take me off here
On Mon, Sep 23, 2013 at 4:44 PM, Marc Schwartz <marc_schwa...@me.com> 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 no longer required and has been replaced by Text::CSV_PP, which is a Pure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.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.
> >
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
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