Vignette problem and CRAN policies

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=3.0 of WriteXLS (current is 3.2.1), that is no longer required and has been replaced by Text::CSV_PP, which is a Pure Perl module and is included in the WriteXLS CRAN package to reduce the dependencies on nonstandard external Perl modules.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