From spencer.graves at prodsyse.com  Mon Sep 23 23:28:26 2013
From: spencer.graves at prodsyse.com (Spencer Graves)
Date: Mon, 23 Sep 2013 14:28:26 -0700
Subject: [Rd] Vignette problem and CRAN policies
In-Reply-To: <523AA11E.2050805@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>
	<523A70F3.4030805@prodsyse.com> <523AA11E.2050805@stats.ox.ac.uk>
Message-ID: <5240B27A.10207@prodsyse.com>

Hello, All:


       Professor Ripley is correct as usual:  I misunderstood his 
original statement of the problem.


       He gave two possible solutions.  I could not make the first 
solution work, and I didn't try the second until someone else on this 
list explained it in slightly more detail.


       The correction passed R CMD check on my local computer.  It has 
been "building" on R-Forge since 2013-09-20 19:19:14+02.  I hope this 
completes soon enough for me to meet Ripley's Sept. 25 deadline for this 
correction to "sos".


       Thanks again to Prof. Ripley and everyone else who took the time 
to read my post.


       Spencer


On 9/19/2013 12:00 AM, Prof Brian Ripley wrote:
> This is nothing to do with CRAN policies (nor R).
>
> The issue is that the current upquote.sty does not play with 'ae' 
> fonts as used by default by Sweave.  The change is in TeX.
>
> And that was what Spencer Graves was informed.
>
>
> On 19/09/2013 04:35, Spencer Graves wrote:
>> 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.



[Rd] Vignette problem and CRAN policies
Spencer Graves