +65 6516 6650 (self)
Faculty of Science                          FAX : +65 6872 3919      
National University of Singapore    
6 Science Drive 2, Blk S16, Level 7          e-mail: [hidden email]
Singapore 117546                    http://www.stat.nus.edu.sg/~statba

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Re: Warning: missing text for item ... in \describe?

Prof Brian Ripley
On Mon, 1 Dec 2008, Berwin A Turlach wrote:

> G'day Spencer,
>
> On Sun, 30 Nov 2008 22:31:54 -0800
> Spencer Graves <[hidden email]> wrote:
>
>> Hello:
>>
>>       What might be the problem generating messages like "Warning:
>> missing text for item ... in \describe" with "R CMD check" and "R CMD
>> install"?
>>
>>       With the current version of "fda" on R-Forge, I get the
>> following:
>>
>>
>> Warning: missing text for item 'fd' in \describe
>> Warning: missing text for item 'fdPar' in \describe
>
> fRegress.Rd, which contains
>
> \item{fd} { ...
> \item{fdPar} {...
>
> Apparently the space between the closing and the opening bracket leads
> to some confusion; remove the space and the warning goes away.
>
> I am not sure why an extra space here leads to problems, would be nicer
> if it would not.  If it have to lead to a problem, then it would be
> nice if the name of the .Rd files that produces the problem is actually
> mentioned. :)

Well, the warning/errors always come out just before the file with the
problem (unless you have stdout buffered and stderr not).  So finding
which file does not seem so hard.

This *is* an error: nothing in the description allows whitespace between
arguments to \item (nor \section).  It seems that only a few people
misread the documentation (sometimes even after their error is pointed out
to them).  What we can do is detect the error, and I am about to commit
code in R-devel to do so.

Note that we don't have a complete description of the Rd language, but
three partial parsers (Rdconv, tools::Rdparse and from R-devel, parseRd).
If Duncan M's work on parseRd comes to fruition we may have a grammar and
a parser, but it is likely to be for 'Rd2' format since no one wants to
enshrine all the quirks of the current format.

> Don't ask me how I found this, let us just say that long live
> find-grep-dired in emacs and perseverance (or should that be
> stubbornness?)
>
> HTH.
>
> Cheers,
>
> Berwin
>
> =========================== Full address =============================
> Berwin A Turlach                            Tel.: +65 6516 4416 (secr)
> Dept of Statistics and Applied Probability        +65 6516 6650 (self)
> Faculty of Science                          FAX : +65 6872 3919
> National University of Singapore
> 6 Science Drive 2, Blk S16, Level 7          e-mail: [hidden email]
> Singapore 117546                    http://www.stat.nus.edu.sg/~statba
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: Warning: missing text for item ... in \describe?

Berwin A Turlach
G'day Brian,

On Fri, 5 Dec 2008 15:35:00 +0000 (GMT)
Prof Brian Ripley <[hidden email]> wrote:

> On Mon, 1 Dec 2008, Berwin A Turlach wrote:
>
> > G'day Spencer,
> >
> > On Sun, 30 Nov 2008 22:31:54 -0800
> > Spencer Graves <[hidden email]> wrote:
> >
> >> Hello:
> >>
> >>       What might be the problem generating messages like "Warning:
> >> missing text for item ... in \describe" with "R CMD check" and "R
> >> CMD install"?
> >>
> >>       With the current version of "fda" on R-Forge, I get the
> >> following:
> >>
> >>
> >> Warning: missing text for item 'fd' in \describe
> >> Warning: missing text for item 'fdPar' in \describe
> >
> > fRegress.Rd, which contains
> >
> > \item{fd} { ...
> > \item{fdPar} {...
[...]
> Well, the warning/errors always come out just before the file with
> the problem (unless you have stdout buffered and stderr not).  So
> finding which file does not seem so hard.

Which platform are we talking here?  I was using linux and "R CMD check
fda", using R 2.8.0, on the command line said:

[...]
* checking for executable files ... OK
* checking whether package 'fda' can be installed ... WARNING
Found the following significant warnings:
  Warning: missing text for item 'fd' in \describe
  Warning: missing text for item 'fd' in \describe
  Warning: missing text for item 'fdPar' in \describe
See '/home/berwin/lang/R/Develop/Others/fda.Rcheck/00install.out' for
details.
* checking package directory ... OK
[...]

And 00install.out said:

[...]
Attaching package: 'zoo'


        The following object(s) are masked from package:base :

         as.Date.numeric

** help
Warning: missing text for item 'fd' in \describe
Warning: missing text for item 'fd' in \describe
Warning: missing text for item 'fdPar' in \describe
 >>> Building/Updating help pages for package 'fda'
     Formats: text html latex example
  CSTR                              text    html    latex   example
  CanadianWeather                   text    html    latex   example
[...]

I am not aware that either stdout or stderr are buffered on my linux
box.

> This *is* an error: nothing in the description allows whitespace
> between arguments to \item (nor \section). It seems that only a few
> people misread the documentation (sometimes even after their error is
> pointed out to them).

But there is also nothing that explicitly forbid such whitespace, is
it?  I guess this comes down to the question whether "everything is
allowed that is not expressively forbidden" or "everything is forbidden
unless it is expressively allowed".  Strangely enough, though I am
German, I don't tend to subscribe to the latter philosophy.  

The language of Rd files, and the notation used, seems to have some
clear roots in (La)TeX;  and in (La)TeX whitespace between arguments to
macros is ignored.  So one may argue that it is a bit of a surprise
that whitespace between arguments to \item matter here.

> What we can do is detect the error, and I am about to commit code in
> R-devel to do so.

Thanks.  I am sure Spencer will be happy about this. :)

Cheers,

        Berwin

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Re: Warning: missing text for item ... in \describe?

Prof Brian Ripley
On Sat, 6 Dec 2008, Berwin A Turlach wrote:

> G'day Brian,
>
> On Fri, 5 Dec 2008 15:35:00 +0000 (GMT)
> Prof Brian Ripley <[hidden email]> wrote:
>
>> On Mon, 1 Dec 2008, Berwin A Turlach wrote:
>>
>>> G'day Spencer,
>>>
>>> On Sun, 30 Nov 2008 22:31:54 -0800
>>> Spencer Graves <[hidden email]> wrote:
>>>
>>>> Hello:
>>>>
>>>>       What might be the problem generating messages like "Warning:
>>>> missing text for item ... in \describe" with "R CMD check" and "R
>>>> CMD install"?
>>>>
>>>>       With the current version of "fda" on R-Forge, I get the
>>>> following:
>>>>
>>>>
>>>> Warning: missing text for item 'fd' in \describe
>>>> Warning: missing text for item 'fdPar' in \describe
>>>
>>> fRegress.Rd, which contains
>>>
>>> \item{fd} { ...
>>> \item{fdPar} {...

> [...]
>> Well, the warning/errors always come out just before the file with
>> the problem (unless you have stdout buffered and stderr not).  So
>> finding which file does not seem so hard.
>
> Which platform are we talking here?  I was using linux and "R CMD check
> fda", using R 2.8.0, on the command line said:

That writes to a file, and writes to a file are buffered.  Try R CMD
INSTALL, where they are not.  We do recommend getting a clean install
before R CMD check.

> [...]
> * checking for executable files ... OK
> * checking whether package 'fda' can be installed ... WARNING
> Found the following significant warnings:
>  Warning: missing text for item 'fd' in \describe
>  Warning: missing text for item 'fd' in \describe
>  Warning: missing text for item 'fdPar' in \describe
> See '/home/berwin/lang/R/Develop/Others/fda.Rcheck/00install.out' for
> details.
> * checking package directory ... OK
> [...]
>
> And 00install.out said:
>
> [...]
> Attaching package: 'zoo'
>
>
>        The following object(s) are masked from package:base :
>
>         as.Date.numeric
>
> ** help
> Warning: missing text for item 'fd' in \describe
> Warning: missing text for item 'fd' in \describe
> Warning: missing text for item 'fdPar' in \describe
> >>> Building/Updating help pages for package 'fda'
>     Formats: text html latex example
>  CSTR                              text    html    latex   example
>  CanadianWeather                   text    html    latex   example
> [...]
>
> I am not aware that either stdout or stderr are buffered on my linux
> box.

Wriitng to a file, stdout almost always is.

>
>> This *is* an error: nothing in the description allows whitespace
>> between arguments to \item (nor \section). It seems that only a few
>> people misread the documentation (sometimes even after their error is
>> pointed out to them).
>
> But there is also nothing that explicitly forbid such whitespace, is
> it?  I guess this comes down to the question whether "everything is
> allowed that is not expressively forbidden" or "everything is forbidden
> unless it is expressively allowed".  Strangely enough, though I am
> German, I don't tend to subscribe to the latter philosophy.

It really doesn't matter: the author of the convertor (not me) decidedly
to silently ignore arguments after whitespace so you get an incorrect
conversion. I also added sentences to the documentation that say that
explicitly.  But if I see documentation that says

\item{foo}{bar}

I don't see why anyone would be surprised that

\item {foo} {bar}

goes haywire.

> The language of Rd files, and the notation used, seems to have some
> clear roots in (La)TeX;  and in (La)TeX whitespace between arguments to

More like texinfo.

> macros is ignored.  So one may argue that it is a bit of a surprise
> that whitespace between arguments to \item matter here.
>
>> What we can do is detect the error, and I am about to commit code in
>> R-devel to do so.
>
> Thanks.  I am sure Spencer will be happy about this. :)
>
> Cheers,
>
> Berwin
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: Warning: missing text for item ... in \describe?

Berwin A Turlach
G'day Brian,

On Fri, 5 Dec 2008 17:32:58 +0000 (GMT)
Prof Brian Ripley <[hidden email]> wrote:

[...]
> > Which platform are we talking here?  I was using linux and "R CMD
> > check fda", using R 2.8.0, on the command line said:
>
> That writes to a file, and writes to a file are buffered.  Try R CMD
> INSTALL, where they are not.  We do recommend getting a clean install
> before R CMD check.

Indeed, forgot about that.  Thanks for reminding me.  With R CMD
INSTALL the messages are right next to the help files with the problems.

> >> This *is* an error: nothing in the description allows whitespace
> >> between arguments to \item (nor \section). It seems that only a few
> >> people misread the documentation (sometimes even after their error
> >> is pointed out to them).
> >
> > But there is also nothing that explicitly forbid such whitespace, is
> > it?  I guess this comes down to the question whether "everything is
> > allowed that is not expressively forbidden" or "everything is
> > forbidden unless it is expressively allowed".  Strangely enough,
> > though I am German, I don't tend to subscribe to the latter
> > philosophy.
>
> It really doesn't matter: the author of the convertor (not me)
> decidedly to silently ignore arguments after whitespace so you get an
> incorrect conversion. I also added sentences to the documentation
> that say that explicitly.  But if I see documentation that says
>
> \item{foo}{bar}
>
> I don't see why anyone would be surprised that
>
> \item {foo} {bar}
>
> goes haywire.

Well, I was. :)  And I guess anybody who knows that the TeX parser does
not care about whitespaces between arguments to macros but forgets
that .Rd files are not directly parsed by the TeX parser would have
been surprised too.

Use of whitespace and indentation is pretty much a matter of taste and
personal style to improve readability; and while there are languages
where they matter (Python, makefiles, &c), and some projects (including
R) have style-guides, usually a developer is left with a lot of
flexibility to suit her or his style.  But I guess only Spencer knows
why a whitespace at this place was desirable and/or improved
readability.
 
Cheers,

        Berwin

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Re: Warning: missing text for item ... in \describe?

Prof Brian Ripley
1) Having run tests on CRAN and BioC overnight, the results are quite
depressing.  There are 112 packages on CRAN and a score on BioC with
incorrectly rendered help pages because of spaces after \item{foo}.  In
two cases (fields and MANOR) the text skipped is invalid, so it is not
simply a case of ignoring the whitespace.


2) On the original subject line, I found a different reason.  E.g. I get
the message on distrMod, which has (sqrt-methods.Rd, also
solve-methods.Rd)

\section{Methods}{\describe{
\item{sqrt}{\code{signature(x = "PosSemDefSymmMatrix")}: produces a
symmetric, p.s.d. matrix \eqn{y} such that  \eqn{x = y^2}}
}}

That is rendered incorrectly, and the issue is that \eqn is a one- or
two-argument macro and the trailing } confuses the Rdconv code.  That is
an Rdconv bug which is proving very tricky to fix.  In any case a fix will
only apply to future versions of R, so the packages affected (at least
distr, geepack, geoR, psychometric, robustbase, uroot) need to be altered.

Note that grammatical help files will almost always have punctation at the
end of an item (even a space will do), and all the examples appropriate
punctuation is missing.


On Sat, 6 Dec 2008, Berwin A Turlach wrote:

> G'day Brian,
>
> On Fri, 5 Dec 2008 17:32:58 +0000 (GMT)
> Prof Brian Ripley <[hidden email]> wrote:
>
> [...]
>>> Which platform are we talking here?  I was using linux and "R CMD
>>> check fda", using R 2.8.0, on the command line said:
>>
>> That writes to a file, and writes to a file are buffered.  Try R CMD
>> INSTALL, where they are not.  We do recommend getting a clean install
>> before R CMD check.
>
> Indeed, forgot about that.  Thanks for reminding me.  With R CMD
> INSTALL the messages are right next to the help files with the problems.
>
>>>> This *is* an error: nothing in the description allows whitespace
>>>> between arguments to \item (nor \section). It seems that only a few
>>>> people misread the documentation (sometimes even after their error
>>>> is pointed out to them).
>>>
>>> But there is also nothing that explicitly forbid such whitespace, is
>>> it?  I guess this comes down to the question whether "everything is
>>> allowed that is not expressively forbidden" or "everything is
>>> forbidden unless it is expressively allowed".  Strangely enough,
>>> though I am German, I don't tend to subscribe to the latter
>>> philosophy.
>>
>> It really doesn't matter: the author of the convertor (not me)
>> decidedly to silently ignore arguments after whitespace so you get an
>> incorrect conversion. I also added sentences to the documentation
>> that say that explicitly.  But if I see documentation that says
>>
>> \item{foo}{bar}
>>
>> I don't see why anyone would be surprised that
>>
>> \item {foo} {bar}
>>
>> goes haywire.
>
> Well, I was. :)  And I guess anybody who knows that the TeX parser does
> not care about whitespaces between arguments to macros but forgets
> that .Rd files are not directly parsed by the TeX parser would have
> been surprised too.
>
> Use of whitespace and indentation is pretty much a matter of taste and
> personal style to improve readability; and while there are languages
> where they matter (Python, makefiles, &c), and some projects (including
> R) have style-guides, usually a developer is left with a lot of
> flexibility to suit her or his style.  But I guess only Spencer knows
> why a whitespace at this place was desirable and/or improved
> readability.
>
> Cheers,
>
> Berwin
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: Warning: missing text for item ... in \describe?

Dr. Peter Ruckdeschel
Hi Brian and Berwin,

thanks for finding the reason for all this trouble.
> 1) Having run tests on CRAN and BioC overnight, the results are
> quite depressing.  There are 112 packages on CRAN and a score
> on BioC with incorrectly rendered help pages because of spaces
> after \item{foo}.
> In two cases (fields and MANOR) the text skipped is invalid, so it
> is not simply a case of ignoring the whitespace.
As you already have found out the "depressing" number of 112, could you
please alert the maintainers of these packages --- I would not be surprised
if I were among them ...
> 2) On the original subject line, I found a different reason.  E.g. I
> get the
> message on distrMod, which has (sqrt-methods.Rd, also
> solve-methods.Rd)
>
> \section{Methods}{\describe{
> \item{sqrt}{\code{signature(x = "PosSemDefSymmMatrix")}: produces a
> symmetric, p.s.d. matrix \eqn{y} such that  \eqn{x = y^2}}
> }}

You indicate that the problem could easily be solved by inserting
punctuation.

I would have no problems with this as a binding restriction, and
probably the same
goes for other maintainers.
So could you perhaps add a corresponding recommendation
to the "Writing R extensions" manual?

I have just uploaded a quick patch for the sqrt() and solve() ".Rd"
files of distrMod
inserting a "." at the closing brace of \eqn{} in both cases.

Should be on CRAN  soon...

Best,
Peter

--
Dr. Peter Ruckdeschel, Abteilung Finanzmathematik, F3.17
Fraunhofer ITWM, Fraunhofer Platz 1, 67663 Kaiserslautern
Telefon:  +49 631/31600-4699
Fax    :  +49 631/31600-5699
E-Mail :  [hidden email]



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Re: Warning: missing text for item ... in \describe?

Prof Brian Ripley
On Mon, 8 Dec 2008, Dr. Peter Ruckdeschel wrote:

> Hi Brian and Berwin,
>
> thanks for finding the reason for all this trouble.
>> 1) Having run tests on CRAN and BioC overnight, the results are
>> quite depressing.  There are 112 packages on CRAN and a score
>> on BioC with incorrectly rendered help pages because of spaces
>> after \item{foo}.
>> In two cases (fields and MANOR) the text skipped is invalid, so it
>> is not simply a case of ignoring the whitespace.

> As you already have found out the "depressing" number of 112, could you
> please alert the maintainers of these packages --- I would not be surprised
> if I were among them ...

Well, needing to do so on that scale is one of the depressing things.
However, I am waiting for the CRAN daily checking to catch up, as this
will appear as warnings in the logs there once they are using a current
R-devel (the last results are for Dec 4's R-devel).  The current list is
for CRAN

AIS AMORE BARD BCE BLCOP BSDA BaM Biodem BootCL ElemStatLearn FactoMineR
FitAR GLDEX GSA Geneland HH Hmisc MBESS MCPAN MSBVAR MiscPsycho
NestedCohort PASWR PHYLOGR PTAk R2HTML RArcInfo RBGL RFOC RGraphics RII
RSEIS RobAStBase Rsge SNPassoc SciViews TinnR VDCutil WaveCGH accuracy ada
ade4 agricolae ars assist bayesm bim bipartite bitops calib candisc
cghFLasso coda colorRamps compositions crq cwhmisc distrTEst dprep emu
equivalence fImport fOptions fields fossil gamlss gclus geiger geometry
gllm gnm impute its kin kknn klaR knnTree lgtdl limSolve locpol logilasso
logspline modeest muStat netmodels nplplot orthopolynom paleoTS pamr pbatR
pcalg phangorn playwith polspline psych rankreg rbugs relaimpo rgl rjacobi
rootSolve samr siar space spectralGP survrec tpr tseriesChaos varSelRF
varmixt

and for BioC-devel

ABarray GSEAlm GeneticsBase Harshlight KCsmart LPEadj MANOR MCRestimate
MassSpecWavelet MeasurementError Mfuzz OLIN PLPE RBGL RankProd SAGx SLGI
VanillaICE affyQCReport affylmGUI cghMCR copa ecolitk explorase flowCore
flowViz gcrma genArise impute limmaGUI lumi made4 pamr rama rflowcyt
rtracklayer simpleaffy snapCGH splicegear sscore


>> 2) On the original subject line, I found a different reason.  E.g. I
>> get the
>> message on distrMod, which has (sqrt-methods.Rd, also
>> solve-methods.Rd)
>>
>> \section{Methods}{\describe{
>> \item{sqrt}{\code{signature(x = "PosSemDefSymmMatrix")}: produces a
>> symmetric, p.s.d. matrix \eqn{y} such that  \eqn{x = y^2}}
>> }}
>
> You indicate that the problem could easily be solved by inserting
> punctuation.
>
> I would have no problems with this as a binding restriction, and
> probably the same
> goes for other maintainers.
> So could you perhaps add a corresponding recommendation
> to the "Writing R extensions" manual?

Yes, I am working on some recommendations for R-exts.  Hopefully more of
these problems can be detected and given as warnings now we are aware of
them.

> I have just uploaded a quick patch for the sqrt() and solve() ".Rd"
> files of distrMod
> inserting a "." at the closing brace of \eqn{} in both cases.
>
> Should be on CRAN  soon...
>
> Best,
> Peter
>
> --
> Dr. Peter Ruckdeschel, Abteilung Finanzmathematik, F3.17
> Fraunhofer ITWM, Fraunhofer Platz 1, 67663 Kaiserslautern
> Telefon:  +49 631/31600-4699
> Fax    :  +49 631/31600-5699
> E-Mail :  [hidden email]
>
>
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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