[Bioc-devel] VariantAnnotation: DNAStringSets for ref/alt alleles in 'VRanges' class
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 and make use of the efficient 'Biostrings' string handling infrastructure. Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] VariantAnnotation: DNAStringSets for ref/alt alleles in 'VRanges' class
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 more complexity, but DNA is by far the most common use case. Are you willing to submit this as a patch? Just out of curiosity, how are you using Biostrings in this case? On Mon, Nov 4, 2013 at 1:12 AM, Julian Gehring julian.gehr...@embl.dewrote: 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 and make use of the efficient 'Biostrings' string handling infrastructure. Best wishes Julian ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?
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 I never have to worry about things being undefined
in the forked subprocess. Therefore I cant really dogfood any of the
stuff that might be implemented as a result of this thread.
-Ryan
On Mon Nov 4 03:48:23 2013, Michael Lawrence wrote:
So what is the best practice for ensuring that something is actually
visible to the worker? If the worker needs functionality from a
package, should the namespace be explicitly referenced via ::? Lazy
users might want to include library() calls in the worker function.
This proposed check will then throw an exception. Probably a good
thing, but is there a way for a user to declare imported namespaces?
I know that BatchJobs allows for passing a list of packages to be
loaded via library() on the worker. That is leveraging the search path
to make sure everything is visible and is a reasonable compromise (::
is always an option). We could essentially reimplement the search path
if we wanted isolation, but the worker is already isolated. Anyway,
somehow those types of declarations should be taken into account.
Moving back to the general discussion, for complex operations, it's
easiest to have the worker in a package. In that case, the worker will
likely rely on other functions, and the cleanest way to get those
functions to the worker is to have them installed as a package. At
least with BatchJobs, when the worker is inside a package namespace,
that namespace is automatically loaded (but not attached), so all
functions are automatically visible, without any extra work by me.
Michael
On Sun, Nov 3, 2013 at 10:46 PM, Ryan r...@thompsonclan.org
mailto:r...@thompsonclan.org wrote:
Ok, here is my attempt at a function to get the list of
user-defined free variables that a function refers to:
https://gist.github.com/__DarwinAwardWinner/7298557
https://gist.github.com/DarwinAwardWinner/7298557
Is uses codetools, so it is subject to the limitations of that
package, but for simple examples, it successfully detects when a
function refers to something in the global env.
On Sun Nov 3 21:14:29 2013, Gabriel Becker wrote:
Ryan (et al),
FYI:
f
function() {
x = rnorm(x)
x
}
findGlobals(f)
[1] = { rnorm
x should be in the list of globals but it isn't.
~G
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] codetools_0.2-8
On Sun, Nov 3, 2013 at 5:37 PM, Ryan r...@thompsonclan.org
mailto:r...@thompsonclan.org
mailto:r...@thompsonclan.org mailto:r...@thompsonclan.org
wrote:
Looking at the codetools package, I think findGlobals is
basically exactly what we want here, right? As you say,
there are
necessarily limitations due to R being a dynamic language,
but the
goal is to catch common errors, not stop people from
tricking the
check.
I think I'll try to code something up soon.
-Ryan
On 11/3/13, 5:10 PM, Gabriel Becker wrote:
Henrik,
See https://github.com/duncantl/__CodeDepends
https://github.com/duncantl/CodeDepends (as used by used by
https://github.com/gmbecker/__RCacheSuite
https://github.com/gmbecker/RCacheSuite). It will identify
necessarily defined symbols (input variables) for code
that is
not doing certain tricks (eg get(), mixing data.frame
columns and
gobal variables in formulas, etc ).
Tierney's codetools package also does things along
these lines
but there are some situations where it has trouble. I
can give
more detail if desired.
~G
On Sun, Nov 3, 2013 at 3:04 PM, Ryan
r...@thompsonclan.org mailto:r...@thompsonclan.org
mailto:r...@thompsonclan.org
mailto:r...@thompsonclan.org wrote:
Another potential easy
Re: [Bioc-devel] VariantAnnotation: DNAStringSets for ref/alt alleles in 'VRanges' class
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 by ref/alt alleles also with respect to the sequence context. Best wishes Julian On 11/04/2013 12:56 PM, Michael Lawrence wrote: 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 more complexity, but DNA is by far the most common use case. Are you willing to submit this as a patch? Just out of curiosity, how are you using Biostrings in this case? On Mon, Nov 4, 2013 at 1:12 AM, Julian Gehring julian.gehr...@embl.de mailto:julian.gehr...@embl.de wrote: 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 and make use of the efficient 'Biostrings' string handling infrastructure. Best wishes Julian _ Bioc-devel@r-project.org mailto:Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?
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 after navigating to the file by going to the repo and changing
the branch and navigating to the file, it now works even when i quit chrome
and restart it. I don't know if it needed me to do that or if there was an
intermittent problem that is now fixed.
Anyway, here is the raw code, the link for which seems to work (in a
browser where I'm not logged into github). If it still doesn't I can just
attach the file here if you want. It doesn't rely on any of the rest of the
CodeDepends machinery.
https://raw.github.com/duncantl/CodeDepends/forCRAN_0.3.5/R/librarySymbols.R
~G
On Mon, Nov 4, 2013 at 11:34 AM, Michael Lawrence lawrence.mich...@gene.com
wrote:
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.
Michael
On Mon, Nov 4, 2013 at 11:05 AM, Gabriel Becker gmbec...@ucdavis.eduwrote:
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 rather, it loads them but does
not
attach them, so no searchpath muddying occurs). You do need a list of
packages to check though (it adds the base ones automatically). It handles
dependency and could be easily extended to handle suggests as well I
think.
When CodeDepends gets pushed to cran (not my call and not high on my
priority list to push for currently) it will actually do exactly what you
want. (the forCRAN_0.3.5 branch already does and I believe it is
documented, so you could use devtools to install it now).
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?
~G
On Mon, Nov 4, 2013 at 7:29 AM, Michel Lang michell...@gmail.com wrote:
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)
}
codetools:::findGlobals(f)
I would suggest to write up some documentation on what the function's
environment contains and how to to define variables accordingly - or
why it
can generally be considered a good idea to pass everything essential as
an
argument. Nevertheless a bpExport function would be a good addition
for
some rare corner cases in my opinion.
Michel
2013/11/3 Henrik Bengtsson h...@biostat.ucsf.edu
Hi,
in BiocParallel, is there a suggested (or planned) best standards for
making *locally* assigned variables (e.g. functions) available to the
applied function when it runs in a separate R process (which will be
the most common use case)? I understand that avoid local variables
should be avoided and it's preferred to put as mush as possible in
packages, but that's not always possible or very convenient.
EXAMPLE:
library('BiocParallel')
library('BatchJobs')
# Here I pick a recursive functions to make the problem a bit harder,
i.e.
# the function needs to call itself (itself = see below)
fib - function(n=0) {
if (n 0) stop(Invalid 'n': , n)
if (n == 0 || n == 1) return(1)
fib(n-2) + fib(n-1)
}
# Executing in the current R session
cluster.functions - makeClusterFunctionsInteractive()
bpParams - BatchJobsParam(cluster.functions=cluster.functions)
register(bpParams)
values - bplapply(0:9, FUN=fib)
## SubmitJobs |++| 100% (00:00:00)
## Waiting [S:0 R:0 D:10 E:0] |+++| 100% (00:00:00)
# Executing in a separate R process, where fib() is not defined
# (not specific to BiocParallel)
cluster.functions - makeClusterFunctionsLocal()
bpParams - BatchJobsParam(cluster.functions=cluster.functions)
register(bpParams)
values - bplapply(0:9, FUN=fib)
## SubmitJobs |++| 100% (00:00:00)
## Waiting [S:0 R:0 D:10 E:0] |+++| 100% (00:00:00)
Error in LastError$store(results = results, is.error = !ok,
throw.error =
TRUE)
:
Errors occurred during execution. First error message:
Error in
Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?
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 easily adapt the same code to return a list of all
packages that a function depends on.
-Ryan
On Nov 4, 2013 11:35 AM, Michael Lawrence lawrence.mich...@gene.com
wrote:
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.
Michael
On Mon, Nov 4, 2013 at 11:05 AM, Gabriel Becker gmbec...@ucdavis.edu
wrote:
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 rather, it loads them but does
not
attach them, so no searchpath muddying occurs). You do need a list of
packages to check though (it adds the base ones automatically). It
handles
dependency and could be easily extended to handle suggests as well I
think.
When CodeDepends gets pushed to cran (not my call and not high on my
priority list to push for currently) it will actually do exactly what you
want. (the forCRAN_0.3.5 branch already does and I believe it is
documented, so you could use devtools to install it now).
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?
~G
On Mon, Nov 4, 2013 at 7:29 AM, Michel Lang michell...@gmail.com
wrote:
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)
}
codetools:::findGlobals(f)
I would suggest to write up some documentation on what the function's
environment contains and how to to define variables accordingly - or
why
it
can generally be considered a good idea to pass everything essential as
an
argument. Nevertheless a bpExport function would be a good addition
for
some rare corner cases in my opinion.
Michel
2013/11/3 Henrik Bengtsson h...@biostat.ucsf.edu
Hi,
in BiocParallel, is there a suggested (or planned) best standards for
making *locally* assigned variables (e.g. functions) available to the
applied function when it runs in a separate R process (which will be
the most common use case)? I understand that avoid local variables
should be avoided and it's preferred to put as mush as possible in
packages, but that's not always possible or very convenient.
EXAMPLE:
library('BiocParallel')
library('BatchJobs')
# Here I pick a recursive functions to make the problem a bit harder,
i.e.
# the function needs to call itself (itself = see below)
fib - function(n=0) {
if (n 0) stop(Invalid 'n': , n)
if (n == 0 || n == 1) return(1)
fib(n-2) + fib(n-1)
}
# Executing in the current R session
cluster.functions - makeClusterFunctionsInteractive()
bpParams - BatchJobsParam(cluster.functions=cluster.functions)
register(bpParams)
values - bplapply(0:9, FUN=fib)
## SubmitJobs |++| 100% (00:00:00)
## Waiting [S:0 R:0 D:10 E:0] |+++| 100% (00:00:00)
# Executing in a separate R process, where fib() is not defined
# (not specific to BiocParallel)
cluster.functions - makeClusterFunctionsLocal()
bpParams - BatchJobsParam(cluster.functions=cluster.functions)
register(bpParams)
values - bplapply(0:9, FUN=fib)
## SubmitJobs |++| 100% (00:00:00)
## Waiting [S:0 R:0 D:10 E:0] |+++| 100% (00:00:00)
Error in LastError$store(results = results, is.error = !ok,
throw.error =
TRUE)
:
Errors occurred during execution. First error message:
Error in FUN(...): could not find function fib
[...]
# The following illustrates that the solution is not always
straightforward.
# (not specific to BiocParallel; must have been discussed previously)
values - bplapply(0:9, FUN=function(n, fib) {
fib(n)
}, fib=fib)
Error in LastError$store(results = results, is.error = !ok,
throw.error = TRUE) :
Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?
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 aren't
available in any of the packages and b) what packages provide the remaining
required symbols. No extra work required.
You do have to give it a list of packages to check, but it is easy to write
a wrapper that automatically passes it all currently attached packages if
desired (a combination of search() and gsub() would be a quick and dirty
way to do this).
All that said, I'm simply trying to help. If you guys don't want to use my
code/approach that is your perogative as I'm not currently working on
BiocParallel myself.
~G
On Mon, Nov 4, 2013 at 11:54 AM, Ryan Thompson r...@thompsonclan.org wrote:
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 easily adapt the same code to return a list of all
packages that a function depends on.
-Ryan
On Nov 4, 2013 11:35 AM, Michael Lawrence lawrence.mich...@gene.com
wrote:
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.
Michael
On Mon, Nov 4, 2013 at 11:05 AM, Gabriel Becker gmbec...@ucdavis.edu
wrote:
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 rather, it loads them but does
not
attach them, so no searchpath muddying occurs). You do need a list of
packages to check though (it adds the base ones automatically). It
handles
dependency and could be easily extended to handle suggests as well I
think.
When CodeDepends gets pushed to cran (not my call and not high on my
priority list to push for currently) it will actually do exactly what
you
want. (the forCRAN_0.3.5 branch already does and I believe it is
documented, so you could use devtools to install it now).
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?
~G
On Mon, Nov 4, 2013 at 7:29 AM, Michel Lang michell...@gmail.com
wrote:
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)
}
codetools:::findGlobals(f)
I would suggest to write up some documentation on what the function's
environment contains and how to to define variables accordingly - or
why
it
can generally be considered a good idea to pass everything essential
as
an
argument. Nevertheless a bpExport function would be a good addition
for
some rare corner cases in my opinion.
Michel
2013/11/3 Henrik Bengtsson h...@biostat.ucsf.edu
Hi,
in BiocParallel, is there a suggested (or planned) best standards
for
making *locally* assigned variables (e.g. functions) available to
the
applied function when it runs in a separate R process (which will be
the most common use case)? I understand that avoid local variables
should be avoided and it's preferred to put as mush as possible in
packages, but that's not always possible or very convenient.
EXAMPLE:
library('BiocParallel')
library('BatchJobs')
# Here I pick a recursive functions to make the problem a bit
harder,
i.e.
# the function needs to call itself (itself = see below)
fib - function(n=0) {
if (n 0) stop(Invalid 'n': , n)
if (n == 0 || n == 1) return(1)
fib(n-2) + fib(n-1)
}
# Executing in the current R session
cluster.functions - makeClusterFunctionsInteractive()
bpParams - BatchJobsParam(cluster.functions=cluster.functions)
register(bpParams)
values - bplapply(0:9, FUN=fib)
## SubmitJobs |++| 100% (00:00:00)
## Waiting [S:0 R:0 D:10 E:0] |+++| 100% (00:00:00)
# Executing in a separate R process, where fib() is
Re: [Bioc-devel] disappearing .tex file when running R CMD Sweave on a new vignette
On Mon, Nov 4, 2013 at 12:46 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
- Original Message -
From: Tim Triche, Jr. tim.tri...@gmail.com
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
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: Anonymous - do.call - Anonymous - Anonymous
Execution halted
This is bizarre because 1) the file is still there, and 2) all the
heavy
lifting is done.
sessionInfo(), etc. is included properly and the vignette concludes
with
\end{document}, but nothing I do seems to resolve this driver error.
Any suggestions would be most appreciated.
Probably has to do with calling setwd() in the vignette? Maybe you need an
on.exit() that restores the original directory. My guess is that you changed
directory and then R can't see the tex file because it's in a different
directory. See
http://stackoverflow.com/questions/12162092/r-sweave-output-error
tools::buildVignettes(), which is used by 'R CMD build', tries to
protect against this by always resetting the working directory after
weave:ing and tangle:ing a vignette, cf.
http://svn.r-project.org/R/trunk/src/library/tools/R/Vignettes.R.
tools::buildVignette() [no plural 's'], which is used by 'R CMD
Sweave' (which is what Tim uses), should also do this, but looking at
the code, this may only work properly if argument 'dir' is an absolute
path, which it may not be the case (not sure). I've just submitted a
bug report PR#15530
[https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15530] with a
patch on this.
There may also be related issues in the utils::Sweave drivers (looks
like code running during garbage collection) - I'll let someone else
look into that. But, undoing setwd():s in the vignette should solve
this, iff that's what behind this in the first place.
/Henrik
Dan
Thanks,
--t
*He that would live in peace and at ease, *
*Must not speak all he knows, nor judge all he sees.*
Benjamin Franklin, Poor Richard's
Almanackhttp://archive.org/details/poorrichardsalma00franrich
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Re: [Bioc-devel] BiocParallel: Best standards for passing locally assigned variables/functions, e.g. a bpExport()?
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 different issue. We want to detect when a function depends on variables outside that function in the user's workspace, or variables defined in a pacakge that the user has loaded. I think we can assume that R child processes will be of the same version with the same set of installed packages, so package-defined variables will not have different values in child processes. For user variables, I think the goal should be to prevent (or at least highly discourage) dependencies on them entirely, so I don't think it matters what their value may be in the child. I realize this is somewhat counter to the question that started this thread, which was about exporting variables to the children, but I think it is the most straightforward approach. As I believe someone noted earlier in the thread, Henrik's original problem of a recursive function is properly solved by using the Recall function. -Ryan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Rd] R 3.1.0 and C++11
Le 03/11/2013 22:45, Michael Kane a écrit : I'd like to echo Whit's sentiment and hopefully warm up this thread. C++11's new features and functionality give R users low-level tools (like threads, mutexes, futures, date-time, and atomic types) that work across platforms and wouldn't require other external libraries like boost. +1 portability is really important. One of the points is that by giving means to assume a certain standard, we can write more portable code. There has been lots of discussion about Boost.Thread, etc ... no need for that if you have C++11. Romain, will you be taking pull requests? Yes. Definitely. I will carefully review them. Can give you write access too. I'm getting a good feel of what C++11 brings while developping Rcpp11. But I think it makes a lot of sense to write such an article with other people as well. Romain -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] ggplot2: Add '+' operator for aes (uneval) objects
Dear all,
Is there a reason, why there is no +-operator for aes (i.e. uneval) objects (as
there is for themes and gg objects)? I had a couple of cases where such an
operator would be useful, for instance to combine the result of aes and
aes_string in functions. Any flaws with the following proposition:
`+.uneval` - function(e1, e2) {
dup - names(e1) %in% names(e2)
if (any(dup)) {
duplist - paste(sQuote(names(e1)[dup]), collapse = , )
msg - sprintf(ngettext(length(dup),
element %s occurs in both summands - second one gets
precedence,
elements %s occur in both summands - second one gets
precedence),
duplist)
warning(msg, domain = NA)
}
res - c(e1[!dup], e2)
class(res) - uneval
res
}
Any thoughts on that?
Kind Regards,
Thorn Thaler
NRC Lausanne
Applied Mathematics
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Re: [Rd] ggplot2: Add '+' operator for aes (uneval) objects
This seems like a conversation to have with the package's maintainer
(Hadley), as suggested by the posting guide:
http://www.r-project.org/posting-guide.html
If the question relates to a contributed package , e.g., one downloaded
from CRAN, try contacting the package maintainer first.
and not R-devel.
Regards,
Brian
On 11/04/2013 03:54 AM, Thaler,Thorn,LAUSANNE,Applied Mathematics wrote:
Dear all,
Is there a reason, why there is no +-operator for aes (i.e. uneval) objects (as
there is for themes and gg objects)? I had a couple of cases where such an
operator would be useful, for instance to combine the result of aes and
aes_string in functions. Any flaws with the following proposition:
`+.uneval` - function(e1, e2) {
dup - names(e1) %in% names(e2)
if (any(dup)) {
duplist - paste(sQuote(names(e1)[dup]), collapse = , )
msg - sprintf(ngettext(length(dup),
element %s occurs in both summands - second one gets
precedence,
elements %s occur in both summands - second one gets
precedence),
duplist)
warning(msg, domain = NA)
}
res - c(e1[!dup], e2)
class(res) - uneval
res
}
Any thoughts on that?
Kind Regards,
Thorn Thaler
NRC Lausanne
Applied Mathematics
__
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[Rd] Determining files opened by an R session
I'm using R in a regulated environment and one of the requirements is to be able to trace how a result is arrived at. I would like to be able to determine which files are opened in read or write mode by an R session, for example when a program uses source, sink, file, open, read.table, write.table or any of the other functions which can be used to read or write files. I'm also interested in output to graphics devices. I've looked in the documentation but only found information relating to profiling. Looking through the source code it seems that much file i/o is done via the C functions *_open in main/connections.c but don't see anything there that looks like logging. Could someone let me know if it is possible to log which files are opened? Regards, Martin Gregory __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Determining files opened by an R session
I am not sure R can do what you want (others may), but have a look at ?history for R's history mechanism, which keeps a record of all commands that you have entered and so might satisfy your needs. Note that there are various 3rd party GUI's/IDE's (e.g. RStudio) that might be more to your liking. The CRAN web site should contain information on at least some of them. Cheers, Bert On Mon, Nov 4, 2013 at 1:32 PM, Martin Gregory grego...@t-online.de wrote: I'm using R in a regulated environment and one of the requirements is to be able to trace how a result is arrived at. I would like to be able to determine which files are opened in read or write mode by an R session, for example when a program uses source, sink, file, open, read.table, write.table or any of the other functions which can be used to read or write files. I'm also interested in output to graphics devices. I've looked in the documentation but only found information relating to profiling. Looking through the source code it seems that much file i/o is done via the C functions *_open in main/connections.c but don't see anything there that looks like logging. Could someone let me know if it is possible to log which files are opened? Regards, Martin Gregory __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Determining files opened by an R session
If you have the code in a parseable form then CodeDepends will try to do
this:
library(CodeDepends)
code
[1] w = rnorm(10); t = read.csv('mycsv.csv'); lm(y~x, data = t)
scr = readScript(dummy, type = R, txt = code)
inp = getInputs(scr)
length(inp)
[1] 3
inp[[2]]@files
[1] mycsv.csv
The package is not currently on CRAN, but is available from the author
Duncan Temple Lang's github account:
https://github.com/duncantl/CodeDepends
There is also work going on for a more comprehensive solution:
https://github.com/karthikram/rProvenance
HTH,
~G
On Mon, Nov 4, 2013 at 1:52 PM, Bert Gunter gunter.ber...@gene.com wrote:
I am not sure R can do what you want (others may), but have a look at
?history
for R's history mechanism, which keeps a record of all commands that
you have entered and so might satisfy your needs.
Note that there are various 3rd party GUI's/IDE's (e.g. RStudio) that
might be more to your liking. The CRAN web site should contain
information on at least some of them.
Cheers,
Bert
On Mon, Nov 4, 2013 at 1:32 PM, Martin Gregory grego...@t-online.de
wrote:
I'm using R in a regulated environment and one of the requirements is to
be
able to trace how a result is arrived at. I would like to be able to
determine which files are opened in read or write mode by an R session,
for
example when a program uses source, sink, file, open, read.table,
write.table or any of the other functions which can be used to read or
write
files. I'm also interested in output to graphics devices.
I've looked in the documentation but only found information relating to
profiling. Looking through the source code it seems that much file i/o is
done via the C functions *_open in main/connections.c but don't see
anything
there that looks like logging.
Could someone let me know if it is possible to log which files are
opened?
Regards,
Martin Gregory
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis
[[alternative HTML version deleted]]
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Re: [Rd] Determining files opened by an R session
Most operating systems have tools which allow you to audit the resources used by a running process, for example the 'lsof' (list open files) command on Unix and MacOS X. Or, for more complex dynamic tracing, the DTrace framework again on MacOS X or BSD Unix. Not sure what the Windows equivalent would be, or what platform you are using, but given the number of ways that code in packages and such may be accessing files in C code possibly based on environment variables or other configuration parameters, I would want to lean heavily on the operating systems tools for things like this rather than rely on parsing your R code looking for specific file access. - Murray On Mon, Nov 4, 2013 at 1:32 PM, Martin Gregory grego...@t-online.de wrote: I'm using R in a regulated environment and one of the requirements is to be able to trace how a result is arrived at. I would like to be able to determine which files are opened in read or write mode by an R session, for example when a program uses source, sink, file, open, read.table, write.table or any of the other functions which can be used to read or write files. I'm also interested in output to graphics devices. I've looked in the documentation but only found information relating to profiling. Looking through the source code it seems that much file i/o is done via the C functions *_open in main/connections.c but don't see anything there that looks like logging. Could someone let me know if it is possible to log which files are opened? Regards, Martin Gregory __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Determining files opened by an R session
On 4 November 2013 at 14:31, Murray Stokely wrote: | Most operating systems have tools which allow you to audit the resources | used by a running process, for example the 'lsof' (list open files) command | on Unix and MacOS X. Or, for more complex dynamic tracing, the DTrace | framework again on MacOS X or BSD Unix. And strace is standard on Linux. | Not sure what the Windows equivalent would be, or what platform you are | using, but given the number of ways that code in packages and such may be | accessing files in C code possibly based on environment variables or other | configuration parameters, I would want to lean heavily on the operating | systems tools for things like this rather than rely on parsing your R code | looking for specific file access. Yep. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
