From spencer.graves at prodsyse.com  Tue Sep 24 00:04:02 2013
From: spencer.graves at prodsyse.com (Spencer Graves)
Date: Mon, 23 Sep 2013 15:04:02 -0700
Subject: [Rd] Vignette problem and CRAN policies
In-Reply-To: <A47334DB-484B-42A3-9094-B363CDFF55F2@me.com>
References: <522D7285.8030205@stats.ox.ac.uk> <522E469C.2030902@stat.wisc.edu>
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	<523AA11E.2050805@stats.ox.ac.uk> <5240B27A.10207@prodsyse.com>
	<A47334DB-484B-42A3-9094-B363CDFF55F2@me.com>
Message-ID: <5240BAD2.8030607@prodsyse.com>

Hi, Marc:


       That's great.  I just did update.packages, then tried 
"writeFindFn2xls", and it worked!  "writeFindFn2xls" is programmed to 
try WriteXLS.  Previously, it failed on my 64-bit installation of R, 
because of that very problem.


       I was planning to modify "writeFindFn2xls" to try 
write.xlsx{xlsx}.  I think I'll not bother with that now.


       Thanks again.


       Spencer


On 9/23/2013 2:44 PM, Marc Schwartz wrote:
> 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=3.0 of WriteXLS (current is 3.2.1), that is no longer required and has been replaced by Text::CSV_PP, which is a Pure Perl module and is included in the WriteXLS CRAN package to reduce the dependencies on nonstandard external Perl modules.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.
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>


-- 
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