Re: [Rd] segfault issue with parallel::mclapply and download.file() on Mac OS X

and they got similar crashes - though I'm not sure which version of macOS they are on. Based on Gábor's recommendation I did quit using the default libcurl backend (default on my machine at least). Using download.file(url, path, method = curl) has been working great for my use c

Re: [Rd] segfault issue with parallel::mclapply and download.file() on Mac OS X

ent can be attributed to I/O multiplexing for the downloading portion using your recommendations. Seth Trimmed reply from Gábor Csárdi : > > Fork without exec is not supported by macOS, basically any calls to > system libraries might crash. (Ie. not just HTTP-related calls.) For >

[Rd] segfault issue with parallel::mclapply and download.file() on Mac OS X

talled via homebrew with "brew install r --with-java --with-openblas" Also, the provided example code works as expected on Linux. Also, if I provide a non-default download method to the download.file() call such as: res <- parallel::mclapply(files, fun

Re: [Rd] SVN vs DVCS

m 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 -- Seth F

[Rd] R CMD check

one to go after it. Thanks a lot for the help. Regards, Sahil Seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Resolving functions using R's namespace mechanism can double runtime

, 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

Re: [Rd] suggestion how to use memcpy in duplicate.c

vectors 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? + seth -- Seth Falcon | @sfalcon | http://userprimary.net/ __ R-devel@r-p

Re: [Rd] transient memory allocation and external pointers

ght pattern of allocation such that data will be written over the memory that your invalid external pointer points to. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] transient memory allocation and external pointers

xternal pointer 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. + seth -- Seth Falc

Re: [Rd] generic '[' for a non-exported class

e on an internal API Rd page. Create an Rd file like yourPkg-internal-api.Rd and add the appropriate \alias{} lines to it. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] as(1:4, "numeric") versus as.numeric(1:4, "numeric")

h unless documented to do so. I'm also suspicious of the behavior of the strict argument: > class(as(1:4, "numeric")) [1] "integer" > class(as(1:4, "numeric", strict = TRUE)) [1] "integer" > class(as(1:4, "numeric", strict = FALSE)) [1] "integer" Is that intended? + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Difference Linux / Windows

quires editing the Rd files to make the contents sensible (you can't just remove the #ifdef's). Patches along these lines would be welcome. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] update.packages(1)

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 >>

Re: [Rd] Suggestion: Not having to export .conflicts.OK in name spaces

On 3/22/10 3:57 AM, Martin Maechler wrote: "SF" == Seth Falcon on Fri, 19 Mar 2010 13:47:17 -0700 writes: SF> On 3/17/10 9:11 AM, Henrik Bengtsson wrote: >> Currently library() and attach() fail to locate an >> existing '.conflicts.O

Re: [Rd] list_files() memory corruption?

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 co

Re: [Rd] list_files() memory corruption?

the patch is the easy/quick part and making sure that one hasn't introduced new infelicities or unintended behavior is the hard part. I will try to take another look at your latest patch. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Suggestion: Not having to export .conflicts.OK in name spaces

methods should look 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? + seth -- Seth Falcon | @sf

Re: [Rd] DESCRIPTION: Imports: assertion of version?

rent lack of checking is a "feature". I would be interested in a patch (with testing) for this. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] list_files() memory corruption?

And there are some performance characteristics to consider in terms of both run time and memory profile. Does making a single pass through the files make up for the allocations/data copying that result from lengthgets? Is it worth possibly requiring twice the memory for the worst case? + seth

Re: [Rd] list_files() memory corruption?

post the patch tomorrow. Is there interest in my patch? I'm curious to know if this is a problem you have encountered while using R. My initial thought is that there isn't much benefit of making this part of the code smarter. If your patch simplifies things

Re: [Rd] list_files() memory corruption?

write past the > length of the allocated vector? Good catch. I've added a length check to prevent a problem. Cheers, + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Segfault Problem c++ R interface (detailed)

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. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] [PATCH] R ignores PATH_MAX and fails in long directories (PR#14228)

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. + seth -- Seth Falcon | @sfalcon | http

Re: [Rd] shash in unique.c

might be saved to disk now or in the future. I agree with your reading: this is a temporary hash table and there would be little reason to want to save it (it is not saved now). + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Rubbish values written with zero-length vectors (PR#14217)

hesub, length(x), 0, &newname, recursed ? len-1 : -1, R_NilValue); if (isVectorList(x) && isNull(y)) { x = DeleteOneVectorListItem(x, offset); + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Rubbish values written with zero-length vectors (PR#14217)

hesub, length(x), 0, &newname, recursed ? len-1 : -1, R_NilValue); if (isVectorList(x) && isNull(y)) { x = DeleteOneVectorListItem(x, offset); + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R_LIBS_USER bugs

to a value longer than 1024 and retrieve it again. But if I have such a value in my shell, it gets overwritten. I'm not yet sure what is going on. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Unexpected behaviour of x[i] when i is a matrix, on Windows

the dimension names. NA indices are propagated to the result. Unmatched values and "" are not allowed and result in an error. Cheers, + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ R-devel@r-project

Re: [Rd] Compiling R projects with multiple external libraries

n example. Quote from manual: 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) + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __

Re: [Rd] src/main/platform.c (PR#14198)

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

Re: [Rd] calling setGeneric() twice

sing valueClass, I don't think you will need any class definitions. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] calling setGeneric() twice

on why you are using multiple calls to setGeneric. That seems like a very odd thing to do. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] optional package dependency

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) >> ... >

Re: [Rd] optional package dependency

at case, perhaps the deafult value should change. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] optional package dependency

;t make proper use of name spaces for any optional functionality. I'm willing to help work on and test a solution if we can arrive at some consensus as to what the solution looks like. Best, + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] How x[, 'colname1'] is implemented?

uot;, "D", "E") >> The definition of "large" and "small" here appears to be such that: >> >> 457: Rboolean usehashing = in && ( ((ns > 1000 && nx) || (nx > 1000 && >> ns)) || (ns * nx > 15*nx + ns)

Re: [Rd] Error in namespaceExport(ns, exports) :

d files. I 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

Re: [Rd] How to generate dependency file that can be used by gnu make?

7;t think there is a feasible general solution. You might have more success with a convention-based approach for your scripts that would allow a simple parser to identify output files by name convention, for example. + seth __ R-devel@r-project.or

Re: [Rd] error checks

{ f(TRUE) # this will raise an error FALSE # only get here if no error }, error = function(e) TRUE) ## verify we saw an error stopifnot(res) + seth -- Seth Falcon | @sfalcon | http://userprimary.net/users ___

Re: [Rd] typo in docs for unlink()

e inconvenience of finding doc during a search for something that only works on another platform -- hey, that still might be useful as it would tell you what platform you should use ;-) + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] parse_Rd and/or lazyload problem

doesn't make any difference which file I process first; the error comes the second time round. If I adjust this example in terms of paths and run on OS X, I get the following error on the second run: > as.list(e) # Splat Error in as.list.environment(e) : internal error -3 in R_decompress

Re: [Rd] memory misuse in subscript code when rep() is called in odd way

ipt.c:658) A little investigation seems to suggest that the problem is originating earlier. Debugging in seq.c:do_rep I see the following: > rep(1:4, 1:8, each=2) Breakpoint 1, do_rep (call=0x102de0068, op=unavailable, due to optimizations>, args=due to optimizations>, rho=0x1018829f0

Re: [Rd] Help with lang4

t, arg4Elt); Reading Rinlinedfuns.h should help some. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Help with lang4

lang4 can handle? If you take a look at the source code for those functions, something may suggest itself. R function calls at the C level are composed like in lisp: a pair-list starting with the function cons'ed with the args. + seth __ R-de

Re: [Rd] (PR#14012)

purpose of Rscript is to enable R script execution on unix-like systems like: #!/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 file

Re: [Rd] how to document stuff most users don't want to see

. Users would need to learn how to tune the help system. Developers would need to learn and follow the system of variable verbosity. This time would be better spent by developers simply improving the documentation and by users by simply reading the improved documentation. My $0.02. + seth

Re: [Rd] unit testing for R packages?

e R session in which you are doing development. The vignette in svUnit has an interesting approach for integrating unit testing into R CMD check via examples in an Rd file within the package. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] build time dependency

ckage? Making it easy to do so is great, but in general if you can find a way to reduce dependencies and have your package work, that is better. :-) + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] crash with NAs in subscripted assignment of a raw vector

2009/9/24 Hervé Pagès : >  > 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. --

Re: [Rd] Rcmdr package dependencies

1", Rcmdr.Suggests) havePkgs <- installed.packages()[, "Package"] wantPkgs <- wantPkgs[!(wantPkgs %in% havePkgs)] install.packages(wantPkgs) + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] asking for suggestions: interface for a C++ class

m. One slot should be an external pointer which will give you the ability to define a finalizer to clean up when the R level object gets gc'd. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Conditional dependency between packages

pkg1"]] <- TRUE } } * Then your methods can check PKG_INFO[["pkg1"]]. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] bug in Rf_PrintValue ?

ng. CHARSXPs should never be exposed at the user level and should instead be elements of a character vector (STRSXP). + seth -- Seth Falcon http://userprimary.net/user __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Side-effects of require() vs library() on x86_64 aka amd64

at, one would have to look at the sources. 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. + seth -- Seth Falcon | http://userprimary.net/user/ _

Re: [Rd] Side-effects of require() vs library() on x86_64 aka amd64

ifferent run paths resulted in different allocation patterns, one of which triggered the bug. + seth -- Seth Falcon | http://userprimary.net/user/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R crashes on sprintf with bad format specification (PR#13285)

intf (call=0x10cb470, op=0x1018924, args=, env=0x10a40b0) at ../../../../R-devel-all/src/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 + seth -- Seth Falcon | http://us

Re: [Rd] R crashes on sprintf with bad format specification (PR#13283)

intf (call=0x10cb470, op=0x1018924, args=, env=0x10a40b0) at ../../../../R-devel-all/src/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 + seth -- Seth Falcon | http://us

Re: [Rd] S4 coercion responsibility

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: libra

Re: [Rd] S4 coercion responsibility

* 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","

Re: [Rd] S4 coercion responsibility

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 amo

Re: [Rd] S4 coercion responsibility

is-a integer. The fact that the as() method dispatch doesn't match that of SQLiteConnection should really be that surprising. I don't see how this could be the responsibility of the author of the class you've subclassed. I would also quest

Re: [Rd] how to install header files in package

ovided by pkgA, then you can use the LinkingTo field in the DESCRIPTION file as described in Writing R Extensions in the "Registering native routines" section. + seth -- Seth Falcon | http://userprimary.net/user/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] RSQLite 0.6-9 uploaded to CRAN [was: RSQLite bug fix for install with icc]

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 -- Seth Falcon | http://userprimary.net/user

Re: [Rd] RSQLite bug fix for install with icc

> in > RSQLite/src/RS-DBI.h I will see about 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 up

Re: [Rd] NAMESPACE & methods guidance, please

of namespaces, looking > in the search list seems a bad idea in principle. I agree that using the dynamic lookup when the static lookup is available is bad programming practice. However, given the flexibility of the current tools, it seems not unreasonable to expect that picking up a method via the se

Re: [Rd] R 2.7.0, match() and strings containing \0 - bug?

majority of R's internal string processing functions use standard C semantics and truncated at first nul there has always been some room for "interesting" behavior. The change in R-2.7 was an attempt to start resolving these inconsistencies. Since then the core team has agr

Re: [Rd] Suggestion: isLoaded() to test if a package is loaded (without loading it)

ckageName(package, version); > } > pattern <- sprintf("package:%s", package); > (pattern %in% s); > } This only tests whether or not the given package is attached to the search path. You also (I think) want to search loaded namespaces. Bu

Re: [Rd] segfault in gregexpr()

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 -- Seth Falcon | [EMAI

Re: [Rd] segfault in gregexpr()

gexpr("", "abc", fixed=TRUE) [[1]] [1] 1 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 + seth -- Seth Falcon | [EMAI

Re: [Rd] isOpen on closed connections

= { > close(con) > }) This doesn't address isOpen, but why do you have the call to close inside the tryCatch block? Isn't the idea that finally will always be run and so you can be reasonably sure that close gets called once? If your real

Re: [Rd] package installation order

Loading required package: RBGL > ## > CRANdeps <- makeDepGraph(repos["cran"], type="source") > ## > getInstallOrder("Rmetrics", CRANdeps, needed.only=FALSE) > > worked for me. I meant to add some code for Graphviz visualization (or look > for it, Seth et a

Re: [Rd] RSQLite indexing

he_size=64000 and synchronous=0 and that this was determined 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 sho

Re: [Rd] warning upon automatic close of connection

quot;yes" can write "yes" ## start new R session for (i in 1:75) file("foo") gc() warnings()[1:3] > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 149603 4.0 35 9.4 35 9.4 Vcells 101924 0.8 786432 6.0 486908 3.8 There w

Re: [Rd] R CMD check recursive copy of tests/

at R CMD check doesn't recurse really isn't a problem. You can have a driver script at the top-level that runs as many of the tests in subdirs as you want. And this is really a good thing since as you mentioned later in your response, some tests take a long time to run and prob

Re: [Rd] R CMD check: Error in function (env) : could not find function "finalize"

narrow it down, gctorture may help or running the examples under valgrind. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] .Call and to reclaim the memory by allocVector

ding up with multiple copies of the object on the R side during some of your operations. 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.

Re: [Rd] [R] Suspected memory leak with R v.2.5.x and large matrices with dimnames set

you from getting things done, or just 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 di

Re: [Rd] Overriding S4 methods in an installed package

ly, 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. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] package dependencies

eck can not be executed. The error 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. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center Bi

Re: [Rd] Convert multiple C strings into an R character vector

i; SEXP cvect; PROTECT(cvect = allocVector(STRSXP, numStrings)); for (i = 0; i < numStrings; i++) { SET_STRING_ELT(cvect, i, mkChar(yourStrings[i])); } UNPROTECT(cvect); return cvect; + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer

Re: [Rd] Using R_MakeExternalPtr

reateSession(attributes); > void* temp = session; It isn't clear from your example, 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,

Re: [Rd] dict package: dictionary data structure for R

gate other hashing functions since computing the next prime and doing so for resizes will take longer than not having to do it and it will add complexity to the code. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http:

Re: [Rd] dict package: dictionary data structure for R

t it might actually be useful to people. It's main use may turn out to be for investigating hash functions behavior and for a test tool it may be sufficient as-is. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] dict package: dictionary data structure for R

is what we see with an environment: > e = new.env(hash=T, size=2^14) > for (k in keys2) e[[k]] = k > summary(env.profile(e)$counts) Min. 1st Qu.Median Mean 3rd Qu. Max. 0.0.0.0.79350. 2700. -- Se

[Rd] dict package: dictionary data structure for R

userprimary.net/software/dict_0.0.4.tar.gz Windows binary: R-2.5.x: http://userprimary.net/software/dict_0.0.4.zip + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-devel@r-project.o

Re: [Rd] X11() dies in remote background

omplicate your desire to use X11(), but perhaps with Xvfb 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. + seth -- Seth Falcon | Computational Biology |

Re: [Rd] S4 coerce

uot; > > setAs("TSconnection", "DBIConnection", def = function(from) [EMAIL > PROTECTED]) I think things work as you expect up until this pint. > > setIs("TSconnection", "DBIConnection", coerce = function(x) > > [EMAIL PROTECTED]) I'

Re: [Rd] Getting param names of primitives

ake sense so making it work seems like 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. + seth -- Seth Falcon | Computational Biology | Fred Hut

Re: [Rd] PATCH: install inst/ before doing lazyload on Windows

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 o

Re: [Rd] step() in sink() and Sweave()

tter to have outdated documents than crippled documents. I'm not trying to argue that the function shouldn't change, but if it is so annoying, you can also resolve this problem by defining your own step function and calling it (forgetting about withC

[Rd] PATCH: install inst/ before doing lazyload on Windows

/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

Re: [Rd] bug in R environments? Was: [BioC] 'recursive default argument' error...

nt contains environments. The lazy loading db is important at runtime when users may only need to access one or two of the environments. We generate the lazy-loading dbs by hand so that users installing from source do not have to repeat the process themselves. Since the environments are lar

Re: [Rd] package check note: no visible global function definition (in functions using Tcl/Tk)

silenced. [Note 1: I don't have any 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] + seth -- Seth Falcon | Computational Bio

Re: [Rd] missing IntegerFromString()

CHARSXP, it does not work. > > So, how could I get the actual values in the column names? How about: SEXP colnums; int *ivals; PROTECT(colnums = coerceVector(cl, INTSXP)); ivals = INTEGER(colnums); Here you convert the STRSXP cl into an INTSXP. If you want the actual int

Re: [Rd] missing IntegerFromString()

#includes other stuff that I don't have and I am > afraid to mess things about by doing things I don't understand. Or > perhaps there is another function that is intended to be used > instead? I think you want asInteger (which calls IntegerFromString). This is in RHOME/incl

Re: [Rd] HTML vignette browser

vailable to them -- I just had a question from someone who wanted to know how to make a plot that appeared in a vignette, for example. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

Re: [Rd] Possible changes to connections

> > http://wiki.r-project.org/rwiki/doku.php?id=developers:r_connections_api I wanted to voice a "me too" for wanting to see an interface 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

Re: [Rd] Possible changes to connections

e when coding R and it would be nice to make it work for connections. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Possible changes to connections

lected when no R object refers to them. This would 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). +

Re: [Rd] S4 assignment \alias and \usage

"TSdoc") <- value ; x }) > > setGeneric("TSdoc", >def= function(x) 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 TSd

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