From spencer.graves at prodsyse.com  Thu Sep 19 05:35:15 2013
From: spencer.graves at prodsyse.com (Spencer Graves)
Date: Wed, 18 Sep 2013 20:35:15 -0700
Subject: [Rd] Vignette problem and CRAN policies
In-Reply-To: <5232C11A.7070705@stats.ox.ac.uk>
References: <522D7285.8030205@stats.ox.ac.uk> <522E469C.2030902@stat.wisc.edu>
	<5232BEFA.8090308@prodsyse.com> <5232C11A.7070705@stats.ox.ac.uk>
Message-ID: <523A70F3.4030805@prodsyse.com>

Hello, All:


	  The vignette with the sos package used "upquote.sty", required for R 
Journal when it was published in 2009.  Current CRAN policy disallows 
"upquote.sty", and I've so far not found a way to pass "R CMD check" 
with sos without upquote.sty.


	  I changed sos.Rnw per an email exchange with Prof. Ripley without 
solving the problem; see below.  The key error messages (see the results 
of "R CMD build" below) appear to be "sos.tex:16: LaTeX Error: 
Environment article undefined" and " sos.tex:558: LaTeX Error: 
\begin{document} ended by \end{article}."  When the article worked, it 
had bot \begin{document} and \begin{article}, with matching \end 
statements for both.  I've tried commenting out either without success.


	  The current nonworking code is available on R-Forge via anonymous SVN 
checkout using "svn checkout 
svn://svn.r-forge.r-project.org/svnroot/rsitesearch/".  Any suggestions 
on how to fix this would be greatly appreciated.


        Thanks,
        Spencer


###### COMPLETE RESULTS FROM R CMD check ########


Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

C:\Users\sgraves>cd 2013
C:\Users\sgraves\2013>cd R_pkgs
C:\Users\sgraves\2013\R_pkgs>cd sos
C:\Users\sgraves\2013\R_pkgs\sos>cd pkg
C:\Users\sgraves\2013\R_pkgs\sos\pkg>R CMD build sos
* checking for file 'sos/DESCRIPTION' ... OK
* preparing 'sos':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: brew

Attaching package: 'sos'

The following object is masked from 'package:utils':

      ?

Loading required package: WriteXLS
Perl found.

The following Perl modules were not found on this system:

Text::CSV_XS

If you have more than one Perl installation, be sure the correct one was 
used he
re.

Otherwise, please install the missing modules. See the package INSTALL 
file for
more information.

Loading required package: RODBC
Warning in odbcUpdate(channel, query, mydata, coldata[m, ], test = test,  :
    character data 'Adrian Baddeley <Adrian.Baddeley at uwa.edu.au>  and 
Rolf Turner
<r.turner at auckland.ac.nz>       with substantial contributions of code by
Kasper Klitgaard Berthelsen;    Abdollah Jalilian; Marie-Colette van Liesho
ut;     Ege Rubak;      Dominic Schuhmacher;    and     Rasmus 
Waagepetersen.
Additional contributions        by Q.W. Ang;    S. Azaele;      C. Beale;
R. Bernhardt;   T. Bendtsen;    A. Bevan;       B. Biggerstaff; 
R. Bivan
d;      F. Bonneu;      J. Burgos;      S. Byers;       Y.M. Chang; 
J.B. Che
n;      I. Chernayavsky;        Y.C. Chin;      B. Christensen; 
J.-F. Co
eurjolly;       R. Corria Ainslie;      M. de la Cruz;  P. Dalgaard; 
P.J. Dig
gle;    P. Donnelly;    I. Dryden;      S. Eglen; O. Flores;    N. 
Funwi-Gabga;
          A. Gault;       M. Genton;      J. Gilbey;      J. Goldstick; 
   P. Graba
rnik;   C. Graf;        J. Franklin;    U. Hahn;        A. Hardegen; 
M. Herin
g;      M.B. Hansen;    M. Hazelton;    J. Heikkinen;   K. Hornik; 
R. Ihaka
;       A. Jammalamadaka;       R. John-Chandran;       D. Johnson; 
M. Kuhn;
          J. Laake;       F. Lavancier;   T. Lawrence;    R.A. Lamb; 
   J. Lee;
          G.P. Leser; [... truncated]
Warning in odbcUpdate(channel, query, mydata, coldata[m, ], test = test,  :
    character data 'John Fox [aut, cre], Sanford Weisberg [aut], Douglas 
Bates [ct
b], Steve Ellison [ctb], David Firth [ctb], Michael Friendly [ctb], 
Gregor Gorja
nc [ctb], Spencer Graves [ctb], Richard Heiberger [ctb], Rafael 
Laboissiere [ctb
], Georges Monette [ctb], Henric Nilsson [ctb], Derek Ogle [ctb], Brian 
Ripley [
ctb], Achim Zeileis [ctb], R-Core [ctb]' truncated to 255 bytes in 
column 'Autho
r'
Warning in odbcUpdate(channel, query, mydata, coldata[m, ], test = test,  :
    character data 'John Fox [aut, cre], Liviu Andronic [ctb], Michael 
Ash [ctb],
Milan Bouchet-Valat [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], 
Andy Cha
ng [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi 
Pour [c
tb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], 
Uwe Ligg
es [ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert Muenchen 
[ctb], Dunc
an Murdoch [ctb], Erich Neuwirth [ctb], Dan Putler [ctb], Brian Ripley 
[ctb], Mi
roslav Ristic [ctb], Peter Wolf [ctb]' truncated to 255 bytes in column 
'Author'

Perl found.

The following Perl modules were not found on this system:

Text::CSV_XS

If you have more than one Perl installation, be sure the correct one was 
used he
re.

Otherwise, please install the missing modules. See the package INSTALL 
file for
more information.

Warning in odbcUpdate(channel, query, mydata, coldata[m, ], test = test,  :
    character data 'Adrian Baddeley <Adrian.Baddeley at uwa.edu.au>  and 
Rolf Turner
<r.turner at auckland.ac.nz>       with substantial contributions of code by
Kasper Klitgaard Berthelsen;    Abdollah Jalilian; Marie-Colette van Liesho
ut;     Ege Rubak;      Dominic Schuhmacher;    and     Rasmus 
Waagepetersen.
Additional contributions        by Q.W. Ang;    S. Azaele;      C. Beale;
R. Bernhardt;   T. Bendtsen;    A. Bevan;       B. Biggerstaff; 
R. Bivan
d;      F. Bonneu;      J. Burgos;      S. Byers;       Y.M. Chang; 
J.B. Che
n;      I. Chernayavsky;        Y.C. Chin;      B. Christensen; 
J.-F. Co
eurjolly;       R. Corria Ainslie;      M. de la Cruz;  P. Dalgaard; 
P.J. Dig
gle;    P. Donnelly;    I. Dryden;      S. Eglen; O. Flores;    N. 
Funwi-Gabga;
          A. Gault;       M. Genton;      J. Gilbey;      J. Goldstick; 
   P. Graba
rnik;   C. Graf;        J. Franklin;    U. Hahn;        A. Hardegen; 
M. Herin
g;      M.B. Hansen;    M. Hazelton;    J. Heikkinen;   K. Hornik; 
R. Ihaka
;       A. Jammalamadaka;       R. John-Chandran;       D. Johnson; 
M. Kuhn;
          J. Laake;       F. Lavancier;   T. Lawrence;    R.A. Lamb; 
   J. Lee;
          G.P. Leser; [... truncated]
Warning in odbcUpdate(channel, query, mydata, coldata[m, ], test = test,  :
    character data 'John Fox [aut, cre], Sanford Weisberg [aut], Douglas 
Bates [ct
b], Steve Ellison [ctb], David Firth [ctb], Michael Friendly [ctb], 
Gregor Gorja
nc [ctb], Spencer Graves [ctb], Richard Heiberger [ctb], Rafael 
Laboissiere [ctb
], Georges Monette [ctb], Henric Nilsson [ctb], Derek Ogle [ctb], Brian 
Ripley [
ctb], Achim Zeileis [ctb], R-Core [ctb]' truncated to 255 bytes in 
column 'Autho
r'
Warning in odbcUpdate(channel, query, mydata, coldata[m, ], test = test,  :
    character data 'John Fox [aut, cre], Liviu Andronic [ctb], Michael 
Ash [ctb],
Milan Bouchet-Valat [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], 
Andy Cha
ng [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi 
Pour [c
tb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], 
Uwe Ligg
es [ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert Muenchen 
[ctb], Dunc
an Murdoch [ctb], Erich Neuwirth [ctb], Dan Putler [ctb], Brian Ripley 
[ctb], Mi
roslav Ristic [ctb], Peter Wolf [ctb]' truncated to 255 bytes in column 
'Author'

Warning: running command 
'"C:\PROGRA~2\MIKTEX~1.9\miktex\bin\texi2dvi.exe" --qui
et --pdf "sos.tex"  -I 
"C:/Users/sgraves/pgms/R/R-3.0.1/share/texmf/tex/latex" -
I "C:/Users/sgraves/pgms/R/R-3.0.1/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'sos.tex' failed

LaTeX errors:
sos.tex:16: LaTeX Error: Environment article undefined.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help
Your command was ignored.
sos.tex:558: LaTeX Error: \begin{document} ended by \end{article}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help
Your command was ignored.
Execution halted


On 9/13/2013 12:39 AM, Prof Brian Ripley wrote:
> On 13/09/2013 08:30, Spencer Graves wrote:
>> Dear Prof. Ripley:
>>
>>
>>        What do you recommend I do with the vignette that comes with that
>> package?
>>
>>
>>        That vignette is a copy of the article published in the R Journal
>> vol. 1/2, Dec. 2009.  That publication seemed to require me to use
>> RJournal.sty.  When I removed RJournal.sty from the vignette
>> subdirectory, "R CMD build" failed.  I have no idea what you want me to
>> do to fix this problem.  Further assistance would be appreciated.
>
> Don't spam all the other addressees!
>
> The issue is using RJournal.sty in a vignette with ae fonts.  I am
> guessing that
>
> \usepackage[noae]{Sweave}
>
> might work: otherwise you need to remove the reference to upquote.sty
> in RJournal.sty.
>
>
>>
>>
>>        Thanks,
>>        Spencer Graves
>>
>>
>> p.s.  I understand reasonably well R and the *.Rd documentation
>> standard, thanks in part to your book on "Modern Applied Statistics with
>> S" and the documentation that ships with R. However, this is the only
>> vignette I've written, and I have not used LaTeX much for anything else
>> apart from Ramsay, Hooker and Graves (2009) Functional Data Analysis
>> with R and Matlab (Springer).
>>
>>
>> On 9/9/2013 3:07 PM, Brian S Yandell wrote:
>>> Brian,
>>> I am making changes, downloading new version of Sweave.sty and
>>> upquote.sty. However, it is not clear to me how to properly credit
>>> Fritz Leisch and others for Sweave. Do you mean in the sweave document
>>> (*.Rnw)? Or is there a place in the package assembly for this? (it
>>> seems not in DESCRIPTION or CITATION, but where else). I could not
>>> find anything about this in "Writing R Extensions".
>>> Thanks for any guidance,
>>> Brian
>>> On 9/9/13 12:02 AM, Prof Brian Ripley wrote:
>>>> Earlier versions of Sweave.sty and Rd.sty only work with the
>>>> upquote.sty in earlier versions of R and not that currently being
>>>> distributed in TeX distributions. R >= 3.0.2 will not contain any
>>>> version of upquote.sty.
>>>>
>>>> In particular, they do not work with the 'ae' fonts which are the
>>>> default for Sweave vignettes.   Packages
>>>>
>>>> boolfun calibrate popReconstruct qtlnet
>>>>
>>>> have copies in vignettes and now fail.
>>>>
>>>> Please remove them. Note too that you did not comply with the CRAN
>>>> policies on giving credit by including them in your package but not
>>>> crediting their authors: do check very carefully that there are no
>>>> other missing credits.
>>>>
>>>> Package PSM has vignettes which include upquote.sty.
>>>>
>>>> Packages makeR and sos include RJournal.sty which includes
>>>> upquote.sty: same problem.
>>>>
>>>> Please update your package as soon as possible and definitely before
>>>> the release of 3.0.2 on Sept 25.
>>>>
>>>
>>
>>
>
>


-- 
Spencer Graves, PE, PhD
President and Chief Technology Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San Jos?, CA 95126
ph:  408-655-4567
web:  www.structuremonitoring.com



[Rd] Vignette problem and CRAN policies
Spencer Graves