[Rd] 'library' or 'require' call to package which was already attached by Depends
Hello, I'm receiving the following NOTE during recent checks of the rmgarch package: 'library' or 'require' call to 'rugarch' which was already attached by Depends. which I traced to the recent changes in R 3.02 Utilities: • packages which are used in ‘library()’ or ‘requires()’ calls in the R code but were already put on the search path _via_ ‘Depends’. However, the code uses the 'library()' call (of a package which is in 'Depends') inside the 'parallel::clusterEvalQ' function which is given as an option to users for running certain routines in parallel. Would it be possible to make allowances for this instance of the use of 'library()' or suggest a way to call 'clusterEvalQ' with 'library' without triggering the NOTE? Thanks, Alexios __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Why does duplicate() make deep copies?
On Sep 5, 2013, at 12:31 AM, Peter Meilstrup wrote:
Some experimentation with the below function should convince you that the
runtime of the bit inside sys.time is proportional to size*number*times. I
think it should only be proportional to number*times. The function is only
manipulating a list of references to vectors and not trying to make changes
to the vectors themselves.
overcopying - function(size, number, times) {
#Make a list of NUMBER vectors of SIZE, then reorder the list. The
#vectors themselves are never touched, only their references are
#moved around. If R implements copy on write correctly the
#elapsed time should be ~number*times.
L - replicate(number, list(vector(numeric, size)), simplify=FALSE)
system.time(for (i in 1:times) {
L[sample(number)] - L
})
}
I see that duplicate.c makes a recursive copy of each element when it
encounters a VECSXP or a LISTSXP, which it seems there should be no need
for (it should be sufficient to make a shallow copy and ensure NAMED is set
on the elements.)
Why is R making apparently unnecessary deep copies?
Because ref counting is not recursive. Changing that breaks a quite a few
packages that abuse the fact that copies are currently deep. Main problem with
that is that it's pretty much impossible to detect it ahead of time. That said,
there are efforts underway by Luke Tierney and Michael Lawrence to see how far
we can go without breaking everything.
Cheers,
Simon
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Re: [Rd] libR.so: cannot open shared object file
First of all, thanks for your help. I did all the things you told me. I was able to load the library, but then Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/lustre/work/gjona2/Wrap/BayesWrap/libs/BayesWrap.so': libR.so: cannot open shared object file: No such file or directory In addition: Warning message: package 'BayesWrap' was built under R version 2.15.2 Error: package/namespace load failed for 'BayesWrap' Execution halted what does it means? G.M. Il 04/09/13 22:42, Prof Brian Ripley ha scritto: On 04/09/2013 19:58, Geoff Jentry wrote: Can you add some details? Suppose i have the package Model.tar.gz and my writable are is in user/area, what i have to do next to install the package? What I was picturing was something like this (forgive me if syntax isn't 100%): mkdir user/area/myRLib R CMD INSTALL --library=user/area/myRLib Model.tar.gz and then in R: library(Model, lib.loc=user/area/myRLib) Note though Brian Ripley's response to me where he indicates that this is handled automatically. Yes, install.packages(Model.tar.gz) should suffice. -J __ 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
Re: [Rd] Comments requested on changedFiles function
On 13-09-04 11:36 PM, Scott Kostyshak wrote:
On Wed, Sep 4, 2013 at 1:53 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
In a number of places internal to R, we need to know which files have
changed (e.g. after building a vignette). I've just written a general
purpose function changedFiles that I'll probably commit to R-devel.
Comments on the design (or bug reports) would be appreciated.
The source for the function and the Rd page for it are inline below.
This looks like a useful function. Thanks for writing it. I have only
one (picky) comment below.
- changedFiles.R:
changedFiles - function(snapshot, timestamp = tempfile(timestamp),
file.info = NULL,
md5sum = FALSE, full.names = FALSE, ...) {
dosnapshot - function(args) {
fullnames - do.call(list.files, c(full.names = TRUE, args))
names - do.call(list.files, c(full.names = full.names, args))
if (isTRUE(file.info) || (is.character(file.info)
length(file.info))) {
info - file.info(fullnames)
rownames(info) - names
if (isTRUE(file.info))
file.info - c(size, isdir, mode, mtime)
} else
info - data.frame(row.names=names)
if (md5sum)
info - data.frame(info, md5sum = tools::md5sum(fullnames))
list(info = info, timestamp = timestamp, file.info = file.info,
md5sum = md5sum, full.names = full.names, args = args)
}
if (missing(snapshot) || !inherits(snapshot, changedFilesSnapshot)) {
if (length(timestamp) == 1)
file.create(timestamp)
if (missing(snapshot)) snapshot - .
pre - dosnapshot(list(path = snapshot, ...))
pre$pre - pre$info
pre$info - NULL
pre$wd - getwd()
class(pre) - changedFilesSnapshot
return(pre)
}
if (missing(timestamp)) timestamp - snapshot$timestamp
if (missing(file.info) || isTRUE(file.info)) file.info -
snapshot$file.info
if (identical(file.info, FALSE)) file.info - NULL
if (missing(md5sum))md5sum - snapshot$md5sum
if (missing(full.names)) full.names - snapshot$full.names
pre - snapshot$pre
savewd - getwd()
on.exit(setwd(savewd))
setwd(snapshot$wd)
args - snapshot$args
newargs - list(...)
args[names(newargs)] - newargs
post - dosnapshot(args)$info
prenames - rownames(pre)
postnames - rownames(post)
added - setdiff(postnames, prenames)
deleted - setdiff(prenames, postnames)
common - intersect(prenames, postnames)
if (length(file.info)) {
preinfo - pre[common, file.info]
postinfo - post[common, file.info]
changes - preinfo != postinfo
}
else changes - matrix(logical(0), nrow = length(common), ncol = 0,
dimnames = list(common, character(0)))
if (length(timestamp))
changes - cbind(changes, Newer = file_test(-nt, common,
timestamp))
if (md5sum) {
premd5 - pre[common, md5sum]
postmd5 - post[common, md5sum]
changes - cbind(changes, md5sum = premd5 != postmd5)
}
changes1 - changes[rowSums(changes, na.rm = TRUE) 0, , drop = FALSE]
changed - rownames(changes1)
structure(list(added = added, deleted = deleted, changed = changed,
unchanged = setdiff(common, changed), changes = changes), class =
changedFiles)
}
print.changedFilesSnapshot - function(x, ...) {
cat(changedFiles snapshot:\n timestamp = \, x$timestamp, \\n
file.info = ,
if (length(x$file.info)) paste(paste0('', x$file.info, ''),
collapse=,),
\n md5sum = , x$md5sum, \n args = , deparse(x$args, control =
NULL), \n, sep=)
x
}
print.changedFiles - function(x, ...) {
if (length(x$added)) cat(Files added:\n, paste0( , x$added,
collapse=\n), \n, sep=)
if (length(x$deleted)) cat(Files deleted:\n, paste0( , x$deleted,
collapse=\n), \n, sep=)
changes - x$changes
changes - changes[rowSums(changes, na.rm = TRUE) 0, , drop=FALSE]
changes - changes[, colSums(changes, na.rm = TRUE) 0, drop=FALSE]
if (nrow(changes)) {
cat(Files changed:\n)
print(changes)
}
x
}
--
--- changedFiles.Rd:
\name{changedFiles}
\alias{changedFiles}
\alias{print.changedFiles}
\alias{print.changedFilesSnapshot}
\title{
Detect which files have changed
}
\description{
On the first call, \code{changedFiles} takes a snapshot of a selection of
files. In subsequent
calls, it takes another snapshot, and returns an object containing data on
the
differences between the two snapshots. The snapshots need not be the same
directory;
this could be used to compare two directories.
}
\usage{
changedFiles(snapshot, timestamp = tempfile(timestamp), file.info = NULL,
md5sum = FALSE, full.names = FALSE, ...)
}
\arguments{
\item{snapshot}{
The path to record, or a previous snapshot. See the Details.
}
\item{timestamp}{
The name of
Re: [Rd] ASCII art in function documentation?
On 09/05/2013 09:10 AM, Rainer M Krug wrote:
want to include ascii art in a function documentation which should
look as follow:
,
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
to keep the monospaced font even in html, I decided to use \code{}:
Wouldn't it be best to use the relatively new \figure markup with
alternate text?
http://cran.r-project.org/doc/manuals/R-exts.html#Figures
Regards,
Brian
--
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http://braverock.com/brian/
Ph: 773-459-4973
IM: bgpbraverock
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Re: [Rd] ASCII art in function documentation - difference html and text output?
Found a solution.
putting \cr at the end of each line inserts a carriage return, but no
additional empty line. So
,
| \code{+--+--+--+} \cr
| \code{| 1/16 | 1/16 | 1/16 |} \cr
| \code{+--+--+--+} \cr
| \code{| 1/16 | 8/16 | 1/16 |} \cr
| \code{+--+--+--+} \cr
| \code{| 1/16 | 1/16 | 1/16 |} \cr
| \code{+--+--+--+} \cr
`
produces the desired output.
But interestingly,
,
| \code{
| +--+--+--+ \cr
| | 1/16 | 1/16 | 1/16 | \cr
| +--+--+--+ \cr
| | 1/16 | 8/16 | 1/16 | \cr
| +--+--+--+ \cr
| | 1/16 | 1/16 | 1/16 | \cr
| +--+--+--+ \cr
| }
`
produces the correct output in html,
,
| /p
| pcode +--+--+--+ br | 1/16 | 1/16 | 1/16 |
| br +--+--+--+ br | 1/16 | 8/16 | 1/16 | br
| +--+--+--+ br | 1/16 | 1/16 | 1/16 | br
| +--+--+--+ br /code
| /p
`
but
,
| ' +--+--+--+
| | 1/16 | 1/16 | 1/16 |
|
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
in the text version - is there a bug somewhere?
Thanks,
Rainer
Rainer M Krug rai...@krugs.de writes:
Sarah Goslee sarah.gos...@gmail.com writes:
Untested, but did you try wrapping the whole thing in a single code block:
Nope - also in one line.
Rainer
\code{
all
the
things
}
Sarah
On Thu, Sep 5, 2013 at 10:10 AM, Rainer M Krug rai...@krugs.de wrote:
Hi
I want to include ascii art in a function documentation which should
look as follow:
,
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
to keep the monospaced font even in html, I decided to use \code{}:
,
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 8/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
`
But the result was an empty line between each text:
,
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 8/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
`
and when no empty lines were included obviously put everything behind
each other.
My question:
Is there a way that I can achieve the ASCII art as shown above? Is there
a way of having a \linebreak which does not insert a new line?
Thanks,
Rainer
--
#secure method=pgpmime mode=sign
#secure method=pgpmime mode=sign
--
Rainer M. Krug
email: RMKrugatgmaildotcom
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Re: [Rd] ASCII art in function documentation?
Now that I'm at the computer with my R code, I've used both
\preformatted{}
and \cr to force line breaks.
Some combination of those may work for you.
Sarah
On Thu, Sep 5, 2013 at 11:10 AM, Rainer M Krug rai...@krugs.de wrote:
Sarah Goslee sarah.gos...@gmail.com writes:
Untested, but did you try wrapping the whole thing in a single code block:
Nope - also in one line.
Rainer
\code{
all
the
things
}
Sarah
On Thu, Sep 5, 2013 at 10:10 AM, Rainer M Krug rai...@krugs.de wrote:
Hi
I want to include ascii art in a function documentation which should
look as follow:
,
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
to keep the monospaced font even in html, I decided to use \code{}:
,
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 8/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
`
But the result was an empty line between each text:
,
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 8/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
`
and when no empty lines were included obviously put everything behind
each other.
My question:
Is there a way that I can achieve the ASCII art as shown above? Is there
a way of having a \linebreak which does not insert a new line?
Thanks,
Rainer
--
#secure method=pgpmime mode=sign
--
Rainer M. Krug
email: RMKrugatgmaildotcom
--
Sarah Goslee
http://www.functionaldiversity.org
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Re: [Rd] Comments requested on changedFiles function
On 05/09/2013 12:32 PM, Dr Gregory Jefferis wrote:
Dear Duncan,
This certainly looks useful. Might you consider adding the ability to
supply an alternative digest function? Details below.
Thanks, that's a good idea.
Duncan Murdoch
I often use a homemade make type function which starts by looking at
modification times e.g. in a private package
https://github.com/jefferis/nat.utils/blob/master/R/make.r
For some of my work, I use hash functions. However because I typically
work with many large files I often use a special digest process e.g.
using the crc checksum embedded in a gzip file directly or hashing only
the part of a large file that is (almost) certain to change.
Perhaps (code unchecked) along the lines of:
changedFiles - function(snapshot, timestamp = tempfile(timestamp),
file.info = NULL,
digest = FALSE, digestfun=NULL, full.names = FALSE, ...)
if(digest){
if(is.null(digestfun)) digestfun=tools::md5sum
else digestfun=match.fun(digestfun)
info - data.frame(info, digest = digestfun(fullnames))
}
etc
OR alternatively using only one argument:
changedFiles - function(snapshot, timestamp = tempfile(timestamp),
file.info = NULL,
digest = FALSE, full.names = FALSE, ...)
if(is.logical(digest)){
if(digest) digestfun=tools::md5sum
} else {
# Assume that digest specifies a function that we want to use
digestfun=match.fun(digest)
digest=TRUE
}
if(digest)
info - data.frame(info, digest = digestfun(fullnames))
etc
Many thanks,
Greg.
On 4 Sep 2013, at 18:53, Duncan Murdoch wrote:
In a number of places internal to R, we need to know which files have
changed (e.g. after building a vignette). I've just written a general
purpose function changedFiles that I'll probably commit to R-devel.
Comments on the design (or bug reports) would be appreciated.
The source for the function and the Rd page for it are inline below.
- changedFiles.R:
changedFiles - function(snapshot, timestamp = tempfile(timestamp),
file.info = NULL,
md5sum = FALSE, full.names = FALSE, ...) {
dosnapshot - function(args) {
fullnames - do.call(list.files, c(full.names = TRUE, args))
names - do.call(list.files, c(full.names = full.names, args))
if (isTRUE(file.info) || (is.character(file.info)
length(file.info))) {
info - file.info(fullnames)
rownames(info) - names
if (isTRUE(file.info))
file.info - c(size, isdir, mode, mtime)
} else
info - data.frame(row.names=names)
if (md5sum)
info - data.frame(info, md5sum = tools::md5sum(fullnames))
list(info = info, timestamp = timestamp, file.info = file.info,
md5sum = md5sum, full.names = full.names, args = args)
--
Gregory Jefferis, PhD Tel: 01223 267048
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK
http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://flybrain.stanford.edu
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[Rd] ASCII art in function documentation?
Hi
I want to include ascii art in a function documentation which should
look as follow:
,
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
to keep the monospaced font even in html, I decided to use \code{}:
,
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 8/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
`
But the result was an empty line between each text:
,
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 8/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
`
and when no empty lines were included obviously put everything behind
each other.
My question:
Is there a way that I can achieve the ASCII art as shown above? Is there
a way of having a \linebreak which does not insert a new line?
Thanks,
Rainer
--
Rainer M. Krug
email: RMKrugatgmaildotcom
__
R-devel@r-project.org mailing list
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Re: [Rd] ASCII art in function documentation?
Untested, but did you try wrapping the whole thing in a single code block:
\code{
all
the
things
}
Sarah
On Thu, Sep 5, 2013 at 10:10 AM, Rainer M Krug rai...@krugs.de wrote:
Hi
I want to include ascii art in a function documentation which should
look as follow:
,
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
to keep the monospaced font even in html, I decided to use \code{}:
,
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 8/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
`
But the result was an empty line between each text:
,
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 8/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
`
and when no empty lines were included obviously put everything behind
each other.
My question:
Is there a way that I can achieve the ASCII art as shown above? Is there
a way of having a \linebreak which does not insert a new line?
Thanks,
Rainer
--
--
Sarah Goslee
http://www.functionaldiversity.org
__
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Re: [Rd] ASCII art in function documentation?
OK - it boils down to an roxygen problem.
I will send a separate email for it.
Thanks,
Rainer
Sarah Goslee sarah.gos...@gmail.com writes:
Now that I'm at the computer with my R code, I've used both
\preformatted{}
and \cr to force line breaks.
Some combination of those may work for you.
Sarah
On Thu, Sep 5, 2013 at 11:10 AM, Rainer M Krug rai...@krugs.de wrote:
Sarah Goslee sarah.gos...@gmail.com writes:
Untested, but did you try wrapping the whole thing in a single code block:
Nope - also in one line.
Rainer
\code{
all
the
things
}
Sarah
On Thu, Sep 5, 2013 at 10:10 AM, Rainer M Krug rai...@krugs.de wrote:
Hi
I want to include ascii art in a function documentation which should
look as follow:
,
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
to keep the monospaced font even in html, I decided to use \code{}:
,
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 8/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
`
But the result was an empty line between each text:
,
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 8/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
`
and when no empty lines were included obviously put everything behind
each other.
My question:
Is there a way that I can achieve the ASCII art as shown above? Is there
a way of having a \linebreak which does not insert a new line?
Thanks,
Rainer
--
#secure method=pgpmime mode=sign
--
Rainer M. Krug
email: RMKrugatgmaildotcom
#secure method=pgpmime mode=sign
--
Rainer M. Krug
email: RMKrugatgmaildotcom
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Comments requested on changedFiles function
Dear Duncan,
This certainly looks useful. Might you consider adding the ability to
supply an alternative digest function? Details below.
I often use a homemade make type function which starts by looking at
modification times e.g. in a private package
https://github.com/jefferis/nat.utils/blob/master/R/make.r
For some of my work, I use hash functions. However because I typically
work with many large files I often use a special digest process e.g.
using the crc checksum embedded in a gzip file directly or hashing only
the part of a large file that is (almost) certain to change.
Perhaps (code unchecked) along the lines of:
changedFiles - function(snapshot, timestamp = tempfile(timestamp),
file.info = NULL,
digest = FALSE, digestfun=NULL, full.names = FALSE, ...)
if(digest){
if(is.null(digestfun)) digestfun=tools::md5sum
else digestfun=match.fun(digestfun)
info - data.frame(info, digest = digestfun(fullnames))
}
etc
OR alternatively using only one argument:
changedFiles - function(snapshot, timestamp = tempfile(timestamp),
file.info = NULL,
digest = FALSE, full.names = FALSE, ...)
if(is.logical(digest)){
if(digest) digestfun=tools::md5sum
} else {
# Assume that digest specifies a function that we want to use
digestfun=match.fun(digest)
digest=TRUE
}
if(digest)
info - data.frame(info, digest = digestfun(fullnames))
etc
Many thanks,
Greg.
On 4 Sep 2013, at 18:53, Duncan Murdoch wrote:
In a number of places internal to R, we need to know which files have
changed (e.g. after building a vignette). I've just written a general
purpose function changedFiles that I'll probably commit to R-devel.
Comments on the design (or bug reports) would be appreciated.
The source for the function and the Rd page for it are inline below.
- changedFiles.R:
changedFiles - function(snapshot, timestamp = tempfile(timestamp),
file.info = NULL,
md5sum = FALSE, full.names = FALSE, ...) {
dosnapshot - function(args) {
fullnames - do.call(list.files, c(full.names = TRUE, args))
names - do.call(list.files, c(full.names = full.names, args))
if (isTRUE(file.info) || (is.character(file.info)
length(file.info))) {
info - file.info(fullnames)
rownames(info) - names
if (isTRUE(file.info))
file.info - c(size, isdir, mode, mtime)
} else
info - data.frame(row.names=names)
if (md5sum)
info - data.frame(info, md5sum = tools::md5sum(fullnames))
list(info = info, timestamp = timestamp, file.info = file.info,
md5sum = md5sum, full.names = full.names, args = args)
--
Gregory Jefferis, PhD Tel: 01223 267048
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK
http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://flybrain.stanford.edu
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Re: [Rd] ASCII art in function documentation?
Sarah Goslee sarah.gos...@gmail.com writes:
Untested, but did you try wrapping the whole thing in a single code block:
Nope - also in one line.
Rainer
\code{
all
the
things
}
Sarah
On Thu, Sep 5, 2013 at 10:10 AM, Rainer M Krug rai...@krugs.de wrote:
Hi
I want to include ascii art in a function documentation which should
look as follow:
,
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
to keep the monospaced font even in html, I decided to use \code{}:
,
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 8/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
`
But the result was an empty line between each text:
,
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 8/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
`
and when no empty lines were included obviously put everything behind
each other.
My question:
Is there a way that I can achieve the ASCII art as shown above? Is there
a way of having a \linebreak which does not insert a new line?
Thanks,
Rainer
--
#secure method=pgpmime mode=sign
--
Rainer M. Krug
email: RMKrugatgmaildotcom
__
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Re: [Rd] libR.so: cannot open shared object file
just for completion i need to use library(Model, lib.loc=user/area/myRLib) because if i use library(Model) i get this message Error in library(BayesWrap) : there is no package called 'BayesWrap' Il 05/09/13 11:59, gianluca.mastranto...@yahoo.it ha scritto: First of all, thanks for your help. I did all the things you told me. I was able to load the library, but then Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/lustre/work/gjona2/Wrap/BayesWrap/libs/BayesWrap.so': libR.so: cannot open shared object file: No such file or directory In addition: Warning message: package 'BayesWrap' was built under R version 2.15.2 Error: package/namespace load failed for 'BayesWrap' Execution halted what does it means? G.M. Il 04/09/13 22:42, Prof Brian Ripley ha scritto: On 04/09/2013 19:58, Geoff Jentry wrote: Can you add some details? Suppose i have the package Model.tar.gz and my writable are is in user/area, what i have to do next to install the package? What I was picturing was something like this (forgive me if syntax isn't 100%): mkdir user/area/myRLib R CMD INSTALL --library=user/area/myRLib Model.tar.gz and then in R: library(Model, lib.loc=user/area/myRLib) Note though Brian Ripley's response to me where he indicates that this is handled automatically. Yes, install.packages(Model.tar.gz) should suffice. -J __ 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
Re: [Rd] Comments requested on changedFiles function
On Thu, Sep 5, 2013 at 6:48 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
On 13-09-04 11:36 PM, Scott Kostyshak wrote:
On Wed, Sep 4, 2013 at 1:53 PM, Duncan Murdoch murdoch.dun...@gmail.com
wrote:
In a number of places internal to R, we need to know which files have
changed (e.g. after building a vignette). I've just written a general
purpose function changedFiles that I'll probably commit to R-devel.
Comments on the design (or bug reports) would be appreciated.
The source for the function and the Rd page for it are inline below.
This looks like a useful function. Thanks for writing it. I have only
one (picky) comment below.
- changedFiles.R:
changedFiles - function(snapshot, timestamp = tempfile(timestamp),
file.info = NULL,
md5sum = FALSE, full.names = FALSE, ...) {
dosnapshot - function(args) {
fullnames - do.call(list.files, c(full.names = TRUE, args))
names - do.call(list.files, c(full.names = full.names, args))
if (isTRUE(file.info) || (is.character(file.info)
length(file.info))) {
info - file.info(fullnames)
rownames(info) - names
if (isTRUE(file.info))
file.info - c(size, isdir, mode, mtime)
} else
info - data.frame(row.names=names)
if (md5sum)
info - data.frame(info, md5sum = tools::md5sum(fullnames))
list(info = info, timestamp = timestamp, file.info = file.info,
md5sum = md5sum, full.names = full.names, args = args)
}
if (missing(snapshot) || !inherits(snapshot,
changedFilesSnapshot)) {
if (length(timestamp) == 1)
file.create(timestamp)
if (missing(snapshot)) snapshot - .
pre - dosnapshot(list(path = snapshot, ...))
pre$pre - pre$info
pre$info - NULL
pre$wd - getwd()
class(pre) - changedFilesSnapshot
return(pre)
}
if (missing(timestamp)) timestamp - snapshot$timestamp
if (missing(file.info) || isTRUE(file.info)) file.info -
snapshot$file.info
if (identical(file.info, FALSE)) file.info - NULL
if (missing(md5sum))md5sum - snapshot$md5sum
if (missing(full.names)) full.names - snapshot$full.names
pre - snapshot$pre
savewd - getwd()
on.exit(setwd(savewd))
setwd(snapshot$wd)
args - snapshot$args
newargs - list(...)
args[names(newargs)] - newargs
post - dosnapshot(args)$info
prenames - rownames(pre)
postnames - rownames(post)
added - setdiff(postnames, prenames)
deleted - setdiff(prenames, postnames)
common - intersect(prenames, postnames)
if (length(file.info)) {
preinfo - pre[common, file.info]
postinfo - post[common, file.info]
changes - preinfo != postinfo
}
else changes - matrix(logical(0), nrow = length(common), ncol = 0,
dimnames = list(common, character(0)))
if (length(timestamp))
changes - cbind(changes, Newer = file_test(-nt, common,
timestamp))
if (md5sum) {
premd5 - pre[common, md5sum]
postmd5 - post[common, md5sum]
changes - cbind(changes, md5sum = premd5 != postmd5)
}
changes1 - changes[rowSums(changes, na.rm = TRUE) 0, , drop =
FALSE]
changed - rownames(changes1)
structure(list(added = added, deleted = deleted, changed = changed,
unchanged = setdiff(common, changed), changes = changes), class
=
changedFiles)
}
print.changedFilesSnapshot - function(x, ...) {
cat(changedFiles snapshot:\n timestamp = \, x$timestamp, \\n
file.info = ,
if (length(x$file.info)) paste(paste0('', x$file.info, ''),
collapse=,),
\n md5sum = , x$md5sum, \n args = , deparse(x$args, control
=
NULL), \n, sep=)
x
}
print.changedFiles - function(x, ...) {
if (length(x$added)) cat(Files added:\n, paste0( , x$added,
collapse=\n), \n, sep=)
if (length(x$deleted)) cat(Files deleted:\n, paste0( ,
x$deleted,
collapse=\n), \n, sep=)
changes - x$changes
changes - changes[rowSums(changes, na.rm = TRUE) 0, , drop=FALSE]
changes - changes[, colSums(changes, na.rm = TRUE) 0, drop=FALSE]
if (nrow(changes)) {
cat(Files changed:\n)
print(changes)
}
x
}
--
--- changedFiles.Rd:
\name{changedFiles}
\alias{changedFiles}
\alias{print.changedFiles}
\alias{print.changedFilesSnapshot}
\title{
Detect which files have changed
}
\description{
On the first call, \code{changedFiles} takes a snapshot of a selection of
files. In subsequent
calls, it takes another snapshot, and returns an object containing data
on
the
differences between the two snapshots. The snapshots need not be the
same
directory;
this could be used to compare two directories.
}
\usage{
changedFiles(snapshot, timestamp =
Re: [Rd] libR.so: cannot open shared object file
On 05/09/2013 21:28, gianluca.mastranto...@yahoo.it wrote: just for completion i need to use library(Model, lib.loc=user/area/myRLib) because if i use library(Model) i get this message Error in library(BayesWrap) : there is no package called 'BayesWrap' For the record: not if you follow my suggestion. See ?.libPaths for why. Il 05/09/13 11:59, gianluca.mastranto...@yahoo.it ha scritto: First of all, thanks for your help. I did all the things you told me. I was able to load the library, but then Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/lustre/work/gjona2/Wrap/BayesWrap/libs/BayesWrap.so': libR.so: cannot open shared object file: No such file or directory In addition: Warning message: package 'BayesWrap' was built under R version 2.15.2 Error: package/namespace load failed for 'BayesWrap' Execution halted what does it means? G.M. Il 04/09/13 22:42, Prof Brian Ripley ha scritto: On 04/09/2013 19:58, Geoff Jentry wrote: Can you add some details? Suppose i have the package Model.tar.gz and my writable are is in user/area, what i have to do next to install the package? What I was picturing was something like this (forgive me if syntax isn't 100%): mkdir user/area/myRLib R CMD INSTALL --library=user/area/myRLib Model.tar.gz and then in R: library(Model, lib.loc=user/area/myRLib) Note though Brian Ripley's response to me where he indicates that this is handled automatically. Yes, install.packages(Model.tar.gz) should suffice. -J __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Comments requested on changedFiles function
This approach does have the difficulty that users could attempt to compare snapshots that were taken with different options and that can't be compared, but that should be an easy error to detect. FYI I implemented that approach in testthat: https://github.com/hadley/testthat/blob/master/R/watcher.r - it's a bit more general, because it just sits in the background and listens for changes, dispatching to a callback. Hadley -- Chief Scientist, RStudio http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] ASCII art in function documentation - difference html and text output?
Rainer,
Have you tried:
\preformatted{...}
which is documented in R-exts to preserve line breaks:
Indicate text that is a literal example of a piece of a program. Text is
displayed using typewriter font if possible. Formatting, e.g. line breaks, is
preserved. (Note that this includes a line break after the initial {, so
typically text should start on the same line as the command.)
Due to limitations in LaTeX as of this writing, this macro may not be nested
within other markup macros other than \dQuote and \sQuote, as errors or bad
formatting may result.
I have not used it myself, but might be worth a try, plus or minus the \cr use.
Regards,
Marc Schwartz
On Sep 5, 2013, at 10:23 AM, Rainer M Krug rai...@krugs.de wrote:
Found a solution.
putting \cr at the end of each line inserts a carriage return, but no
additional empty line. So
,
| \code{+--+--+--+} \cr
| \code{| 1/16 | 1/16 | 1/16 |} \cr
| \code{+--+--+--+} \cr
| \code{| 1/16 | 8/16 | 1/16 |} \cr
| \code{+--+--+--+} \cr
| \code{| 1/16 | 1/16 | 1/16 |} \cr
| \code{+--+--+--+} \cr
`
produces the desired output.
But interestingly,
,
| \code{
| +--+--+--+ \cr
| | 1/16 | 1/16 | 1/16 | \cr
| +--+--+--+ \cr
| | 1/16 | 8/16 | 1/16 | \cr
| +--+--+--+ \cr
| | 1/16 | 1/16 | 1/16 | \cr
| +--+--+--+ \cr
| }
`
produces the correct output in html,
,
| /p
| pcode +--+--+--+ br | 1/16 | 1/16 | 1/16 |
| br +--+--+--+ br | 1/16 | 8/16 | 1/16 | br
| +--+--+--+ br | 1/16 | 1/16 | 1/16 | br
| +--+--+--+ br /code
| /p
`
but
,
| ' +--+--+--+
| | 1/16 | 1/16 | 1/16 |
|
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
in the text version - is there a bug somewhere?
Thanks,
Rainer
Rainer M Krug rai...@krugs.de writes:
Sarah Goslee sarah.gos...@gmail.com writes:
Untested, but did you try wrapping the whole thing in a single code block:
Nope - also in one line.
Rainer
\code{
all
the
things
}
Sarah
On Thu, Sep 5, 2013 at 10:10 AM, Rainer M Krug rai...@krugs.de wrote:
Hi
I want to include ascii art in a function documentation which should
look as follow:
,
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
to keep the monospaced font even in html, I decided to use \code{}:
,
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 8/16 | 1/16 |}
|
| \code{+--+--+--+}
|
| \code{| 1/16 | 1/16 | 1/16 |}
|
| \code{+--+--+--+}
`
But the result was an empty line between each text:
,
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 8/16 | 1/16 |'
|
| '+--+--+--+'
|
| '| 1/16 | 1/16 | 1/16 |'
|
| '+--+--+--+'
`
and when no empty lines were included obviously put everything behind
each other.
My question:
Is there a way that I can achieve the ASCII art as shown above? Is there
a way of having a \linebreak which does not insert a new line?
Thanks,
Rainer
--
#secure method=pgpmime mode=sign
#secure method=pgpmime mode=sign
--
Rainer M. Krug
email: RMKrugatgmaildotcom
__
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Re: [Rd] ASCII art in function documentation?
Brian G. Peterson br...@braverock.com writes:
On 09/05/2013 09:10 AM, Rainer M Krug wrote:
want to include ascii art in a function documentation which should
look as follow:
,
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
| | 1/16 | 8/16 | 1/16 |
| +--+--+--+
| | 1/16 | 1/16 | 1/16 |
| +--+--+--+
`
to keep the monospaced font even in html, I decided to use \code{}:
Wouldn't it be best to use the relatively new \figure markup with
alternate text?
http://cran.r-project.org/doc/manuals/R-exts.html#Figures
Thanks - mus't have overlooked it.
This would definitely work, but in this case I think ASCII art would be
the better solution.
Thanks,
Rainer
Regards,
Brian
#secure method=pgpmime mode=sign
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email: RMKrugatgmaildotcom
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