Hello,
I am working on building a package under Windows. Everything works
well;
only if I do not provide the pdf version of the vignette in the
'inst/doc' directory I get the following warning when running Rcmd
check:
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF
Also then the pdf is not built with Rcmd build.
I have seen on the daily check results page of the development
packages
that many packages get this warning.
How can I avoid this warning or can I ignore it? Or do I have to
provide
the pdf (which is not recommended)?
Thank you very much
Best regards
Manuela Hummel
Hi Manuela,
On 15 Sep 2005, hummel at ibe.med.uni-muenchen.de wrote:
> I am working on building a package under Windows. Everything works
> well; only if I do not provide the pdf version of the vignette in
> the 'inst/doc' directory I get the following warning when running
> Rcmd check:
>
> * checking package vignettes in 'inst/doc' ... WARNING
> Package vignettes without corresponding PDF
Yes, R CMD check wants to see a pdf corresponding to each Rnw file in
the inst/doc package location.
> Also then the pdf is not built with Rcmd build.
If the proper tools (MikTeX) are installed, R CMD build foo/ should
"build" the package's vignettes, that is, create the pdf.
> I have seen on the daily check results page of the development
> packages that many packages get this warning. How can I avoid this
> warning or can I ignore it? Or do I have to provide the pdf (which
> is not recommended)?
The warnings are because the pdf isn't getting generated. In many
cases, the pdf isn't getting generated because there are problems
during the vignette processing --- so the best solution is to make it
so that the vignettes can be built on Windows (this does work for many
packages, so we know that it is possible).
Hope that helps some,
+ seth
PS: Next time, send this sort of question to bioc-devel. If you are
writing packages for BioC, you should subscribe to this list and post
development related questions there.
On 16 Sep 2005, huber at ebi.ac.uk wrote:
> as far as I understand, you can safely ignore this Warning.
I have a different opinion. Vignettes are an important component of
BioC packages. If R CMD build isn't building them, that usually
indicates a problem that needs fixing.
If we can help get the vignette building, post some details about what
is going on.
Best,
+ seth
> I have a different opinion. Vignettes are an important component of
> BioC packages. If R CMD build isn't building them, that usually
> indicates a problem that needs fixing.
It depends on the situation, that warning can mean various things. It
is
entirely likely that the vignettes can and do build when one gets that
warning (and this is the situation that I think Wolfgang was referring
to). A few versions of R back 'check' started looking to make sure a
.pdf
was *already* present in /inst/doc for every vignette file.
Personally I
don't really agree w/ that behavior but I don't make the rules. :)
That was actually part of the reason behind all the pre-building/etc
before checks are run in the daily package checking code (which I'm
guessing has changed radically since I last saw it, but also guessing
the
general flow of activity is similar in this regard).
-J
Hi Manuela,
as far as I understand, you can safely ignore this Warning. It seems
there are different opinions around what should constitute a warning,
ranging from "look at this interesting factoid" to "here's something
that is not acceptable for a bioconductor package", which are not the
same.
However, "R CMD build" should produce the PDF file for the vignette -
why does this go wrong? Do have details?
Best wishes
Wolfgang
Manuela Hummel wrote:
> Hello,
>
> I am working on building a package under Windows. Everything works
well;
> only if I do not provide the pdf version of the vignette in the
> 'inst/doc' directory I get the following warning when running Rcmd
check:
>
> * checking package vignettes in 'inst/doc' ... WARNING
> Package vignettes without corresponding PDF
>
> Also then the pdf is not built with Rcmd build.
> I have seen on the daily check results page of the development
packages
> that many packages get this warning.
> How can I avoid this warning or can I ignore it? Or do I have to
provide
> the pdf (which is not recommended)?
>
> Thank you very much
> Best regards
> Manuela Hummel
>
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax: +44 1223 494486
Http: www.ebi.ac.uk/huber
Hi Wolfgang,
thank you for your reply. So this warning should not be the problem -
but the fact that no vignette can be built...
When I build a zip file everything is normal except that no pdf is
created.
When building a tar.gz file there is something strange:
Z:\GlobalAncova>Rcmd build z:/GA_Subversion/GlobalAncova
* checking for file 'z:/GA_Subversion/GlobalAncova/DESCRIPTION' ... OK
* preparing 'z:/GA_Subversion/GlobalAncova':
* creating vignettes ... OK
* removing junk files
* building 'GlobalAncova_1.2.tar.gz'
tar: GlobalAncova/inst/doc/Rplots.ps: file changed as we read it
tar: Error exit delayed from previous errors
Do you know what can be the reason?
Best regards
Manuela
Wolfgang Huber schrieb:
> Hi Manuela,
>
> as far as I understand, you can safely ignore this Warning. It seems
> there are different opinions around what should constitute a
warning,
> ranging from "look at this interesting factoid" to "here's something
> that is not acceptable for a bioconductor package", which are not
the
> same.
>
> However, "R CMD build" should produce the PDF file for the vignette
-
> why does this go wrong? Do have details?
>
> Best wishes
> Wolfgang
>
> Manuela Hummel wrote:
>
>> Hello,
>>
>> I am working on building a package under Windows. Everything works
>> well; only if I do not provide the pdf version of the vignette in
the
>> 'inst/doc' directory I get the following warning when running Rcmd
>> check:
>>
>> * checking package vignettes in 'inst/doc' ... WARNING
>> Package vignettes without corresponding PDF
>>
>> Also then the pdf is not built with Rcmd build.
>> I have seen on the daily check results page of the development
>> packages that many packages get this warning.
>> How can I avoid this warning or can I ignore it? Or do I have to
>> provide the pdf (which is not recommended)?
>>
>> Thank you very much
>> Best regards
>> Manuela Hummel
>>
>
>
> -------------------------------------
> Wolfgang Huber
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Cambridge CB10 1SD
> England
> Phone: +44 1223 494642
> Fax: +44 1223 494486
> Http: www.ebi.ac.uk/huber
> -------------------------------------
On 19 Sep 2005, hummel at ibe.med.uni-muenchen.de wrote:
> When I build a zip file everything is normal except that no pdf is
> created. When building a tar.gz file there is something strange:
>
> Z:\GlobalAncova>Rcmd build z:/GA_Subversion/GlobalAncova
> * checking for file 'z:/GA_Subversion/GlobalAncova/DESCRIPTION' ...
> OK
> * preparing 'z:/GA_Subversion/GlobalAncova':
> * creating vignettes ... OK
> * removing junk files
> * building 'GlobalAncova_1.2.tar.gz'
> tar: GlobalAncova/inst/doc/Rplots.ps: file changed as we read it
> tar: Error exit delayed from previous errors
The first thing I would try is running R CMD build again on a clean
source dir. Make sure all generated files are removed first.
If this is 100% reproducible, then my guess would be that your Rnw
file is doing something funny with figures. Do you have Rgraphviz
installed for Windows?
+ seth
I recognized that I forgot updating the system path to the new R
version... So I guess this was the reason something went wrong (for
example with Rgraphviz). Now the pdf is created correctly.
Thank you, kind regards
Manuela
Seth Falcon schrieb:
>On 19 Sep 2005, hummel at ibe.med.uni-muenchen.de wrote:
>
>
>>When I build a zip file everything is normal except that no pdf is
>>created. When building a tar.gz file there is something strange:
>>
>>Z:\GlobalAncova>Rcmd build z:/GA_Subversion/GlobalAncova
>>* checking for file 'z:/GA_Subversion/GlobalAncova/DESCRIPTION' ...
>> OK
>>* preparing 'z:/GA_Subversion/GlobalAncova':
>>* creating vignettes ... OK
>>* removing junk files
>>* building 'GlobalAncova_1.2.tar.gz'
>>tar: GlobalAncova/inst/doc/Rplots.ps: file changed as we read it
>>tar: Error exit delayed from previous errors
>>
>>
>
>The first thing I would try is running R CMD build again on a clean
>source dir. Make sure all generated files are removed first.
>
>If this is 100% reproducible, then my guess would be that your Rnw
>file is doing something funny with figures. Do you have Rgraphviz
>installed for Windows?
>
>+ seth
>
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