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longer required and has been replaced by Text::CSV_PP, which is a Pure Perl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.gra...@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.badde...@uwa.edu.au> and
>>> Rolf Turner
>>> <r.tur...@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.badde...@uwa.edu.au> and
>>> Rolf Turner
>>> <r.tur...@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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