Thanks much to everyone for the helpful suggestions. It was indeed a
setwd() issue as suspected. However, I still have one curious little
niggle that remains:
when I run pdflatex on the generated .tex file, it stops with an error.
! Extra alignment tab has been changed to \cr.
\endtemplate
l.2
On 11/4/13, 11:05 AM, Gabriel Becker wrote:
As a side note, I'm not sure that existence of a symbol is sufficient (it
certainly is necessary). What about situations where the symbol exists but
is stale compared to the value in the parent? Are we sure that can never
happen?
I think this is a diff
On Mon, Nov 4, 2013 at 12:46 PM, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Tim Triche, Jr."
>> To: bioc-devel@r-project.org
>> Sent: Monday, November 4, 2013 12:25:19 PM
>> Subject: [Bioc-devel] disappearing .tex file when running R CMD Sweave on a
>> new vignette
>>
>>
That's got to be it. Thanks!
--t
> On Nov 4, 2013, at 12:46 PM, Dan Tenenbaum wrote:
>
>
>
> - Original Message -
>> From: "Tim Triche, Jr."
>> To: bioc-devel@r-project.org
>> Sent: Monday, November 4, 2013 12:25:19 PM
>> Subject: [Bioc-devel] disappearing .tex file when running R CM
Gabriel,
Thanks for the clarification. I was avoiding depending on CodeDepends
because I'm fairly certain that a BioC package can't depend on a package
that isn't in either CRAN or Bioconductor. Since you point out that the
librarySymbols code doesn't depend on any other part of the package, I
- Original Message -
> From: "Tim Triche, Jr."
> To: bioc-devel@r-project.org
> Sent: Monday, November 4, 2013 12:25:19 PM
> Subject: [Bioc-devel] disappearing .tex file when running R CMD Sweave on a
> new vignette
>
> I get a bizarre error when compiling a newly-added Methylumi
> v
I get a bizarre error when compiling a newly-added Methylumi vignette:
10 : echo keep.source term verbatim (label = sessioninfo,
methylumi450k.Rnw:136)
Error in driver$finish(drobj) :
the output file 'methylumi450k.tex' has disappeared
Calls: -> do.call -> ->
Execution halted
This is bizarre
Ryan,
I agree that in some sense it is a different problem, but my point is with
a different approach we can easily answer both. The code I posted returns a
named character vector of symbol names with package name being the name.
This makes it a trivial lookup to determine both a) what symbols ar
The code that I wrote intentionally avoids checking for package variables,
since I consider that a separate problem. Package variables can be provided
to the child by leading the package, whereas user-defined variables must be
serialized in the parent and sent to the child.
I think I could fairly
Weird, I guess it needs to be logged in or something. I don't know if the
issue is that its in a non-master branch or waht. The repo is fully public
and the forCRAN_0.3.5 in branch definitely exists on github.
I started chrome (where I'm not logged into github) and got the same 404
error but afte
The dynamic nature of R limits the extent of these checks. But as Ryan has
noted, a simple sanity check goes a long way. If what he has done could be
extended to the rest of the search path (people always forget to attach
packages), I think we've hit the 80% with 20%. Got a 404 on that URL btw.
Mi
Hey guys,
Here is code that I have written which resolves library names into a full
list of symbols:
https://github.com/duncantl/CodeDepends/blob/forCRAN_0.3.5/R/librarySymbols.RNote
this does not require that the packages actually be loaded at the time
of the check, and does not load them (or rat
You might want to consider using Recall() for recursion which should solve
this. Determining the required variables using heuristics as codetools will
probably lead to some confusion when using functions which include calls
to, e.g., with():
f = function() {
with(iris, Sepal.Length + Sepal.Width
Hi Michael,
Sure, I'll try to dig into it and construct a patch that adds this feature.
I stumbled upon this after converting data between the 'VCF' and
'VRanges' class. The primary use case I had in mind is having a more
efficient storing and processing for short InDels, or defining variants
Actually, the check that I proposed is only supposed to check for usage
of user-defined variables, not variables from packages. Truthfully,
though, I guess I'm not the right person to work on this, since in
practice I use forked processes for the vast majority of my inside-R
parallelization, so
This was a consideration. I guess I've never got much use out of them being
DNAStringSets, so I just went with the simple character vectors. It makes
sense to support DNAStringSet. I could imagine someone e.g. wanting to
represent mutations at the protein-level, and structural variants will
require
Hi,
Would it be reasonable to (optionally) allow storing the reference and
alternative alleles in the 'VRanges' class as a 'DNAStringSet'?
Currently, 'character' and 'Rle' are possible. Having a 'DNAStringSet'
would make it more consistent with the rest of the 'VariantAnnotation'
framework a
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