the initial repo clone, working via git-svn was
noticeably faster than straight svn client (!) -- I think related to how
the tools organize the working copy and how many fstat calls they make.
- I find the log reviewing functionality much better suited to reviewing
changes.
+ seth
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,
you could do:
myfoo - pkgname::foo
And then later call myfoo() and I don't think you will see the added cost.
You can formalize the above approach in package code by renaming
function in the importFrom directive where I believe you can do:
importFrom(pkgname, myfoo=foo)
+ seth
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is something that I would expect to happen fairly
often in many applications of R.
Is for() faster on small blocks by enough that one would want to branch
based on size?
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of allocation such that data will be written over the memory
that your invalid external pointer points to.
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that will
do any required cleanup and then call Free.
If instead you want to have an externally managed SEXP, you could put it
in the protected slot of the external pointer, but then you should
allocate it using standard R allocation functions.
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{} lines to it.
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On 3/31/10 4:52 PM, John Chambers wrote:
The example is confusing and debatable, but not an obvious bug. And
your presentation of it is the cause of much of the confusion
(unintentionally I'm sure).
To restate the issue (I think):
In a new R session if you happen to call:
sensible (you can't just remove the
#ifdef's). Patches along these lines would be welcome.
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On 3/27/10 1:43 PM, Duncan Murdoch wrote:
On 25/03/2010 3:16 PM, Arni Magnusson wrote:
I'm relaying a question from my institute's sysadmin:
Would it be possible to modify update.packages() and related functions
so that 'lib.loc' accepts integer values to specify a library from the
On 3/20/10 2:03 PM, Seth Falcon wrote:
On 3/20/10 1:36 PM, Alistair Gee wrote:
I fixed my build problems. I also noticed that my patch wasn't
correct, so I have attached a new version.
This fix still grows the vector by doubling it until it is big enough,
but the length is reset to the correct
that .conflicts.OK is OK. Are there
package authors who realize they do not know what they are doing enough
to keep the warning messages :-P
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On 3/20/10 1:36 PM, Alistair Gee wrote:
I fixed my build problems. I also noticed that my patch wasn't
correct, so I have attached a new version.
This fix still grows the vector by doubling it until it is big enough,
but the length is reset to the correct size at the end once it is
known.
in a patch (with testing) for this.
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for
'.conflicts.OK' even if it is not exported.
I guess I agree that there is no real value in forcing .conflicts.OK to
be exported. OTOH, this seems like a dubious feature to begin. When is
it a good idea to use it?
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On 3/17/10 7:16 AM, Alistair Gee wrote:
Yes. I had noticed that R occasionally segfaults (especially when I
run many concurrent R processes), so I used valgrind to log every use
of R. In the valgrind logs, I tracked the problem to list_files().
I attached a patch to platform.c (for trunk).
Hi,
First thing to observe is that you are calling RSymbReg via .Call, but
that function does not return SEXP as is required by the .Call interface.
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Hi Alistair,
On 3/12/10 4:37 PM, Alistair Gee wrote:
I am using R-2-10 from subversion.
In the implementation of do_listfiles() in platform.c, it appears to
allocate a vector of length count where count is calculated by
count_files(). It then proceeds to call list_files(), passing in the
On 3/15/10 8:37 PM, Alistair Gee wrote:
I think I have a fix that avoids the problem by just growing the
vector as necessary as the directory is traversed (and no longer uses
count_lines()).
I don't have access to the code at the moment, but I should be able to
post the patch tomorrow. Is
On 3/11/10 12:45 AM, Henrik Bengtsson wrote:
Thanks for the troubleshooting,
I just want to second this patch; it would be great if PATH_MAX could
be used everywhere.
The patch, or at least something quite similar, was applied in r51229.
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be little reason to want to save it (it is not saved now).
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On 2/20/10 7:50 AM, Peter Dalgaard wrote:
You don't want to understand, believe me! ;-)
It's a bug, probably not the very worst kind, but accessing memory that
isn't yours is potentially harmful (but writing to it is considerably
worse).
Looks like the issue only concerns the right hand
Hi,
On 2/16/10 10:31 AM, Jens Elkner wrote:
Having currently a big problem with R 2.10.1 vanilla (Solaris):
As soon as the R_LIBS_USER env var gets bigger than 1023 chars R
completely ignores it and uses the default:
I guess the first question is, why do need such a long list of library
names. NA indices are propagated to the
result. Unmatched values and are not allowed and result in
an error.
Cheers,
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:
If you want to create and then link to a library, say using code in a
subdirectory, use something like
.PHONY: all mylibs
all: $(SHLIB) $(SHLIB): mylibs
mylibs: (cd subdir; make)
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On 1/28/10 3:50 AM, a.r.runna...@kent.ac.uk wrote:
At line 312 in src/main/platform.c (at the latest svn revision, 51039):
if (length(tl)= 1 || !isNull(STRING_ELT(tl, 0)))
should not '||' read ''? Likewise four lines later.
Thanks, I'll fix this up.
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to setGeneric. That seems like a very odd thing to do.
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On 1/19/10 11:19 AM, Ross Boylan wrote:
If files that were read in later in the sequence extended an existing
generic, I omitted the setGeneric().
I had to resequence the order in which the files were read to avoid some
undefined slot classes warnings. The resequencing created other
problems,
On 1/15/10 7:51 AM, Uwe Ligges wrote:
the Windows checks for CRAN run with that setting, i.e.
_R_CHECK_FORCE_SUGGESTS_=false
Hence the multicore issue mentioned below actually does not exist.
I did not know that the Windows checks for CRAN used this setting.
My concern was initiated by a
On 1/15/10 7:47 AM, Simon Urbanek wrote:
On Jan 15, 2010, at 10:22 , Seth Falcon wrote:
I believe another option is:
pkg - somePkg
pkgAvail - require(pkg, character.only = TRUE)
if (pkgAvail)
...
else
...
That is not an option - that is the code you usually use
On 1/15/10 12:19 AM, Kurt Hornik wrote:
Jeff Ryan writes:
Hi Ross,
The quantmod package makes available routines from a variety of
contributed packages, but gets around your issues with a bit of, um,
trickery.
Take a look here (unless your name is Kurt ;-) ):
I believe another option
On 1/1/10 1:40 PM, Peng Yu wrote:
On Fri, Jan 1, 2010 at 6:52 AM, Barry Rowlingson
b.rowling...@lancaster.ac.uk wrote:
On Thu, Dec 31, 2009 at 11:27 PM, Peng Yu pengyu...@gmail.com wrote:
I don't see where describes the implementation of '[]'.
For example, if x is a matrix or a data.frame,
also can't
find them in any other function or help file.
So does anybody know where these functions are still listed that causes this
error?
Are you sure they are not in your NAMESPACE file?
--
Seth Falcon
Program in Computational Biology | Fred Hutchinson Cancer Research Center
On 11/17/09 5:02 AM, Peng Yu wrote:
This may not easy to do, when the filename are not hard coded strings.
For example, the variable 'filename' is a vector of strings.
for (i in 1:length(filename)){
do something...
save(,file=filename[i])
}
That's right. I don't think there is a
) # this will raise an error
FALSE # only get here if no error
},
error = function(e) TRUE)
## verify we saw an error
stopifnot(res)
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On 11/11/09 2:36 AM, Duncan Murdoch wrote:
On 10/11/2009 11:16 PM, Tony Plate wrote:
PS, I should have said that I'm reading the docs for unlink in
R-2.10.0 on a Linux system. The docs that appear in a Windows
installation of R are different (the Windows docs do not mention that
not all systems
Hi,
On 11/3/09 2:28 PM, William Dunlap wrote:
The following odd call to rep()
gives somewhat random results:
rep(1:4, 1:8, each=2)
I've committed a fix for this to R-devel.
I admit that I had to reread the rep man page as I first thought this
was not a valid call to rep since times (1:8)
Hi,
On 11/3/09 6:51 PM, mark.braving...@csiro.au wrote:
file.copy( 'd:/temp/Rdiff.Rd', 'd:/temp/scrunge.Rd') # Rdiff.Rd from 'tools'
package source
eglist- list( scrunge=parse_Rd( 'd:/temp/scrunge.Rd'))
tools:::makeLazyLoadDB( eglist, 'd:/temp/ll')
e- new.env()
lazyLoad( 'd:/temp/ll', e)
On 10/29/09 7:00 AM, Abhijit Bera wrote:
Hi
I seem to have run into a situation where I have more than 3 arguments to
pass to a function from C.
the following functions help me build an expression for evaluation:
lang
lang2
lang3
lang4
What should one do if there are more arguments than
On 10/29/09 7:38 AM, Abhijit Bera wrote:
Can't find the source to Rf_lang* series of functions. :|
But I'm thinking it should be like this correct me if I'm wrong:
PROTECT(e=lang4(install(myfunction),arg1,arg2,arg3);
PROTECT(SETCAR(CDR(e),portConstraints));
:
#!/path/to/Rscript --vanilla
print(1:10)
So then I'm not sure how useful it is for Rscript to handle such
files. Why not convert to a more common and portable line termination
for your R script files?
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an interesting approach for integrating
unit testing into R CMD check via examples in an Rd file within the
package.
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find a way to reduce
dependencies and have your package work, that is better. :-)
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2009/9/24 Hervé Pagès hpa...@fhcrc.org:
x - charToRaw(ABCDEFGx)
x[c(1:3, NA, 6)] - x[8]
*** caught segfault ***
address 0x8402423f, cause 'memory not mapped'
Thanks for the report. I have a fix which I will commit after some testing.
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)]
install.packages(wantPkgs)
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up when the R level object
gets gc'd.
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Hi Jon,
* On 2009-06-30 at 15:27 +0200 Jon Olav Skoien wrote:
I work on two packages, pkg1 and pkg2 (in two different projects). pkg1 is
quite generic, pkg2 tries to solve a particular problem within same field
(geostatistics). Therefore, there might be users who want to use pkg2 as an
).
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in different allocation patterns, one of which triggered the
bug.
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. But the above helps explain the behavior you saw; a
--quite R will suppress some output and that will make a difference
in terms of memory allocation.
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/main/sprintf.c:179
#5 0x003fe1af in do_internal (call=0x10cb4a8, op=0x100fc38, args=0x10a40e8,
env=0x10a40b0) at ../../../../R-devel-all/src/main/names.c:1140
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A couple more comments...
* On 2008-09-15 at 10:07 -0700 Seth Falcon wrote:
The example is with RSQLite but the same thing happens with
RMySQL, and other DBI packages.
The use of as() within the various DBI packages should be
re-evaluated. I suspect some of that code was among the first
* On 2008-09-17 at 19:25 -0700 Seth Falcon wrote:
In the latest R-devel code (svn r46542), this behaves differently (and
works as you were hoping). I get:
library(RSQLite)
setClass(SQLConPlus, contains=c(SQLiteConnection,integer))
dd = data.frame(a=1:3, b=letters[1:3])
con
Continuing to talk to myself here...
* On 2008-09-17 at 21:06 -0700 Seth Falcon wrote:
*argh* I'm certain this was working for me and yet when I try to
reproduce in a new R shell it errors out.
This looks like an infelicity in the methods caching.
To make it work:
library(RSQLite
choice. Why not extend SQLiteConnection and add
extra slots as you like. The dispatch will in this case be much
easier to reason about.
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in the DESCRIPTION file as described in Writing R Extensions
in the Registering native routines section.
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Hi all,
A new version of RSQLite has been uploaded to CRAN and should be
available soon. This update contains a minor change to the C code
that should improve compatibility on various unix OS.
+ seth
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making such a change. I suspect the correct fix is
one that tweaks configure to determine where things are based on the
current system (the current code is correct for gcc I believe).
Anyhow, thanks for the report. I will try to have an update within a
week.
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tools, it seems not unreasonable to expect that
picking up a method via the search path would work in a package just
as it does (should?) interactively.
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for embedded nul in character strings --
raw can be used when this is desired, and having nul terminated
strings will make the code more consistent and easier to maintain
going forward.
Best Wishes,
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Hi again,
Herve wrote:
gregexpr(, abc, fixed=TRUE)
*** caught segfault ***
address 0x1c09000, cause 'memory not mapped'
This should be fixed in latest svn. Thanks for the report.
+ seth
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2 3
attr(,match.length)
[1] 0 0 0
gregexpr(, abc, perl=TRUE)
[[1]]
[1] 1 2 3
attr(,match.length)
[1] 0 0 0
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), error=function(e) FALSE)
You could do similar with myClose and close a connection as many
times as you'd like :-)
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by a
handful of experiments on typical annotation dbs.
Columns with few levels may not benefit from an index. See this
thread:
http://thread.gmane.org/gmane.comp.db.sqlite.general/23683/focus=23693
But your column with many levels should suffer this problem :-)
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75 (foo)`
NULL
$`closing unused connection 74 (foo)`
NULL
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thing since as you mentioned later in
your response, some tests take a long time to run and probably are
best not automatically run during R CMD check.
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BioC: http://bioconductor.org/
Blog: http
.
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. I would
recommend recompiling with --enable-memory-profiling and using
tracemem() to see if you can identify places where copies of your
large object are occurring. You can also take a look at
Rprof(memory.profile=TRUE).
+ seth
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environment (omit the where arg) and
test it that way.
OTOH, if foo is used by pkg internally, then it will be much easier to
simply edit the source for pkg, reinstall and test. If you find and
fix a bug, most package maintainers will be quite happy to integrate
your fix.
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a concern that there is a leak that needs fixing? It is worth
noting that the internal handling of character vectors has changed in
R-devel and so IMO testing there would make sense before persuing this
further, I suspect your results will be different.
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message is:
Instead of require(pkgname), simply list pkgname in the Depends field
of your package's DESCRIPTION file. See the Writing R Extensions
manual for details.
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Blog: http
;
PROTECT(cvect = allocVector(STRSXP, numStrings));
for (i = 0; i numStrings; i++) {
SET_STRING_ELT(cvect, i, mkChar(yourStrings[i]));
}
UNPROTECT(cvect);
return cvect;
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, are you sure that temp is valid at
this point?
SEXP out = R_MakeExternalPtr(temp, R_NilValue, R_NilValue);
I was expecting to see:
SEXP out = R_MakeExternalPtr((void *)sesPtr, R_NilValue, R_NilValue);
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run from the screen session things will work. Do
all of the graphics devices require access to X11()? I thought you
could use pdf() for example, without X11() but I'm not certain.
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http://bioconductor.org
/software/dict_0.0.4.tar.gz
Windows binary:
R-2.5.x: http://userprimary.net/software/dict_0.0.4.zip
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summary(env.profile(e)$counts)
Min. 1st Qu.Median Mean 3rd Qu. Max.
0.0.0.0.79350. 2700.
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to be a DBIConnection, why wouldn't you use inheritance?
setClass(TSconnection, contains=DBIConnection, ...)
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a good idea. I'll
agree that it working might encourage someone to try formals-(), but
the fact that it cannot do anything but error seems like a strange
reason not to make formals() work.
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http
withCallingHandlers).
Clearly not ideal, but at the same time in the spirit of open source,
no?
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Seth Falcon [EMAIL PROTECTED] writes:
On Windows, package files in the inst/ subdir are installed after the
lazyload creation. This differs from Linux where inst/ is installed
_before_ lazyload creation.
Since packages may need data in inst, I think the order on Windows
should be changed
/MakePkg -s
lazyload
endif
- @$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s
$(DPKG)/demo $(DPKG)/exec $(DPKG)/inst $(DATA)
ifeq ($(strip $(LAZYDATA)),true)
@$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s
lazydata
endif
--
Seth Falcon
ideas at the moment for how this could
work.]
[Note 2: Despite the false-positives, I've already caught a handful of
bugs by reading over these NOTEs and think they provide a lot of value
to the check process]
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(cl, INTSXP));
ivals = INTEGER(colnums);
Here you convert the STRSXP cl into an INTSXP. If you want the actual
integer values, use the ivals pointer.
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how to make a plot that appeared in a vignette, for example.
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for connections.
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added for
working with connections from C in package code. There are a number
of places where this would be useful and provide cleaner solution than
what is possible today.
The proposed interface looks useful.
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codoc, etc,
checks.
If you have your own generic TSdoc-, then I think you want:
\alias{TSdoc-}
\alias{TSdoc-,someClass,anotherClass-method}
You may not be allowed to specify usage, but I think the issue only
arises when setting methods for a generic documented elsewhere.
+ seth
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) standardGeneric(TSdoc),
useAsDefault= function(x) attr(x, TSdoc))
Aside:
It seems odd to me to define such defaults. How do you know x is
going to have a TSdoc attribute?
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allow
for example
readLines(gzfile(foo.gz))
I think this would be a nice improvement as it matches what many
people already assume happens as well as matches what some other
languages do (in particular, Python).
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16831859 128.5 45712717 348.8 39456690 301.1
Best Wishes,
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Andrew Clausen [EMAIL PROTECTED] writes:
Hi Seth,
On Mon, May 21, 2007 at 05:15:10PM -0700, Seth Falcon wrote:
I will also add that the notion of a default argument on a generic
function seems a bit odd to me. If an argument is available for
dispatch, I just don't see what sense it makes
Hi again,
Robert has committed the proposed patch to R-devel. So [[ now has an
'exact' argument and the behavior is as described:
Seth Falcon [EMAIL PROTECTED] writes:
1. [[ gains an 'exact' argument with default value NA
2. Behavior of 'exact' argument:
exact=NA
at the vsn package in Bioconductor which uses a
Makefile to avoid R CMD check from building its vignette because it is
too time consuming...
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__
R
matching the missing class.
What often does make sense is to define a generic function where some
argument are not available for dispatch. For example:
setGeneric(foo, signature=flesh,
function(flesh, skeleton=attr(flesh, skeleton)
standardGeneric(foo)))
+ seth
--
Seth
. The recent integration of the completion code
gives less typing and complete names.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
__
R-devel@r-project.org mailing list
https://stat.ethz.ch
. Comments from
others in this thread suggest that there is a desire that this be an
opt-in feature for package authors [I don't really understand this
desire as it seems to me it should be a feature/decision of the GUI]
and again vignette() doesn't help.
+ seth
--
Seth Falcon | Computational Biology
, item, paste(shell.exec(\,
as.character(i), \), sep = ))
}
} ## else
ans - TRUE
} else {
ans - FALSE
}
ans
}
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
into modifying the existing function to handle this.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
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R-devel@r-project.org mailing list
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is a hackish workaround.
setMethod($, Foo, function(x, name)
eval(substitute([EMAIL PROTECTED], list(FOO=name
[1] $
f$bo
[1] 1
f$al
[1] 2
Other suggestions for workarounds? Is this a bug?
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer
might expect each import to be in the chain of
parent environments. Instead all imports are merged into a single
environment that is the parent of the package env.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
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