From marc_schwartz at me.com  Mon Sep 23 23:44:15 2013
From: marc_schwartz at me.com (Marc Schwartz)
Date: Mon, 23 Sep 2013 16:44:15 -0500
Subject: [Rd] Vignette problem and CRAN policies
In-Reply-To: <5240B27A.10207@prodsyse.com>
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>
	<5240B27A.10207@prodsyse.com>
Message-ID: <A47334DB-484B-42A3-9094-B363CDFF55F2@me.com>

Spencer,

FYI. I just noted in your post below the error message from WriteXLS regarding TEXT::CSV_XS missing.

Please note that in version >=3.0 of WriteXLS (current is 3.2.1), that is no longer required and has been replaced by Text::CSV_PP, which is a Pure Perl module and is included in the WriteXLS CRAN package to reduce the dependencies on nonstandard external Perl modules.

Regards,

Marc Schwartz


On Sep 23, 2013, at 4:28 PM, Spencer Graves <spencer.graves at prodsyse.com> wrote:

> 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.
> 
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[Rd] Vignette problem and CRAN policies
Marc Schwartz