From josh.m.ulrich at gmail.com  Tue Sep 24 00:01:15 2013
From: josh.m.ulrich at gmail.com (Joshua Ulrich)
Date: Mon, 23 Sep 2013 17:01:15 -0500
Subject: [Rd] Vignette problem and CRAN policies
In-Reply-To: <CAJVuBM=-NiphVa17Q9BYe5Ao_1gdKq1+v+LcMOhDrPKQiTgsfQ@mail.gmail.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>
	<A47334DB-484B-42A3-9094-B363CDFF55F2@me.com>
	<CAJVuBM=-NiphVa17Q9BYe5Ao_1gdKq1+v+LcMOhDrPKQiTgsfQ@mail.gmail.com>
Message-ID: <CAPPM_gR_sQyrQJLZ=86ORF2oNUdGtwX=y78Lam+5vB3F-v1bew@mail.gmail.com>

As Berend Hasselman already told you, "Then surf to the address given
at the end of each posting; go to the bottom of that page and follow
the instructions for unsubscribing."

Here's the link, so you don't have to scroll to the bottom of this
message: https://stat.ethz.ch/mailman/listinfo/r-devel
--
Joshua Ulrich  |  about.me/joshuaulrich
FOSS Trading  |  www.fosstrading.com


On Mon, Sep 23, 2013 at 4:57 PM, Eric Malitz <eric.malitz at gmail.com> wrote:
> take me off here
>
>
> On Mon, Sep 23, 2013 at 4:44 PM, Marc Schwartz <marc_schwartz at 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 no longer required and has been replaced by Text::CSV_PP, which is a Pure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.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
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] Vignette problem and CRAN policies
Joshua Ulrich