R CMD check and error in an \Sexpr in an Rd file
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R CMD check and error in an \Sexpr in an Rd file
 
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Hi,
another Rd related issue I encountered is that if an error occurs in an \Sexpr in an Rd file, then on get the following error: * checking for portable compilation flags in Makevars ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking examples ... ERROR Error in paste(before, x, after, sep = "") : object 'exfile' not found Execution halted To reproduce, put a call like this in an Rd section: \Sexpr[results=verbatim, stage=render]{x <- 1; stop("sexpr error")} The strange thing is that it occurs at the example checking step. Not sure why it does not break before. Thank you. Renaud PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu (64-bit) -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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On 28/10/2011 10:49 AM, Renaud Gaujoux wrote:
> Hi, > > another Rd related issue I encountered is that if an error occurs in an > \Sexpr in an Rd file, then on get the following error: > > * checking for portable compilation flags in Makevars ... OK > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK > * checking examples ... ERROR > Error in paste(before, x, after, sep = "") : object 'exfile' not found > Execution halted > > To reproduce, put a call like this in an Rd section: > > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} > > The strange thing is that it occurs at the example checking step. > Not sure why it does not break before. > > Thank you. > > Renaud > > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu (64-bit) > I would update to 2.13.2 patched, or the release candidate of 2.14.0. Duncan Murdoch ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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On 28/10/2011 10:53 AM, Duncan Murdoch wrote:
> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: > > Hi, > > > > another Rd related issue I encountered is that if an error occurs in an > > \Sexpr in an Rd file, then on get the following error: > > > > * checking for portable compilation flags in Makevars ... OK > > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK > > * checking examples ... ERROR > > Error in paste(before, x, after, sep = "") : object 'exfile' not found > > Execution halted > > > > To reproduce, put a call like this in an Rd section: > > > > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} > > > > The strange thing is that it occurs at the example checking step. > > Not sure why it does not break before. > > > > Thank you. > > > > Renaud > > > > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu (64-bit) > > > > I would update to 2.13.2 patched, or the release candidate of 2.14.0. Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. 2.14.0 is what you should get. Duncan Murdoch ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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Thank you Duncan.
I tried with: * using R version 2.14.0 RC (2011-10-24 r57417) * using platform: x86_64-unknown-linux-gnu (64-bit) But I still get the errors for verbatim multiline and the strange error if an error occurs in \Sexpr. Is your patch included in this version? I will try now with R-rc_2011-10-27_r57452.tar.gz. Renaud On 28/10/2011 17:25, Duncan Murdoch wrote: > On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >> > Hi, >> > >> > another Rd related issue I encountered is that if an error occurs >> in an >> > \Sexpr in an Rd file, then on get the following error: >> > >> > * checking for portable compilation flags in Makevars ... OK >> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK >> > * checking examples ... ERROR >> > Error in paste(before, x, after, sep = "") : object 'exfile' not >> found >> > Execution halted >> > >> > To reproduce, put a call like this in an Rd section: >> > >> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >> > >> > The strange thing is that it occurs at the example checking step. >> > Not sure why it does not break before. >> > >> > Thank you. >> > >> > Renaud >> > >> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >> (64-bit) >> > >> >> I would update to 2.13.2 patched, or the release candidate of 2.14.0. > > Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. > 2.14.0 is what you should get. > > Duncan Murdoch ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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On 31.10.2011 13:13, Renaud Gaujoux wrote: > Thank you Duncan. > > I tried with: > * using R version 2.14.0 RC (2011-10-24 r57417) > * using platform: x86_64-unknown-linux-gnu (64-bit) > > But I still get the errors for verbatim multiline and the strange error > if an error occurs in \Sexpr. > Is your patch included in this version? I will try now with > R-rc_2011-10-27_r57452.tar.gz. Try R-2.14.0, it is already released. Or R-devel. Best, Uwe Ligges > > Renaud > > On 28/10/2011 17:25, Duncan Murdoch wrote: >> On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >>> > Hi, >>> > >>> > another Rd related issue I encountered is that if an error occurs >>> in an >>> > \Sexpr in an Rd file, then on get the following error: >>> > >>> > * checking for portable compilation flags in Makevars ... OK >>> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK >>> > * checking examples ... ERROR >>> > Error in paste(before, x, after, sep = "") : object 'exfile' not found >>> > Execution halted >>> > >>> > To reproduce, put a call like this in an Rd section: >>> > >>> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >>> > >>> > The strange thing is that it occurs at the example checking step. >>> > Not sure why it does not break before. >>> > >>> > Thank you. >>> > >>> > Renaud >>> > >>> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >>> (64-bit) >>> > >>> >>> I would update to 2.13.2 patched, or the release candidate of 2.14.0. >> >> Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. 2.14.0 >> is what you should get. >> >> Duncan Murdoch > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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I do not see it on main CRAN home page.
Do you mean http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz ? On 31/10/2011 14:19, Uwe Ligges wrote: > > > On 31.10.2011 13:13, Renaud Gaujoux wrote: >> Thank you Duncan. >> >> I tried with: >> * using R version 2.14.0 RC (2011-10-24 r57417) >> * using platform: x86_64-unknown-linux-gnu (64-bit) >> >> But I still get the errors for verbatim multiline and the strange error >> if an error occurs in \Sexpr. >> Is your patch included in this version? I will try now with >> R-rc_2011-10-27_r57452.tar.gz. > > Try R-2.14.0, it is already released. Or R-devel. > > Best, > Uwe Ligges > > >> >> Renaud >> >> On 28/10/2011 17:25, Duncan Murdoch wrote: >>> On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >>>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >>>> > Hi, >>>> > >>>> > another Rd related issue I encountered is that if an error occurs >>>> in an >>>> > \Sexpr in an Rd file, then on get the following error: >>>> > >>>> > * checking for portable compilation flags in Makevars ... OK >>>> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) >>>> ... OK >>>> > * checking examples ... ERROR >>>> > Error in paste(before, x, after, sep = "") : object 'exfile' not >>>> found >>>> > Execution halted >>>> > >>>> > To reproduce, put a call like this in an Rd section: >>>> > >>>> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >>>> > >>>> > The strange thing is that it occurs at the example checking step. >>>> > Not sure why it does not break before. >>>> > >>>> > Thank you. >>>> > >>>> > Renaud >>>> > >>>> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >>>> (64-bit) >>>> > >>>> >>>> I would update to 2.13.2 patched, or the release candidate of 2.14.0. >>> >>> Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. 2.14.0 >>> is what you should get. >>> >>> Duncan Murdoch >> >> ______________________________________________ >> [hidden email] mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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On 31.10.2011 13:23, Renaud Gaujoux wrote: > I do not see it on main CRAN home page. > Do you mean http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz ? Home page is not yet updated, see today's announcement by Peter Dalgaard who said it is at: http://cran.r-project.org/src/base/R-2/R-2.14.0.tar.gz Uwe Ligges > On 31/10/2011 14:19, Uwe Ligges wrote: >> >> >> On 31.10.2011 13:13, Renaud Gaujoux wrote: >>> Thank you Duncan. >>> >>> I tried with: >>> * using R version 2.14.0 RC (2011-10-24 r57417) >>> * using platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> But I still get the errors for verbatim multiline and the strange error >>> if an error occurs in \Sexpr. >>> Is your patch included in this version? I will try now with >>> R-rc_2011-10-27_r57452.tar.gz. >> >> Try R-2.14.0, it is already released. Or R-devel. >> >> Best, >> Uwe Ligges >> >> >>> >>> Renaud >>> >>> On 28/10/2011 17:25, Duncan Murdoch wrote: >>>> On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >>>>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >>>>> > Hi, >>>>> > >>>>> > another Rd related issue I encountered is that if an error occurs >>>>> in an >>>>> > \Sexpr in an Rd file, then on get the following error: >>>>> > >>>>> > * checking for portable compilation flags in Makevars ... OK >>>>> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) >>>>> ... OK >>>>> > * checking examples ... ERROR >>>>> > Error in paste(before, x, after, sep = "") : object 'exfile' not >>>>> found >>>>> > Execution halted >>>>> > >>>>> > To reproduce, put a call like this in an Rd section: >>>>> > >>>>> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >>>>> > >>>>> > The strange thing is that it occurs at the example checking step. >>>>> > Not sure why it does not break before. >>>>> > >>>>> > Thank you. >>>>> > >>>>> > Renaud >>>>> > >>>>> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >>>>> (64-bit) >>>>> > >>>>> >>>>> I would update to 2.13.2 patched, or the release candidate of 2.14.0. >>>> >>>> Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. 2.14.0 >>>> is what you should get. >>>> >>>> Duncan Murdoch >>> >>> ______________________________________________ >>> [hidden email] mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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In reply to this post by Renaud Gaujoux
On Mon, 31 Oct 2011, Renaud Gaujoux wrote:
> I do not see it on main CRAN home page. No, but see the announcement on R-announce this morning: https://stat.ethz.ch/pipermail/r-help/2011-October/294203.html Things which need human intervention can take some hours: the CRAN front page and binary distributions are two of those. > Do you mean http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz ? > > On 31/10/2011 14:19, Uwe Ligges wrote: >> >> >> On 31.10.2011 13:13, Renaud Gaujoux wrote: >>> Thank you Duncan. >>> >>> I tried with: >>> * using R version 2.14.0 RC (2011-10-24 r57417) >>> * using platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> But I still get the errors for verbatim multiline and the strange error >>> if an error occurs in \Sexpr. >>> Is your patch included in this version? I will try now with >>> R-rc_2011-10-27_r57452.tar.gz. >> >> Try R-2.14.0, it is already released. Or R-devel. >> >> Best, >> Uwe Ligges >> >> >>> >>> Renaud >>> >>> On 28/10/2011 17:25, Duncan Murdoch wrote: >>>> On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >>>>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >>>>> > Hi, >>>>> > >>>>> > another Rd related issue I encountered is that if an error occurs >>>>> in an >>>>> > \Sexpr in an Rd file, then on get the following error: >>>>> > >>>>> > * checking for portable compilation flags in Makevars ... OK >>>>> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK >>>>> > * checking examples ... ERROR >>>>> > Error in paste(before, x, after, sep = "") : object 'exfile' not found >>>>> > Execution halted >>>>> > >>>>> > To reproduce, put a call like this in an Rd section: >>>>> > >>>>> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >>>>> > >>>>> > The strange thing is that it occurs at the example checking step. >>>>> > Not sure why it does not break before. >>>>> > >>>>> > Thank you. >>>>> > >>>>> > Renaud >>>>> > >>>>> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >>>>> (64-bit) >>>>> > >>>>> >>>>> I would update to 2.13.2 patched, or the release candidate of 2.14.0. >>>> >>>> Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. 2.14.0 >>>> is what you should get. >>>> >>>> Duncan Murdoch >>> >>> ______________________________________________ >>> [hidden email] mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Brian D. Ripley, [hidden email] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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In reply to this post by Renaud Gaujoux
On Oct 31, 2011, at 13:23 , Renaud Gaujoux wrote: > I do not see it on main CRAN home page. > Do you mean http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz ? Links need to be updated. Have a look in http://cran.r-project.org/src/base/R-2 > > On 31/10/2011 14:19, Uwe Ligges wrote: >> >> >> On 31.10.2011 13:13, Renaud Gaujoux wrote: >>> Thank you Duncan. >>> >>> I tried with: >>> * using R version 2.14.0 RC (2011-10-24 r57417) >>> * using platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> But I still get the errors for verbatim multiline and the strange error >>> if an error occurs in \Sexpr. >>> Is your patch included in this version? I will try now with >>> R-rc_2011-10-27_r57452.tar.gz. >> >> Try R-2.14.0, it is already released. Or R-devel. >> >> Best, >> Uwe Ligges >> >> >>> >>> Renaud >>> >>> On 28/10/2011 17:25, Duncan Murdoch wrote: >>>> On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >>>>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >>>>> > Hi, >>>>> > >>>>> > another Rd related issue I encountered is that if an error occurs >>>>> in an >>>>> > \Sexpr in an Rd file, then on get the following error: >>>>> > >>>>> > * checking for portable compilation flags in Makevars ... OK >>>>> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK >>>>> > * checking examples ... ERROR >>>>> > Error in paste(before, x, after, sep = "") : object 'exfile' not found >>>>> > Execution halted >>>>> > >>>>> > To reproduce, put a call like this in an Rd section: >>>>> > >>>>> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >>>>> > >>>>> > The strange thing is that it occurs at the example checking step. >>>>> > Not sure why it does not break before. >>>>> > >>>>> > Thank you. >>>>> > >>>>> > Renaud >>>>> > >>>>> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >>>>> (64-bit) >>>>> > >>>>> >>>>> I would update to 2.13.2 patched, or the release candidate of 2.14.0. >>>> >>>> Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. 2.14.0 >>>> is what you should get. >>>> >>>> Duncan Murdoch >>> >>> ______________________________________________ >>> [hidden email] mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: [hidden email] Priv: [hidden email] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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In reply to this post by Prof Brian Ripley
Thank you very much Duncan, Uwe and Peter.
Sorry if I missed the announcement, I follow more r-devel than r-help, which I find a bit hard to quickly read. Will try now on the 2.14.0. Renaud On 31/10/2011 14:28, Prof Brian Ripley wrote: > On Mon, 31 Oct 2011, Renaud Gaujoux wrote: > >> I do not see it on main CRAN home page. > > No, but see the announcement on R-announce this morning: > https://stat.ethz.ch/pipermail/r-help/2011-October/294203.html > > Things which need human intervention can take some hours: the CRAN > front page and binary distributions are two of those. > >> Do you mean >> http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz ? >> >> On 31/10/2011 14:19, Uwe Ligges wrote: >>> >>> >>> On 31.10.2011 13:13, Renaud Gaujoux wrote: >>>> Thank you Duncan. >>>> >>>> I tried with: >>>> * using R version 2.14.0 RC (2011-10-24 r57417) >>>> * using platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> But I still get the errors for verbatim multiline and the strange >>>> error >>>> if an error occurs in \Sexpr. >>>> Is your patch included in this version? I will try now with >>>> R-rc_2011-10-27_r57452.tar.gz. >>> >>> Try R-2.14.0, it is already released. Or R-devel. >>> >>> Best, >>> Uwe Ligges >>> >>> >>>> >>>> Renaud >>>> >>>> On 28/10/2011 17:25, Duncan Murdoch wrote: >>>>> On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >>>>>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >>>>>> > Hi, >>>>>> > >>>>>> > another Rd related issue I encountered is that if an error occurs >>>>>> in an >>>>>> > \Sexpr in an Rd file, then on get the following error: >>>>>> > >>>>>> > * checking for portable compilation flags in Makevars ... OK >>>>>> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) >>>>>> ... OK >>>>>> > * checking examples ... ERROR >>>>>> > Error in paste(before, x, after, sep = "") : object 'exfile' >>>>>> not found >>>>>> > Execution halted >>>>>> > >>>>>> > To reproduce, put a call like this in an Rd section: >>>>>> > >>>>>> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >>>>>> > >>>>>> > The strange thing is that it occurs at the example checking step. >>>>>> > Not sure why it does not break before. >>>>>> > >>>>>> > Thank you. >>>>>> > >>>>>> > Renaud >>>>>> > >>>>>> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >>>>>> (64-bit) >>>>>> > >>>>>> >>>>>> I would update to 2.13.2 patched, or the release candidate of >>>>>> 2.14.0. >>>>> >>>>> Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. >>>>> 2.14.0 >>>>> is what you should get. >>>>> >>>>> Duncan Murdoch >>>> >>>> ______________________________________________ >>>> [hidden email] mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> ______________________________________________ >> [hidden email] mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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> Thank you very much Duncan, Uwe and Peter. Sorry if I > missed the announcement, I follow more r-devel than > r-help, which I find a bit hard to quickly read. But please --- this concerns every one on R-devel --- if you do not subscribe to R-help, then do subscribe to R-announce -- that one has about one posting *per month* and is really only for important announcements (and basically reserved for R-core to post). See a list of *all* R-announce postings of 2011 : https://stat.ethz.ch/pipermail/r-announce/2011/date.html with the 2.14.0 announcement at the end. Martin Maechler, ETH Zurich > Will try now on the 2.14.0. > Renaud > On 31/10/2011 14:28, Prof Brian Ripley wrote: >> On Mon, 31 Oct 2011, Renaud Gaujoux wrote: >> >>> I do not see it on main CRAN home page. >> >> No, but see the announcement on R-announce this morning: >> https://stat.ethz.ch/pipermail/r-help/2011-October/294203.html >> >> Things which need human intervention can take some hours: >> the CRAN front page and binary distributions are two of >> those. >> >>> Do you mean >>> http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz >>> ? >>> >>> On 31/10/2011 14:19, Uwe Ligges wrote: >>>> >>>> >>>> On 31.10.2011 13:13, Renaud Gaujoux wrote: >>>>> Thank you Duncan. >>>>> >>>>> I tried with: * using R version 2.14.0 RC (2011-10-24 >>>>> r57417) * using platform: x86_64-unknown-linux-gnu >>>>> (64-bit) >>>>> >>>>> But I still get the errors for verbatim multiline and >>>>> the strange error if an error occurs in \Sexpr. Is >>>>> your patch included in this version? I will try now >>>>> with R-rc_2011-10-27_r57452.tar.gz. >>>> >>>> Try R-2.14.0, it is already released. Or R-devel. >>>> >>>> Best, Uwe Ligges >>>> >>>> >>>>> >>>> Renaud >>>> >>>> On 28/10/2011 17:25, Duncan Murdoch wrote: >>>>> On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >>>>>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >>>>>> > Hi, >>>>>> > >>>>>> > another Rd related issue I encountered is that if an error occurs >>>>>> in an >>>>>> > \Sexpr in an Rd file, then on get the following error: >>>>>> > >>>>>> > * checking for portable compilation flags in Makevars ... OK >>>>>> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) >>>>>> ... OK >>>>>> > * checking examples ... ERROR >>>>>> > Error in paste(before, x, after, sep = "") : object 'exfile' >>>>>> not found >>>>>> > Execution halted >>>>>> > >>>>>> > To reproduce, put a call like this in an Rd section: >>>>>> > >>>>>> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >>>>>> > >>>>>> > The strange thing is that it occurs at the example checking step. >>>>>> > Not sure why it does not break before. >>>>>> > >>>>>> > Thank you. >>>>>> > >>>>>> > Renaud >>>>>> > >>>>>> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >>>>>> (64-bit) >>>>>> > >>>>>> >>>>>> I would update to 2.13.2 patched, or the release candidate of >>>>>> 2.14.0. >>>>> >>>>> Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. >>>>> 2.14.0 >>>>> is what you should get. >>>>> >>>>> Duncan Murdoch >>>> >>>> ______________________________________________ >>>> [hidden email] mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> ______________________________________________ >> [hidden email] mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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Martin,
I am pretty sure (but I will probably be proven wrong) that when r-announce was created it was stated that every email got sent to both r-help and r-devel, and I see I have received emails from r-announce in the past despite only being subscribed to r-devel and not r-help. For example, I can find the announcement of R-2.13.0 (posted by P Dalgaard) (and many earlier versions), but not R-2.13.1. While I am pretty sure I have only subscribed to r-help for a brief period many years ago, I did switch my r-devel subscription from one email address to another. I infer from your email that r-announce emails are no longer sent to r-devel subscribers (which is consistent with the text on https://stat.ethz.ch/mailman/listinfo/r-announce ). Kasper On Mon, Oct 31, 2011 at 11:42 AM, Martin Maechler <[hidden email]> wrote: > >   > Thank you very much Duncan, Uwe and Peter.  Sorry if I >   > missed the announcement, I follow more r-devel than >   > r-help, which I find a bit hard to quickly read. > > But please --- this concerns every one on R-devel --- > if you do not subscribe to R-help, > then do subscribe to R-announce -- that one has about > one posting *per month* and is really only for important > announcements (and basically reserved for R-core to post). > > See a list of *all*  R-announce postings of  2011 : > >  https://stat.ethz.ch/pipermail/r-announce/2011/date.html > > with the 2.14.0 announcement at the end. > > Martin Maechler, ETH Zurich > > >   > Will try now on the 2.14.0. > >   > Renaud > >   > On 31/10/2011 14:28, Prof Brian Ripley wrote: >   >> On Mon, 31 Oct 2011, Renaud Gaujoux wrote: >   >> >   >>> I do not see it on main CRAN home page. >   >> >   >> No, but see the announcement on R-announce this morning: >   >> https://stat.ethz.ch/pipermail/r-help/2011-October/294203.html >   >> >   >> Things which need human intervention can take some hours: >   >> the CRAN front page and binary distributions are two of >   >> those. >   >> >   >>> Do you mean >   >>> http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz >   >>> ? >   >>> >   >>> On 31/10/2011 14:19, Uwe Ligges wrote: >   >>>> >   >>>> >   >>>> On 31.10.2011 13:13, Renaud Gaujoux wrote: >   >>>>> Thank you Duncan. >   >>>>> >   >>>>> I tried with: * using R version 2.14.0 RC (2011-10-24 >   >>>>> r57417) * using platform: x86_64-unknown-linux-gnu >   >>>>> (64-bit) >   >>>>> >   >>>>> But I still get the errors for verbatim multiline and >   >>>>> the strange error if an error occurs in \Sexpr.  Is >   >>>>> your patch included in this version? I will try now >   >>>>> with R-rc_2011-10-27_r57452.tar.gz. >   >>>> >   >>>> Try R-2.14.0, it is already released. Or R-devel. >   >>>> >   >>>> Best, Uwe Ligges >   >>>> >   >>>> >   >>>>> >>>>> Renaud >>>>> >>>>> On 28/10/2011 17:25, Duncan Murdoch wrote: >>>>>> On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >>>>>>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >>>>>>> > Hi, >>>>>>> > >>>>>>> > another Rd related issue I encountered is that if an error occurs >>>>>>> in an >>>>>>> > \Sexpr in an Rd file, then on get the following error: >>>>>>> > >>>>>>> > * checking for portable compilation flags in Makevars ... OK >>>>>>> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) >>>>>>> ... OK >>>>>>> > * checking examples ... ERROR >>>>>>> > Error in paste(before, x, after, sep = "") : object 'exfile' >>>>>>> not found >>>>>>> > Execution halted >>>>>>> > >>>>>>> > To reproduce, put a call like this in an Rd section: >>>>>>> > >>>>>>> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >>>>>>> > >>>>>>> > The strange thing is that it occurs at the example checking step. >>>>>>> > Not sure why it does not break before. >>>>>>> > >>>>>>> > Thank you. >>>>>>> > >>>>>>> > Renaud >>>>>>> > >>>>>>> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >>>>>>> (64-bit) >>>>>>> > >>>>>>> >>>>>>> I would update to 2.13.2 patched, or the release candidate of >>>>>>> 2.14.0. >>>>>> >>>>>> Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. >>>>>> 2.14.0 >>>>>> is what you should get. >>>>>> >>>>>> Duncan Murdoch >>>>> >>>>> ______________________________________________ >>>>> [hidden email] mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >>> ______________________________________________ >>> [hidden email] mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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Hi Kasper,
On Mon, Oct 31, 2011 at 16:55, Kasper Daniel Hansen <[hidden email]> wrote: > > Martin, > > I am pretty sure (but I will probably be proven wrong) that when > r-announce was created it was stated that every email got sent to both > r-help and r-devel, Hmm, I don't believe you. To the contrary, I'd even bet a bit on that.  Always to R-help, but not to R-devel,... If you have real proof please "present" it.. (but this *is* getting off-topic... we should probably continue off-R-devel ..) Martin > > and I see I have received emails from r-announce > in the past despite only being subscribed to r-devel and not r-help. > For example, I can find the announcement of R-2.13.0 (posted by P > Dalgaard) (and many earlier versions), but not R-2.13.1.  While I am > pretty sure I have only subscribed to r-help for a brief period many > years ago, I did switch my r-devel subscription from one email address > to another. > > I infer from your email that r-announce emails are no longer sent to > r-devel subscribers (which is consistent with the text on >  https://stat.ethz.ch/mailman/listinfo/r-announce > ). > > Kasper > > > On Mon, Oct 31, 2011 at 11:42 AM, Martin Maechler > <[hidden email]> wrote: > > > >   > Thank you very much Duncan, Uwe and Peter.  Sorry if I > >   > missed the announcement, I follow more r-devel than > >   > r-help, which I find a bit hard to quickly read. > > > > But please --- this concerns every one on R-devel --- > > if you do not subscribe to R-help, > > then do subscribe to R-announce -- that one has about > > one posting *per month* and is really only for important > > announcements (and basically reserved for R-core to post). > > > > See a list of *all*  R-announce postings of  2011 : > > > >  https://stat.ethz.ch/pipermail/r-announce/2011/date.html > > > > with the 2.14.0 announcement at the end. > > > > Martin Maechler, ETH Zurich > > > > > >   > Will try now on the 2.14.0. > > > >   > Renaud > > > >   > On 31/10/2011 14:28, Prof Brian Ripley wrote: > >   >> On Mon, 31 Oct 2011, Renaud Gaujoux wrote: > >   >> > >   >>> I do not see it on main CRAN home page. > >   >> > >   >> No, but see the announcement on R-announce this morning: > >   >> https://stat.ethz.ch/pipermail/r-help/2011-October/294203.html > >   >> > >   >> Things which need human intervention can take some hours: > >   >> the CRAN front page and binary distributions are two of > >   >> those. > >   >> > >   >>> Do you mean > >   >>> http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz > >   >>> ? > >   >>> > >   >>> On 31/10/2011 14:19, Uwe Ligges wrote: > >   >>>> > >   >>>> > >   >>>> On 31.10.2011 13:13, Renaud Gaujoux wrote: > >   >>>>> Thank you Duncan. > >   >>>>> > >   >>>>> I tried with: * using R version 2.14.0 RC (2011-10-24 > >   >>>>> r57417) * using platform: x86_64-unknown-linux-gnu > >   >>>>> (64-bit) > >   >>>>> > >   >>>>> But I still get the errors for verbatim multiline and > >   >>>>> the strange error if an error occurs in \Sexpr.  Is > >   >>>>> your patch included in this version? I will try now > >   >>>>> with R-rc_2011-10-27_r57452.tar.gz. > >   >>>> > >   >>>> Try R-2.14.0, it is already released. Or R-devel. > >   >>>> > >   >>>> Best, Uwe Ligges > >   >>>> > >   >>>> > >   >>>>> > >>>>> Renaud > >>>>> > >>>>> On 28/10/2011 17:25, Duncan Murdoch wrote: > >>>>>> On 28/10/2011 10:53 AM, Duncan Murdoch wrote: > >>>>>>> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: > >>>>>>> > Hi, > >>>>>>> > > >>>>>>> > another Rd related issue I encountered is that if an error occurs > >>>>>>> in an > >>>>>>> > \Sexpr in an Rd file, then on get the following error: > >>>>>>> > > >>>>>>> > * checking for portable compilation flags in Makevars ... OK > >>>>>>> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) > >>>>>>> ... OK > >>>>>>> > * checking examples ... ERROR > >>>>>>> > Error in paste(before, x, after, sep = "") : object 'exfile' > >>>>>>> not found > >>>>>>> > Execution halted > >>>>>>> > > >>>>>>> > To reproduce, put a call like this in an Rd section: > >>>>>>> > > >>>>>>> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} > >>>>>>> > > >>>>>>> > The strange thing is that it occurs at the example checking step. > >>>>>>> > Not sure why it does not break before. > >>>>>>> > > >>>>>>> > Thank you. > >>>>>>> > > >>>>>>> > Renaud > >>>>>>> > > >>>>>>> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu > >>>>>>> (64-bit) > >>>>>>> > > >>>>>>> > >>>>>>> I would update to 2.13.2 patched, or the release candidate of > >>>>>>> 2.14.0. > >>>>>> > >>>>>> Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. > >>>>>> 2.14.0 > >>>>>> is what you should get. > >>>>>> > >>>>>> Duncan Murdoch > >>>>> > >>>>> ______________________________________________ > >>>>> [hidden email] mailing list > >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel > >>> > >>> ______________________________________________ > >>> [hidden email] mailing list > >>> https://stat.ethz.ch/mailman/listinfo/r-devel > >>> > >> > > > > ______________________________________________ > > [hidden email] mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > ______________________________________________ > > [hidden email] mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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In reply to this post by Duncan Murdoch-2
Getting back to the \Sexpr issue, I tried with R-2.14.0 and I still see
the following issues: - verbatim multiline is not shown properly on PDF (\Sexpr[results=verbatim, stage=render]{cat("line\nnext line")}) - verbatim with empty lines breaks PDF generation (\Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n\nyet another line")}). Would there be an issue in using a plain Latex verbatim environment for \Sexpr[results=verbatim]? - an error in an \Sexpr (\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")}) gives the following in R CMD check: * checking examples ... ERROR Error in paste(before, x, after, sep = "") : object 'exfile' not found Execution halted The two first issues can be reproduced with a call to R CMD Rd2pdf on the Rd code below. Thank you. Renaud. %%%%%%%%%%% \name{Sexpr} \alias{Sexpr} \title{Error and verbatim in Sexpr} \description{ Testing Sexpr in Rd files %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")} \Sexpr[results=verbatim, stage=render]{cat("line\nnext line")} %\Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n\nyet another line")} } %%%%%%%%%%% -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa On 28/10/2011 17:25, Duncan Murdoch wrote: > On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >> > Hi, >> > >> > another Rd related issue I encountered is that if an error occurs >> in an >> > \Sexpr in an Rd file, then on get the following error: >> > >> > * checking for portable compilation flags in Makevars ... OK >> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK >> > * checking examples ... ERROR >> > Error in paste(before, x, after, sep = "") : object 'exfile' not >> found >> > Execution halted >> > >> > To reproduce, put a call like this in an Rd section: >> > >> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >> > >> > The strange thing is that it occurs at the example checking step. >> > Not sure why it does not break before. >> > >> > Thank you. >> > >> > Renaud >> > >> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >> (64-bit) >> > >> >> I would update to 2.13.2 patched, or the release candidate of 2.14.0. > > Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. > 2.14.0 is what you should get. > > Duncan Murdoch ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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In reply to this post by Renaud Gaujoux
Dear Renaud,
> Getting back to the \Sexpr issue, I tried with R-2.14.0 and I still see > the following issues: > > - verbatim multiline is not shown properly on PDF > (\Sexpr[results=verbatim, stage=render]{cat("line\nnext line")}) You probably meant to use `paste', not `cat'. The latter sends its output somewhere and returns NULL, not the string. Best, Georgi -- Dr Georgi Boshnakov tel: (+44) (0)161 306 3684 School of Mathematics fax: (+44) (0)161 306 3669 Alan Turing Building 1.125 The University of Manchester email: [hidden email] Oxford Road Manchester M13 9PL UK ------------------------------ Message: 18 Date: Tue, 01 Nov 2011 12:22:30 +0200 From: Renaud Gaujoux <[hidden email]> To: Duncan Murdoch <[hidden email]> Cc: Renaud Gaujoux <[hidden email]>, "[hidden email]" <[hidden email]> Subject: Re: [Rd] R CMD check and error in an \Sexpr in an Rd file Message-ID: <[hidden email]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Getting back to the \Sexpr issue, I tried with R-2.14.0 and I still see the following issues: - verbatim multiline is not shown properly on PDF (\Sexpr[results=verbatim, stage=render]{cat("line\nnext line")}) - verbatim with empty lines breaks PDF generation (\Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n\nyet another line")}). Would there be an issue in using a plain Latex verbatim environment for \Sexpr[results=verbatim]? - an error in an \Sexpr (\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")}) gives the following in R CMD check: * checking examples ... ERROR Error in paste(before, x, after, sep = "") : object 'exfile' not found Execution halted The two first issues can be reproduced with a call to R CMD Rd2pdf on the Rd code below. Thank you. Renaud. %%%%%%%%%%% \name{Sexpr} \alias{Sexpr} \title{Error and verbatim in Sexpr} \description{ Testing Sexpr in Rd files %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")} \Sexpr[results=verbatim, stage=render]{cat("line\nnext line")} %\Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n\nyet another line")} } %%%%%%%%%%% -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa On 28/10/2011 17:25, Duncan Murdoch wrote: > On 28/10/2011 10:53 AM, Duncan Murdoch wrote: >> On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: >> > Hi, >> > >> > another Rd related issue I encountered is that if an error occurs >> in an >> > \Sexpr in an Rd file, then on get the following error: >> > >> > * checking for portable compilation flags in Makevars ... OK >> > * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK >> > * checking examples ... ERROR >> > Error in paste(before, x, after, sep = "") : object 'exfile' not >> found >> > Execution halted >> > >> > To reproduce, put a call like this in an Rd section: >> > >> > \Sexpr[results=verbatim, stage=render]{x<- 1; stop("sexpr error")} >> > >> > The strange thing is that it occurs at the example checking step. >> > Not sure why it does not break before. >> > >> > Thank you. >> > >> > Renaud >> > >> > PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu >> (64-bit) >> > >> >> I would update to 2.13.2 patched, or the release candidate of 2.14.0. > > Oops, sorry, 2.13.2 is "final", so I didn't backport the patch. > 2.14.0 is what you should get. > > Duncan Murdoch ------------------------------ _______________________________________________ [hidden email] mailing list DIGESTED https://stat.ethz.ch/mailman/listinfo/r-devel End of R-devel Digest, Vol 105, Issue 1 *************************************** ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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In reply to this post by Renaud Gaujoux
Georgi, I tried with paste() instead of cat(), but I then get the
following in my PDF manual: [1] "line\nnext line" i.e. what would be printed in the R console, which is not what I want. I would like to get something like this in the Latex code: \begin{verbatim} line next line \end{verbatim} Using cat() I get the following in the Latex code: \AsIs{ line next line} which does not render as a new line in the PDF and breaks if empty lines are present in the output text. Besides it will also break on \Sexpr[results=verbatim, stage=render]{list("text", 3)}. But maybe this is not what 'results=verbatim' is supposed to do nor to be used for? Renaud Another test Rd file. %%%%%%%%% \name{Sexpr} \alias{Sexpr} \title{Error and verbatim in Sexpr} \description{ Testing Sexpr in Rd files %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")} Verbatim: 1: \Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n")} 2: \Sexpr[results=verbatim, stage=render]{"line\nnext line\n"} 3: \Sexpr[results=verbatim, stage=render]{list("line\nnext line", 3)} Text: 1: \Sexpr[results=text, stage=render]{cat("line\nnext line\n")} 2: \Sexpr[results=text, stage=render]{"line\nnext line\n"} 3: \Sexpr[results=text, stage=render]{list("line\nnext line", 3)} } %%%%% ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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On 11-11-03 7:58 AM, Renaud Gaujoux wrote:
> Georgi, I tried with paste() instead of cat(), but I then get the > following in my PDF manual: > > [1] "line\nnext line" > > i.e. what would be printed in the R console, which is not what I want. > I would like to get something like this in the Latex code: > > \begin{verbatim} > line > next line > \end{verbatim} I don't think you want that: it forces display mode. You might want verbatim text displayed inline, like \verb does. > > Using cat() I get the following in the Latex code: > > \AsIs{ > line > next line} > > which does not render as a new line in the PDF and breaks if empty lines > are present in the output text. So the problem is with the \AsIs macro. You can see the definition in the Rd.sty file in R_HOME/share/texmf/tex/latex. Can you suggest an improvement? Duncan Murdoch > Besides it will also break on \Sexpr[results=verbatim, > stage=render]{list("text", 3)}. > > But maybe this is not what 'results=verbatim' is supposed to do nor to > be used for? > > Renaud > > Another test Rd file. > > %%%%%%%%% > \name{Sexpr} > \alias{Sexpr} > \title{Error and verbatim in Sexpr} > \description{ > Testing Sexpr in Rd files > > %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")} > > Verbatim: > > 1: \Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n")} > > 2: \Sexpr[results=verbatim, stage=render]{"line\nnext line\n"} > > 3: \Sexpr[results=verbatim, stage=render]{list("line\nnext line", 3)} > > Text: > > 1: \Sexpr[results=text, stage=render]{cat("line\nnext line\n")} > > 2: \Sexpr[results=text, stage=render]{"line\nnext line\n"} > > 3: \Sexpr[results=text, stage=render]{list("line\nnext line", 3)} > > } > %%%%% > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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Although I use Latex quite a lot, I am not literate in Latex macro
languages (e.g. the definition of AsIs). Is there (I am sure there is) a reason why a plain verbatim environment is not used in this case? On 03/11/2011 14:19, Duncan Murdoch wrote: > On 11-11-03 7:58 AM, Renaud Gaujoux wrote: >> Georgi, I tried with paste() instead of cat(), but I then get the >> following in my PDF manual: >> >> [1] "line\nnext line" >> >> i.e. what would be printed in the R console, which is not what I want. >> I would like to get something like this in the Latex code: >> >> \begin{verbatim} >> line >> next line >> \end{verbatim} > > I don't think you want that: it forces display mode. You might want > verbatim text displayed inline, like \verb does. > >> >> Using cat() I get the following in the Latex code: >> >> \AsIs{ >> line >> next line} >> >> which does not render as a new line in the PDF and breaks if empty lines >> are present in the output text. > > So the problem is with the \AsIs macro. You can see the definition in > the Rd.sty file in R_HOME/share/texmf/tex/latex. Can you suggest an > improvement? > > Duncan Murdoch > >> Besides it will also break on \Sexpr[results=verbatim, >> stage=render]{list("text", 3)}. >> >> But maybe this is not what 'results=verbatim' is supposed to do nor to >> be used for? >> >> Renaud >> >> Another test Rd file. >> >> %%%%%%%%% >> \name{Sexpr} >> \alias{Sexpr} >> \title{Error and verbatim in Sexpr} >> \description{ >> Testing Sexpr in Rd files >> >> %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")} >> >> Verbatim: >> >> 1: \Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n")} >> >> 2: \Sexpr[results=verbatim, stage=render]{"line\nnext line\n"} >> >> 3: \Sexpr[results=verbatim, stage=render]{list("line\nnext >> line", 3)} >> >> Text: >> >> 1: \Sexpr[results=text, stage=render]{cat("line\nnext line\n")} >> >> 2: \Sexpr[results=text, stage=render]{"line\nnext line\n"} >> >> 3: \Sexpr[results=text, stage=render]{list("line\nnext line", 3)} >> >> } >> %%%%% >> >> ______________________________________________ >> [hidden email] mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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In reply to this post by Duncan Murdoch-2
Dear Duncan and Renauld,
The error caused by the empty line(s) can be removed by prefixin the macro with \long in Rd.sty: \long\def\Rd@AsIsX#1{\normalfont #1\egroup} but the slash-n's come up in the output. In "text mode" this seems not to be a problem. Following normal TeX rules one needs to enter an empty line, e.g. by \n\n. Having written that, I tried putting two \n's in the verbatim text and it seems to work (see below). I need to consult the TeX book to be sure but the problem with AsIs seems to be that by the time it starts processing its argument it has been tokenized by TeX (hence single newlines have become spaces). Further thought may be needed about the new lines in verbatim. I may have missed again something but it seems that the observed output is consistent with the documentation, which states: "results=verbatim Print the results of the code just as if it was executed at the console, and include the printed results verbatim. (Invisible results will not print.)" And the examples print on the console as they appear in output (with print, not cat). Do we need exception from the general rule? An alternative would be to introduce results=verbatimLines option. Georgi \name{Sexpr} \alias{Sexpr} \title{Error and verbatim in Sexpr} \description{ Testing Sexpr in Rd files %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")} Verbatim: 1: \Sexpr[results=verbatim, stage=render]{cat("line\n\nnext line\n\n and another")} % 1a: \Sexpr[results=text, stage=render]{capture.output(cat(c("line", "next line\n"),sep="\n", collapse="\n"))} 2: \Sexpr[results=verbatim, stage=render]{"line\nnext line\n"} 3: \Sexpr[results=verbatim, stage=render]{list("line\nnext line", 3)} 4: \Sexpr[results=verbatim, stage=render]{list(c("line", "next line"), 3)} Text: 1: \Sexpr[results=text, stage=render]{cat("line\nnext line\n")} 2: \Sexpr[results=text, stage=render]{"line\nnext line\n"} 3: \Sexpr[results=text, stage=render]{list("line\n\nnext line\\\\\\\\ \\\\newline and another", 3)} } -- Dr Georgi Boshnakov tel: (+44) (0)161 306 3684 School of Mathematics fax: (+44) (0)161 306 3669 Alan Turing Building 1.125 The University of Manchester email: [hidden email] Oxford Road Manchester M13 9PL UK ________________________________________ From: Duncan Murdoch [[hidden email]] Sent: 03 November 2011 12:19 To: Renaud Gaujoux Cc: Georgi Boshnakov; [hidden email] Subject: Re: [Rd] R CMD check and error in an \Sexpr in an Rd file On 11-11-03 7:58 AM, Renaud Gaujoux wrote: > Georgi, I tried with paste() instead of cat(), but I then get the > following in my PDF manual: > > [1] "line\nnext line" > > i.e. what would be printed in the R console, which is not what I want. > I would like to get something like this in the Latex code: > > \begin{verbatim} > line > next line > \end{verbatim} I don't think you want that: it forces display mode. You might want verbatim text displayed inline, like \verb does. > > Using cat() I get the following in the Latex code: > > \AsIs{ > line > next line} > > which does not render as a new line in the PDF and breaks if empty lines > are present in the output text. So the problem is with the \AsIs macro. You can see the definition in the Rd.sty file in R_HOME/share/texmf/tex/latex. Can you suggest an improvement? Duncan Murdoch > Besides it will also break on \Sexpr[results=verbatim, > stage=render]{list("text", 3)}. > > But maybe this is not what 'results=verbatim' is supposed to do nor to > be used for? > > Renaud > > Another test Rd file. > > %%%%%%%%% > \name{Sexpr} > \alias{Sexpr} > \title{Error and verbatim in Sexpr} > \description{ > Testing Sexpr in Rd files > > %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")} > > Verbatim: > > 1: \Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n")} > > 2: \Sexpr[results=verbatim, stage=render]{"line\nnext line\n"} > > 3: \Sexpr[results=verbatim, stage=render]{list("line\nnext line", 3)} > > Text: > > 1: \Sexpr[results=text, stage=render]{cat("line\nnext line\n")} > > 2: \Sexpr[results=text, stage=render]{"line\nnext line\n"} > > 3: \Sexpr[results=text, stage=render]{list("line\nnext line", 3)} > > } > %%%%% > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: R CMD check and error in an \Sexpr in an Rd file
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Thank you Georgi.
With the fix \long the output is indeed consistent with the documentation. I think my use of cat() worked by luck as its output should not have been rendered. Would a 'results=tex' (html, text) be possible? or 'results=source' that could be combined with \if{format}{text}? This would allow to generate custom Latex, or HTML code, but it might also be is hazardous... Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa On 03/11/2011 15:50, Georgi Boshnakov wrote: > Dear Duncan and Renauld, > > > The error caused by the empty line(s) can be removed by prefixin the macro with \long > in Rd.sty: > > \long\def\Rd@AsIsX#1{\normalfont #1\egroup} > > but the slash-n's come up in the output. > > In "text mode" this seems not to be a problem. Following normal TeX rules one needs to enter an empty line, e.g. by \n\n. > > Having written that, I tried putting two \n's in the verbatim text and it seems to work (see below). > > I need to consult the TeX book to be sure but the > problem with AsIs seems to be that by the time it starts processing its argument it has been tokenized by TeX > (hence single newlines have become spaces). > > Further thought may be needed about the new lines in verbatim. > I may have missed again something but it seems that the observed output is consistent with the > documentation, which states: > > "results=verbatim Print the results of the code just as if it was executed at the > console, and include the printed results verbatim. (Invisible results will not print.)" > > And the examples print on the console as they appear in output (with print, not cat). > > Do we need exception from the general rule? > > An alternative would be to introduce results=verbatimLines option. > > > Georgi > > \name{Sexpr} > \alias{Sexpr} > \title{Error and verbatim in Sexpr} > \description{ > Testing Sexpr in Rd files > > %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")} > > Verbatim: > > 1: \Sexpr[results=verbatim, stage=render]{cat("line\n\nnext line\n\n and another")} > > % 1a: \Sexpr[results=text, stage=render]{capture.output(cat(c("line", "next line\n"),sep="\n", collapse="\n"))} > > 2: \Sexpr[results=verbatim, stage=render]{"line\nnext line\n"} > > 3: \Sexpr[results=verbatim, stage=render]{list("line\nnext line", 3)} > > 4: \Sexpr[results=verbatim, stage=render]{list(c("line", "next line"), 3)} > > Text: > > 1: \Sexpr[results=text, stage=render]{cat("line\nnext line\n")} > > 2: \Sexpr[results=text, stage=render]{"line\nnext line\n"} > > 3: \Sexpr[results=text, stage=render]{list("line\n\nnext line\\\\\\\\ \\\\newline and another", 3)} > > } > > > > -- > Dr Georgi Boshnakov tel: (+44) (0)161 306 3684 > School of Mathematics fax: (+44) (0)161 306 3669 > Alan Turing Building 1.125 > The University of Manchester email: [hidden email] > Oxford Road > Manchester M13 9PL > UK > > > ________________________________________ > From: Duncan Murdoch [[hidden email]] > Sent: 03 November 2011 12:19 > To: Renaud Gaujoux > Cc: Georgi Boshnakov; [hidden email] > Subject: Re: [Rd] R CMD check and error in an \Sexpr in an Rd file > > On 11-11-03 7:58 AM, Renaud Gaujoux wrote: >> Georgi, I tried with paste() instead of cat(), but I then get the >> following in my PDF manual: >> >> [1] "line\nnext line" >> >> i.e. what would be printed in the R console, which is not what I want. >> I would like to get something like this in the Latex code: >> >> \begin{verbatim} >> line >> next line >> \end{verbatim} > I don't think you want that: it forces display mode. You might want > verbatim text displayed inline, like \verb does. > >> Using cat() I get the following in the Latex code: >> >> \AsIs{ >> line >> next line} >> >> which does not render as a new line in the PDF and breaks if empty lines >> are present in the output text. > So the problem is with the \AsIs macro. You can see the definition in > the Rd.sty file in R_HOME/share/texmf/tex/latex. Can you suggest an > improvement? > > Duncan Murdoch > >> Besides it will also break on \Sexpr[results=verbatim, >> stage=render]{list("text", 3)}. >> >> But maybe this is not what 'results=verbatim' is supposed to do nor to >> be used for? >> >> Renaud >> >> Another test Rd file. >> >> %%%%%%%%% >> \name{Sexpr} >> \alias{Sexpr} >> \title{Error and verbatim in Sexpr} >> \description{ >> Testing Sexpr in Rd files >> >> %\Sexpr[results=verbatim, stage=render]{stop("error in sexpr")} >> >> Verbatim: >> >> 1: \Sexpr[results=verbatim, stage=render]{cat("line\nnext line\n")} >> >> 2: \Sexpr[results=verbatim, stage=render]{"line\nnext line\n"} >> >> 3: \Sexpr[results=verbatim, stage=render]{list("line\nnext line", 3)} >> >> Text: >> >> 1: \Sexpr[results=text, stage=render]{cat("line\nnext line\n")} >> >> 2: \Sexpr[results=text, stage=render]{"line\nnext line\n"} >> >> 3: \Sexpr[results=text, stage=render]{list("line\nnext line", 3)} >> >> } >> %%%%% >> >> ______________________________________________ >> [hidden email] mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
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