Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
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
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Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
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
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
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
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Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
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
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Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
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
__
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
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, UKFax: +44 1865 272595
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Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
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
>>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
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Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
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
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Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
> 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
__
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>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
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Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
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
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
>
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>>>
>>> __
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>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>
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[Rd] Sweave, cairo_pdf, xetex, CJK (Re: Sweave, cairo_pdf, CJK, ghostscript)
I am still doing some cosmetic things (adding annotations with some of the
really minority languages in Sichuan), but here are a few misc tips and quirks
so far:
- cairo_pdf() behaves differently via "R CMD Sweave " vs Sweave("file")
within R. The former produces a lot of warnings about not being able to
determine strwidth and have to substitute. Probably understandable, but still
annoying.
- It generates pdf 1.5 - when used in combination with xetex, - which uses
xdvipdfmx for pdf generation, and xdvipdfmx has the rather disturbing behavior
of *silently* *skipping* included pdf's that's higher than the default (instead
of do it with warning like pdfTeX) so no graphics will be included, unless
xetex is run with -output-driver="xdvipdfmx -V 5"... to declare to output pdf
1.5 .
- xetex needs noae in \usepackage{SWeave}. FWIW, Werner Lemberg's CJK (the
LaTeX package) can work without declaring noae, so that's my preferred choice
at the moment, although I have got both of them working, for doing Chinese in a
LaTeX document.
I think some of these information should go into the man page of cairo_pdf()...
--- On Fri, 28/10/11, Hin-Tak Leung wrote:
> Reading ?RWeaveLatex more carefully,
> I worked out that the outcome I want could be achieved
> without patching R, by having this towards the beginning:
>
> <>=
> cairo <- function(name, width, height, ...)
> grDevices::cairo_pdf(file = paste(name, "pdf", sep =
> "."),
>
> width = width, height =
> height)
> @
>
> Then declaring grdevice= like this:
>
> <>=
> grid.text("\u4F60\u597D", y=2/3,
> gp=gpar(fontfamily="CNS1"))
> @
>
> So all is well. is there any chance of either updating
> ?RWeaveLatex with this actual use-case example, or make it
> easier with the attached patch (and updated version of what
> I did, just adding the corresponding documentation)? I
> thought there might be a a use for cairo_ps() as well, but
> then most people who can do latex could do pdflatex,
> especially those who has cairo installed.
>
> FWIW, besides Chinese, I am doing Tibetan and Arabic as
> well - needed/wanted those two for Sichuan (south-western
> China) and Ningxia (northern western, just south of
> Mongolia).
>
> --- On Sun, 23/10/11, Hin-Tak Leung
> wrote:
>
> > --- On Sat, 22/10/11, Prof Brian
> > Ripley
> > wrote:
> >
> > > On Sat, 22 Oct 2011, Duncan Murdoch
> > > wrote:
> > >
> > > > On 11-10-21 8:57 PM, Hin-Tak Leung wrote:
> > > >> I have had some fun in the last few
> days
> > trying to
> > > put together an annotated map of China with R
> and
> > some
> > > public GIS data:
> > > >>
> > > >> http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download
> > > >>
> > > >> It is done, and rather nice... there are
> a
> > few
> > > issues:
> > > >>
> > > >> - the default pdf() device cannot do
> CJK
> > with
> > > embedded fonts - and cairo_pdf() is not hooked up
> to
> > Sweave
> > > yet. I have had a quick look, and it does not
> look
> > too
> > > complicated, other than the fact that cairo_pdf()
> is
> > > mutually exclusive with pdf(); and the jpeg/png
> are
> > new to
> > > 2.13 so it is probably just nobody has gotten
> round to
> > it.
> > > (and cairo_pdf() also behaves differently with
> the
> > onefile
> > > option). I guess I am almost saying I might get
> my
> > hand
> > > dirty or help somebody else who wants to. So it
> is
> > probably
> > > best to start some discussion.
> > > >
> > > > It is not hard to write your own device
> > functions,
> > > especially in 2.14.0. See rgl::rgl.Sweave for
> an
> > > example.
> > >
> > > And guess what the example in the Sweave manual
> > uses?
> > > cairo_pdf() ...
> >
> > I don't want a new device - I just wanted cairo_pdf()
> to be
> > hooked up to Sweave as an alternative to the default
> pdf().
> > See my later post with the patch against R trunk
> and
> > the worked examples.
> >
> > It looks like cairo_pdf() is just using my current
> > fontconfig settings.
> >
> >
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Re: [Rd] Sweave, cairo_pdf, xetex, CJK (Re: Sweave, cairo_pdf, CJK, ghostscript)
On Oct 31, 2011, at 5:56 PM, Hin-Tak Leung wrote:
> I am still doing some cosmetic things (adding annotations with some of the
> really minority languages in Sichuan), but here are a few misc tips and
> quirks so far:
>
> - cairo_pdf() behaves differently via "R CMD Sweave " vs Sweave("file")
> within R. The former produces a lot of warnings about not being able to
> determine strwidth and have to substitute. Probably understandable, but still
> annoying.
>
> - It generates pdf 1.5 - when used in combination with xetex, - which uses
> xdvipdfmx for pdf generation, and xdvipdfmx has the rather disturbing
> behavior of *silently* *skipping* included pdf's that's higher than the
> default (instead of do it with warning like pdfTeX) so no graphics will be
> included, unless xetex is run with -output-driver="xdvipdfmx -V 5"... to
> declare to output pdf 1.5 .
>
> - xetex needs noae in \usepackage{SWeave}. FWIW, Werner Lemberg's CJK (the
> LaTeX package) can work without declaring noae, so that's my preferred choice
> at the moment, although I have got both of them working, for doing Chinese in
> a LaTeX document.
>
> I think some of these information should go into the man page of
> cairo_pdf()...
>
Well, I don't see how most of the above is in any way relevant. What PDF gets
generated really depends on the cairo version you are using, not on R. Only
most recent versions of Cairo (1.10.x) switched the format to PDF-1.5 and added
format restriction functions, they are not available in general. In addition,
PDF-1.5 is 8 years old, so whatever tools can't deal with it are seriously out
of date.
Cheers,
Simon
> --- On Fri, 28/10/11, Hin-Tak Leung wrote:
>
>> Reading ?RWeaveLatex more carefully,
>> I worked out that the outcome I want could be achieved
>> without patching R, by having this towards the beginning:
>>
>> <>=
>> cairo <- function(name, width, height, ...)
>> grDevices::cairo_pdf(file = paste(name, "pdf", sep =
>> "."),
>>
>>width = width, height =
>> height)
>> @
>>
>> Then declaring grdevice= like this:
>>
>> <>=
>> grid.text("\u4F60\u597D", y=2/3,
>> gp=gpar(fontfamily="CNS1"))
>> @
>>
>> So all is well. is there any chance of either updating
>> ?RWeaveLatex with this actual use-case example, or make it
>> easier with the attached patch (and updated version of what
>> I did, just adding the corresponding documentation)? I
>> thought there might be a a use for cairo_ps() as well, but
>> then most people who can do latex could do pdflatex,
>> especially those who has cairo installed.
>>
>> FWIW, besides Chinese, I am doing Tibetan and Arabic as
>> well - needed/wanted those two for Sichuan (south-western
>> China) and Ningxia (northern western, just south of
>> Mongolia).
>>
>> --- On Sun, 23/10/11, Hin-Tak Leung
>> wrote:
>>
>>> --- On Sat, 22/10/11, Prof Brian
>>> Ripley
>>> wrote:
>>>
On Sat, 22 Oct 2011, Duncan Murdoch
wrote:
> On 11-10-21 8:57 PM, Hin-Tak Leung wrote:
>> I have had some fun in the last few
>> days
>>> trying to
put together an annotated map of China with R
>> and
>>> some
public GIS data:
>>
>> http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download
>>
>> It is done, and rather nice... there are
>> a
>>> few
issues:
>>
>> - the default pdf() device cannot do
>> CJK
>>> with
embedded fonts - and cairo_pdf() is not hooked up
>> to
>>> Sweave
yet. I have had a quick look, and it does not
>> look
>>> too
complicated, other than the fact that cairo_pdf()
>> is
mutually exclusive with pdf(); and the jpeg/png
>> are
>>> new to
2.13 so it is probably just nobody has gotten
>> round to
>>> it.
(and cairo_pdf() also behaves differently with
>> the
>>> onefile
option). I guess I am almost saying I might get
>> my
>>> hand
dirty or help somebody else who wants to. So it
>> is
>>> probably
best to start some discussion.
>
> It is not hard to write your own device
>>> functions,
especially in 2.14.0. See rgl::rgl.Sweave for
>> an
example.
And guess what the example in the Sweave manual
>>> uses?
cairo_pdf() ...
>>>
>>> I don't want a new device - I just wanted cairo_pdf()
>> to be
>>> hooked up to Sweave as an alternative to the default
>> pdf().
>>> See my later post with the patch against R trunk
>> and
>>> the worked examples.
>>>
>>> It looks like cairo_pdf() is just using my current
>>> fontconfig settings.
>>>
>>>
>
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>
>
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Re: [Rd] R CMD check and error in an \Sexpr in an Rd file
Hi Kasper,
On Mon, Oct 31, 2011 at 16:55, Kasper Daniel Hansen
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
> 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
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>
> >>> __
> >>> R-devel@r-project
Re: [Rd] Sweave, cairo_pdf, xetex, CJK (Re: Sweave, cairo_pdf, CJK, ghostscript)
--- On Mon, 31/10/11, Simon Urbanek wrote:
> On Oct 31, 2011, at 5:56 PM, Hin-Tak Leung wrote:
>
> > I am still doing some cosmetic things (adding
> annotations with some of the really minority languages in
> Sichuan), but here are a few misc tips and quirks so far:
> >
> > - cairo_pdf() behaves differently via "R CMD Sweave
> " vs Sweave("file") within R. The former
> produces a lot of warnings about not being able to determine
> strwidth and have to substitute. Probably understandable,
> but still annoying.
> >
> > - It generates pdf 1.5 - when used in combination with
> xetex, - which uses xdvipdfmx for pdf generation, and
> xdvipdfmx has the rather disturbing behavior of *silently*
> *skipping* included pdf's that's higher than the default
> (instead of do it with warning like pdfTeX) so no graphics
> will be included, unless xetex is run with
> -output-driver="xdvipdfmx -V 5"... to declare to output pdf
> 1.5 .
> >
> > - xetex needs noae in \usepackage{SWeave}. FWIW,
> Werner Lemberg's CJK (the LaTeX package) can work without
> declaring noae, so that's my preferred choice at the moment,
> although I have got both of them working, for doing Chinese
> in a LaTeX document.
> >
> > I think some of these information should go into the
> man page of cairo_pdf()...
> >
>
> Well, I don't see how most of the above is in any way
> relevant. What PDF gets generated really depends on the
> cairo version you are using, not on R. Only most recent
> versions of Cairo (1.10.x) switched the format to PDF-1.5
> and added format restriction functions, they are not
> available in general. In addition, PDF-1.5 is 8 years old,
> so whatever tools can't deal with it are seriously out of
> date.
That's ignorant. In terms of visual elements and desktop publishing, the last
major change in the pdf specification was 1.4, which introduces transparency.
Most open-source pdf rendering capbalities are based on either ghostscript or
xpdf/libpoppler . (TexLive/xetex/xdvipdfmx in the latter camp). Granted the
developer od xdivpdfmx made a strange decision - the pdf specification
explicitly state that renderers/readers should ignore features they don't
understand and make "best effort" rather than abort, but what you claimed -
"whatever tools cannot cannot deal with [PDF-1.5] are seriously out of date" is
utterly wrong: neither ghostscript nor libpopper supports that fully. And I
wonder what "tools" you use (other than Acrobat) are not based on those two.
FWIW, have a look at ghostscript's bug database, and search for "cairo".
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Re: [Rd] Sweave, cairo_pdf, xetex, CJK (Re: Sweave, cairo_pdf, CJK, ghostscript)
On Oct 31, 2011, at 7:52 PM, Hin-Tak Leung wrote:
> --- On Mon, 31/10/11, Simon Urbanek wrote:
>
>> On Oct 31, 2011, at 5:56 PM, Hin-Tak Leung wrote:
>>
>>> I am still doing some cosmetic things (adding
>> annotations with some of the really minority languages in
>> Sichuan), but here are a few misc tips and quirks so far:
>>>
>>> - cairo_pdf() behaves differently via "R CMD Sweave
>> " vs Sweave("file") within R. The former
>> produces a lot of warnings about not being able to determine
>> strwidth and have to substitute. Probably understandable,
>> but still annoying.
>>>
>>> - It generates pdf 1.5 - when used in combination with
>> xetex, - which uses xdvipdfmx for pdf generation, and
>> xdvipdfmx has the rather disturbing behavior of *silently*
>> *skipping* included pdf's that's higher than the default
>> (instead of do it with warning like pdfTeX) so no graphics
>> will be included, unless xetex is run with
>> -output-driver="xdvipdfmx -V 5"... to declare to output pdf
>> 1.5 .
>>>
>>> - xetex needs noae in \usepackage{SWeave}. FWIW,
>> Werner Lemberg's CJK (the LaTeX package) can work without
>> declaring noae, so that's my preferred choice at the moment,
>> although I have got both of them working, for doing Chinese
>> in a LaTeX document.
>>>
>>> I think some of these information should go into the
>> man page of cairo_pdf()...
>>>
>>
>> Well, I don't see how most of the above is in any way
>> relevant. What PDF gets generated really depends on the
>> cairo version you are using, not on R. Only most recent
>> versions of Cairo (1.10.x) switched the format to PDF-1.5
>> and added format restriction functions, they are not
>> available in general. In addition, PDF-1.5 is 8 years old,
>> so whatever tools can't deal with it are seriously out of
>> date.
>
> That's ignorant.
Oh, really? I'll leave it to you to verify the canonical source (Adobe) which
lists PDF 1.5 as released in August 2003, more than 8 years ago. Please check
you facts before making such obviously incorrect statements.
Cheers,
Simon
> In terms of visual elements and desktop publishing, the last major change in
> the pdf specification was 1.4, which introduces transparency. Most
> open-source pdf rendering capbalities are based on either ghostscript or
> xpdf/libpoppler . (TexLive/xetex/xdvipdfmx in the latter camp). Granted the
> developer od xdivpdfmx made a strange decision - the pdf specification
> explicitly state that renderers/readers should ignore features they don't
> understand and make "best effort" rather than abort, but what you claimed -
> "whatever tools cannot cannot deal with [PDF-1.5] are seriously out of date"
> is utterly wrong: neither ghostscript nor libpopper supports that fully. And
> I wonder what "tools" you use (other than Acrobat) are not based on those two.
>
> FWIW, have a look at ghostscript's bug database, and search for "cairo".
>
>
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Re: [Rd] Sweave, cairo_pdf, xetex, CJK (Re: Sweave, cairo_pdf, CJK, ghostscript)
--- On Mon, 31/10/11, Simon Urbanek wrote: > Well, I don't see how most of the above is in any way > relevant. What PDF gets generated really depends on the > cairo version you are using, not on R. Only most recent > versions of Cairo (1.10.x) switched the format to PDF-1.5 > and added format restriction functions, they are not > available in general. In addition, PDF-1.5 is 8 years old, > so whatever tools can't deal with it are seriously out of > date. You have completely missed the point. Have a look at both ghostscript's and libpoppler's bug database: neither's support of PDF *1.4* is complete, and that's what, over 10 years old. And I hope you do not used either of them in any form. TeXLive/Evince/xpdf/kpdf/okular used the latter, and linux-based printing used the former. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] weird error
I was just rebuilding a package that has built before and I hit this error Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : cyclic name space dependency detected when loading 'GhcnDaily', already loading 'GhcnDaily' The package built just fine last revision, and the only changes I made were to Rd files How do I track this puppy down [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] weird error
Thanks, found it. never say you only changed one thing. For reference for other folks. There was an errant script in my R subdir for the package that script had a library command for the package. hence the cyclical reference Steve On Mon, Oct 31, 2011 at 8:36 PM, steven mosher wrote: > I was just rebuilding a package that has built before and I hit this error > > Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = > keep.source) : > cyclic name space dependency detected when loading 'GhcnDaily', already > loading 'GhcnDaily' > > The package built just fine last revision, and the only changes I made > were to Rd files > > How do I track this puppy down > > > > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
