Hi,
The following command:
R CMD Rd2pdf --no-preview --output=./tmp.pdf --title=test genefu-package.Rd
run against this file:
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu/man/genefu-package.Rd
(username: readonly; password: readonly)
produces a very verbose error (see below)
On Wed, Mar 14, 2012 at 1:13 PM, Dan Tenenbaum wrote:
> Hi,
>
> The following command:
> R CMD Rd2pdf --no-preview --output=./tmp.pdf --title=test genefu-package.Rd
> run against this file:
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu/man/genefu-pack
On Tue, Mar 20, 2012 at 10:21 AM, Duncan Murdoch
wrote:
> On 12-03-19 10:27 PM, Dan Tenenbaum wrote:
>>
>> Hello,
>>
>> Sorry to repeat myself, but I was wondering if anyone had taken a look at
>> this.
>
>
> No. Could you put together a simple self c
On Tue, Mar 20, 2012 at 10:41 AM, Duncan Murdoch
wrote:
> On 12-03-20 1:25 PM, Dan Tenenbaum wrote:
>>
>> On Tue, Mar 20, 2012 at 10:21 AM, Duncan Murdoch
>> wrote:
>>>
>>> On 12-03-19 10:27 PM, Dan Tenenbaum wrote:
>>>>
>>>>
>&
On Tue, Mar 20, 2012 at 11:51 AM, Duncan Murdoch
wrote:
> On 12-03-20 1:46 PM, Dan Tenenbaum wrote:
>>
>> On Tue, Mar 20, 2012 at 10:41 AM, Duncan Murdoch
>> wrote:
>>>
>>> On 12-03-20 1:25 PM, Dan Tenenbaum wrote:
>>>>
>>>>
>&
On Tue, Mar 20, 2012 at 12:14 PM, Duncan Murdoch
wrote:
> This should now be fixed in R-devel, and shortly in the 2.15.0 beta.
Thanks very much.
Dan
>
> Duncan Murdoch
>
>
> On 12-03-20 2:54 PM, Dan Tenenbaum wrote:
>>
>> On Tue, Mar 20, 2012 at 11:51 AM, Duncan
Hi,
The page
http://cran.r-project.org/bin/windows/base/rtest.html
has a link to:
http://cran.r-project.org/bin/windows/base/R-2.15.0rc-win.exe
However, clicking on that link gives a 404 "Object not found' error.
FYI.
Dan
__
R-devel@r-project.org mail
On Fri, Mar 23, 2012 at 4:52 PM, Daniel Nordlund
wrote:
>> -Original Message-
>> From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org]
>> On Behalf Of Dan Tenenbaum
>> Sent: Friday, March 23, 2012 12:21 PM
>> To: r-devel@r-project.org
&g
gt;>
>>>>
>>>> On 24.03.2012 06:58, Daniel Nordlund wrote:
>>>>>>
>>>>>> -Original Message-
>>>>>> From: Dan Tenenbaum [mailto:dtene...@fhcrc.org]
>>>>>> Sent: Friday, March 23, 2012 5:48 PM
>>>>>> To:
source.
Dan
>
> On 27/03/2012 17:48, Dan Tenenbaum wrote:
>>
>> On Sat, Mar 24, 2012 at 1:07 PM, Duncan Murdoch
>> wrote:
>>>
>>> On 12-03-24 2:31 PM, Simon Urbanek wrote:
>>>>
>>>>
>>>>
>
I'd like to have a way to create reference manuals during R CMD build
(and have them go in the build/ directory of the resulting package
tarball), whether or not any of my Rd files have \Sexpr macros in
them.
It seems like there are a couple of ways to suppress the building of
manuals during R CMD
On Tue, May 22, 2012 at 10:34 AM, Henrik Bengtsson
wrote:
> Hi,
>
> I'd like to spawn of a new R process from within R using system(),
> e.g. system("R -f myScript.R"). However, just specifying "R" as in
> that example is not guaranteed to work, because "R" may not be on the
> OS's search path.
I know this has come up before on R-help
(http://r.789695.n4.nabble.com/7-arguments-passed-to-Internal-identical-which-requires-6-td4548460.html)
but I have a concise reproducible case that I wanted to share.
Also, please note the Bioconductor scenario which is potentially
seriously impacted by th
On Mon, Aug 6, 2012 at 3:01 PM, Mike Lawrence wrote:
> Is there any way to ensure that quotation marks are left as straight
> quotes and not converted to curly quotes in the \usage and \examples
> sections when the pdf versions of the docs are created?
>
Perhaps if the R session that builds the p
On Wed, Oct 24, 2012 at 11:13 AM, Richard D. Morey wrote:
> This question involves Rook, but I think the answer will be general enough
> that it pays to post here. At any rate, I don't know enough to know whether
> this is a Rook only issue or a general R issue.
>
> Here's what I'd like to do (and
On Thu, Oct 25, 2012 at 8:45 AM, Richard D. Morey wrote:
> On 24/10/12 10:55 PM, Simon Urbanek wrote:
>>
>>
>> The point is that you need a separate monitoring process or threads. That
>> process can be R, Rserve or any thing else.
>>
>>
>>
>
> Thanks for the tips. This is what I'm currently conte
> png(tempfile())
Error in .External(C_Quartz, "png", path.expand(filename), width, height, :
Incorrect number of arguments (12), expecting 11 for 'Quartz'
> sessionInfo()
R Under development (unstable) (2013-02-24 r62054)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF
On Mon, Mar 4, 2013 at 2:15 PM, Steve Lianoglou
wrote:
> On Mon, Mar 4, 2013 at 4:28 PM, Aaron Mackey wrote:
>> On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm wrote:
>>
>>> * where do the dragons lurk
>>>
>>
>> webs of interconnected dynamically loaded libraries, identical versions of
>> R compil
On Sat, Mar 9, 2013 at 2:17 PM, Kevin Hendricks
wrote:
> Hi,
> One last quick question ... does anyone archive older CRAN package check
> summaries? I searched the web but could not find any. My package was
> archived in February of this year so any package check summary from earlier
> than t
Hello,
I'm seeing three different vignette-related errors with recent
versions of R-3.0.0 alpha.
First, with the package BitSeq
(http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get
the following when trying to build the package:
Error: processing vignette ’BitSeq.Rnw' failed with
Hi,
After updating to R-3.0 beta r62328, I get the following:
> install.packages("Biobase", type="source",
> repos="http://george2/BBS/2.12/bioc";)
Error in do.call(op, list(v_c, v_t[[op]])) :
could not find function "R (>=2.15.1)"
The problem can be fixed by adding a space after >= in the of
On Thu, Mar 21, 2013 at 9:52 AM, Dan Tenenbaum wrote:
> Hi,
>
> After updating to R-3.0 beta r62328, I get the following:
>
>> install.packages("Biobase", type="source",
>> repos="http://george2/BBS/2.12/bioc";)
> Error in do.call(o
On Thu, Mar 21, 2013 at 10:28 AM, Duncan Murdoch
wrote:
> On 21/03/2013 12:59 PM, Dan Tenenbaum wrote:
>>
>> On Thu, Mar 21, 2013 at 9:52 AM, Dan Tenenbaum wrote:
>> > Hi,
>> >
>> > After updating to R-3.0 beta r62328, I get the following:
>>
On Fri, Mar 22, 2013 at 9:44 AM, Andrew Redd wrote:
> I am developing a package that is only applicable on windows, is there a
> line I can put in the depends field of the DESCRIPTION file to tell that
> this should only be build for windows?
>
OS_type: windows
See
RShowDoc("R-exts")
Section 1
Hi,
>From http://cran.r-project.org/bin/windows/base/rtest.html
I clicked on:
Download R-3.0.0 RC build for Windows
and got Object not found for
http://cran.r-project.org/bin/windows/base/R-3.0.0rc-win.exe
Thanks,
Dan
__
R-devel@r-project.org mailin
Hi,
Every day a few Bioconductor packages (different ones each day) fail
to build, on Windows only, with an error like this:
D:\biocbld\bbs-2.13-bioc\meat>D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD
build --keep-empty-dirs --no-resave-data OrganismDbi
[...]
Error in find_vignette_product(name, by = "
m. Duncan's suggestion about
a virus scanner is a good one, but there is no such software running
on the machine in question.
So it sounds maybe more like what Henrik describes above. Wondering if
there are more insights to be had...
Thanks,
Dan
>>
>> Kasper
>>
>>
&g
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