Re: [Rd] R 2.12.0 beta (r53110) fails make check on Ubuntu hardy
Thanks for the quick answer. We will use the builtin BLAS then. Matthias Prof Brian Ripley wrote, On 10/04/10 15:17: > So your system has a broken BLAS and you need to use the builtin one. > > On Mon, 4 Oct 2010, it-r-de...@ml.epigenomics.com wrote: >> >> Hi! [...] -- Matthias BurgerProject Manager, Assay Transfer Epigenomics AG Kleine Praesidentenstr. 1 10178 Berlin, Germany phone:+49-30-24345-0 fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] RUnit bug?
Romain has already given you the answer. As would have the help page ?defineTestSuite Not a bug, but a user error, I assume. Matthias Dominick Samperi wrote, On 04/22/10 02:19: > There appears to be a bug in RUnit. > > Given a testsuite testsuite.math, say, when I run: > > runTestSuite(testsuite.math) > > this works fine, provided there are no extraneous files in the > unit test subdirectory. > > But if there are any Emacs temp files (with names that > end with '~') then runTestSuite gets confused and tries to > run functions from the temp files as well. > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Matthias Burger Project Manager/ Biostatistician Epigenomics AG Kleine Praesidentenstr. 1 10178 Berlin, Germany phone:+49-30-24345-0 fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R devel repository tarball naming issue
Hi, we noticed that since some time after Aug 24th the daily snapshots provided on ftp://ftp.stat.math.ethz.ch/Software/R/ no longer have their default tarball file name but dropped the date stamp, i.e. R-devel_.tar.bz2 Same for R-patched snapshots. Could one of the maintainers please take a look. We rely on the default naming convention for automatic builds. Regards, Matthias -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-0fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Link to pdf documentation from other package ?
Ulrike Grömping wrote, On 11/18/09 13:28:
> Duncan Murdoch schrieb:
>> Ulrike Groemping wrote:
>>>
>>> Duncan Murdoch-2 wrote:
>>>
Ulrike Groemping wrote:
> Dear developeRs,
>
> I have not found anything recent about how to link to a vignette or
> other
> documentation from within Rd-files. Is this now possible with the new
> help
> system ? For example, I would like to link to the file AlgDesign.pdf
> provided within the doc directory of package AlgDesign.
>
>
Yes, you can do it with a \url{} macro. Use a relative link, acting
as though the starting page is located in
/library/AlgDesign/html/*. So \url{../doc/AlgDesign.pdf}
should work from the same package,
\url{../../AlgDesign/doc/AlgDesign.pdf} from elsewhere. Please let
me know if this doesn't work, I haven't tested.
Duncan Murdoch
>>>
>>> Yes, this works, thanks! Is it also possible to display an
>>> alternative text
>>> instead of the URL itself, like with other links (e.g. show text
>>> "Open pdf"
>>> that operates the link) ?
>>>
>>>
>>
>> There's no optional text in the \url{} tag, but you could embed it in
>> an \ifelse tag, e.g.
>>
>> \ifelse{html}{\url{ }}{ [open pdf ...] }
>>
>> might work. Using the \ifelse tag will make your package depend on R
>> >= 2.10.0.
>>
>> Duncan Murdoch
>>>
> Another thought: the link only works, if the two packages are installed
> in the same library, doesn't it ? Would there be a way to make it work
> independently of this restriction ?
you could use the Sweave like macro to compute the path inside the Rd
environments
\Sexpr{file.path(system.file(package="AlgDesign", "doc"), "AlgDesign.pdf")}
described in 'Writing R extensions' 2.11
> Regards, Ulrike
>
> __
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>
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Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-0fax:+49-30-24345-555
http://www.epigenomics.com matthias.bur...@epigenomics.com
--
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Vorstand: Geert Nygaard (CEO/Vorsitzender)
Oliver Schacht PhD (CFO)
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[Rd] R 2.5.0 devel try issue in conjuntion with S4 method dispatch
Hi,
after updating R 2.5.0 devel yesterday we today observed many new
unexpected failures in our daily package build and test system runs,
which can be traced to recent changes in the implementation in try()
(as noted in NEWS).
Investigating this new implementation I come across an issue in
conjuntion with using S4 classes and methods. try(expr) does not return an
object with attribute 'try-error' in case of method dispatch failure
in the wrapped expression which to me seems not
quite correct.
Examples to reproduce the observation:
## using functions all is well:
f <- function(x) { print(x); ret<-try(stop("forced.")); print(ret)}
f(3)
[1] 3
Error in try(stop("forced.")) : forced.
[1] "Error in try(stop(\"forced.\")) : forced.\n"
attr(,"class")
[1] "try-error"
## using S4 classes and methods
setClass("fooBase",
representation("VIRTUAL",
width = "numeric",
height = "numeric"),
prototype(width = 1024,
height = 1024),
validity = NULL,
where= .GlobalEnv,
sealed = TRUE,
)
if (!isGeneric("plotObject")) {
setGeneric("plotObject",
def=function(x, y, ...) {
value <- standardGeneric("plotObject")
return(value)
},
where=.GlobalEnv,
useAsDefault=TRUE
)
}
setClass("foo",
representation("fooBase"),
validity = NULL,
where= .GlobalEnv,
sealed = TRUE)
plotObject.foo <- function(x, y) {
plot(x,y)
}
setMethod("plotObject", signature=c("foo", "numeric"), plotObject.foo,
where=.GlobalEnv)
fooObject <- new("foo")
## should fail and return object with attribute 'try-error' set
ret <- try(plotObject(fooObject, character(1)))
Error in as.list(call)[[1]] == "doTryCatch" :
comparison (1) is possible only for atomic and list types
>is(ret)
Error in .class1(object) : object "ret" not found
which I belive is in contradiction to the documentation, where in
Details:
The value of the expression if 'expr' is evaluated without error,
but an invisible object of class '"try-error"' containing the
error message if it fails.
This is crucial for our current implementation of check functions in
package RUnit.
Is this new behaviour 'as intended' and only the documentation has not
caught up?
Regards,
Matthias
>sessionInfo()
R version 2.5.0 Under development (unstable) (2007-03-13 r40832)
i686-pc-linux-gnu
locale:
C
attached base packages:
[1] "stats" "graphics" "grDevices" "datasets" "utils" "methods"
[7] "base"
other attached packages:
rcompletionrcompgen
"0.1-2" "0.1-5"
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-371 fax:+49-30-24345-555
http://www.epigenomics.com [EMAIL PROTECTED]
--
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Vorstand: Geert Nygaard (CEO/Vorsitzender), Dr. Kurt Berlin (CSO)
Oliver Schacht PhD (CFO), Christian Piepenbrock (COO)
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Re: [Rd] R 2.5.0 devel try issue in conjuntion with S4 method dispatch
Peter Dalgaard wrote: > Matthias Burger wrote: >> Hi Seth, >> > [...] >> > I have just committed my variation of Seth's patch, so please check the > current r-devel too. For the record: With R 2.5.0 devel (2007-03-18 r40854) the issue I was concerned about has been resolved. Thanks to all of you! Regards, Matthias > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-371 fax:+49-30-24345-555 http://www.epigenomics.com [EMAIL PROTECTED] -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender), Dr. Kurt Berlin (CSO) Oliver Schacht PhD (CFO), Christian Piepenbrock (COO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] ifelse behaviour
Hi! I'm puzzled by the return value of ifelse consider x<-integer(0) ifelse(is(x, "character"), paste(x), x) [1] NA whereas if (is(x, "character")) return(paste(x)) else x [1] integer(0) or x<-integer(1) ifelse(is(x, "character"), paste(x), x) [1] 0 work as I had anticipated. Is this correct behaviour? Regards, Matthias >sessionInfo() R version 2.5.0 (2007-04-23) i686-pc-linux-gnu locale: C attached base packages: [1] "stats" "graphics" "grDevices" "datasets" "utils" "methods" [7] "base" other attached packages: rcompletionrcompgen "0.1-2""0.1-10" -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-371 fax:+49-30-24345-555 http://www.epigenomics.com [EMAIL PROTECTED] -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender), Dr. Kurt Berlin (CSO) Oliver Schacht PhD (CFO), Christian Piepenbrock (COO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] ifelse behaviour
Duncan Murdoch wrote: > On 4/26/2007 9:53 AM, [EMAIL PROTECTED] wrote: >> Hi! >> >> I'm puzzled by the return value of ifelse >> >> consider >> >> x<-integer(0) >> ifelse(is(x, "character"), paste(x), x) >> [1] NA > > The test evaluates to a length 1 logical vector containing FALSE. So > ifelse() tries to return the first entry of x. But x[1] doesn't exist, > so it evaluates to NA, and that's what ifelse() returns. Thank you for the explanation! Regards, Matthias >> >> whereas >> if (is(x, "character")) return(paste(x)) else x >> [1] integer(0) > > This is quite different. It says to return the expression in the else > clause, which is x. >> >> or >> x<-integer(1) >> ifelse(is(x, "character"), paste(x), x) >> [1] 0 >> >> work as I had anticipated. Is this correct behaviour? > > Yes, this is correct. > > Duncan Murdoch > -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-371 fax:+49-30-24345-555 http://www.epigenomics.com [EMAIL PROTECTED] -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender), Dr. Kurt Berlin (CSO) Oliver Schacht PhD (CFO), Christian Piepenbrock (COO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] getNamespaceExports("base") error
Hi!
>getNamespaceExports("base")
Error in ls(NULL, all = TRUE) : using 'as.environment(NULL)' is defunct
getNamespaceExports
function (ns)
{
ns <- asNamespace(ns)
if (isBaseNamespace(ns))
ls(NULL, all = TRUE)
else ls(getNamespaceInfo(ns, "exports"), all = TRUE)
}
One possible way to fix this could be to changed to e.g.
if (isBaseNamespace(ns))
ls(envir=baseenv(), all = TRUE)
Observed with
R 2.5.0 & R 2.6.0 devel (2007-05-12 r41546)
(one has to go back to R 2.3.1 to see it working)
Regards,
Matthias
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-371 fax:+49-30-24345-555
http://www.epigenomics.com [EMAIL PROTECTED]
--
Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861
Vorstand: Geert Nygaard (CEO/Vorsitzender), Dr. Kurt Berlin (CSO)
Oliver Schacht PhD (CFO), Christian Piepenbrock (COO)
Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender)
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Re: [Rd] getNamespaceExports("base") error
Prof Brian Ripley wrote:
> It would seem more logical to use x. Today it has the
> same contents as baseenv() (but a different enclosing env), but that may
> change.
>
> I do wonder why you are using this: the R code clearly doesn't. For
> base is not a normal namespace and is automatically imported into every
> other namespace (or similar words, as 'import' is used in a couple of
> senses in the documentation).
I came across this programmatically applying getNamespaceExports to a
vector of namespaces
where 'base' happend to be a member.
I will use ls(.BaseNamespaceEnv, all=TRUE) instead .
Thank you!
Matthias
> On Tue, 15 May 2007, [EMAIL PROTECTED] wrote:
>
>>
>> Hi!
>>
>> >getNamespaceExports("base")
>> Error in ls(NULL, all = TRUE) : using 'as.environment(NULL)' is defunct
>>
>> getNamespaceExports
>> function (ns)
>> {
>> ns <- asNamespace(ns)
>> if (isBaseNamespace(ns))
>> ls(NULL, all = TRUE)
>> else ls(getNamespaceInfo(ns, "exports"), all = TRUE)
>> }
>>
>>
>> One possible way to fix this could be to changed to e.g.
>>
>> if (isBaseNamespace(ns))
>> ls(envir=baseenv(), all = TRUE)
>>
>> Observed with
>> R 2.5.0 & R 2.6.0 devel (2007-05-12 r41546)
>> (one has to go back to R 2.3.1 to see it working)
>>
>>
>> Regards,
>>
>> Matthias
>>
>>
>>
>
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-371 fax:+49-30-24345-555
http://www.epigenomics.com [EMAIL PROTECTED]
--
Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861
Vorstand: Geert Nygaard (CEO/Vorsitzender), Dr. Kurt Berlin (CSO)
Oliver Schacht PhD (CFO), Christian Piepenbrock (COO)
Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender)
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[Rd] methods::is problem in R 2.7.0 & R 2.8.0 devel
Hi,
x <- 1L
class(x) <- c("myInt", "integer")
is(x)
Error in inherits(x, "factor") :
argument "class2" is missing, with no default
The problem arises when is() is used with only one argument (object)
which has more than one class reported by class(object).
In the code is() does use variable "class2" before checking for its
presence.
Reversing the order of checks
is2 <- function(object, class2) {
cl <- class(object)
if (missing(class2))
return(extends(cl))
if (length(cl) > 1)
return(class2 %in% cl)
if (.identC(cl, class2) || .identC(class2, "ANY"))
return(TRUE)
ext <- possibleExtends(cl, class2)
if (is.logical(ext))
ext
else if ([EMAIL PROTECTED])
TRUE
else [EMAIL PROTECTED](object)
}
is2(x)
[1] "myInt" "integer"
This is not sufficient, though:
utils::data(npk, package="MASS")
ret <- aov(yield ~ block + N*P*K, npk)
is2(ret)
[1] "aov" "lm" "lm" "mlm" "oldClass" "oldClass"
with duplicate class names
due to
extends(class(ret))
[1] "aov" "lm" "lm" "mlm" "oldClass" "oldClass"
so something different would be needed.
Best,
Matthias
> sessionInfo()
R version 2.7.0 RC (2008-04-15 r45347)
i686-pc-linux-gnu
locale:
[EMAIL
PROTECTED];LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=C;[EMAIL
PROTECTED];LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL
PROTECTED];LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
--
Matthias Burger Project Manager/ Biostatistician
Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-371 fax:+49-30-24345-555
http://www.epigenomics.com [EMAIL PROTECTED]
--
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Vorstand: Geert Nygaard (CEO/Vorsitzender), Dr. Kurt Berlin (CSO)
Oliver Schacht PhD (CFO), Christian Piepenbrock (COO)
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[Rd] R 2.9.0 devel: package installation with configure-args option
Hi, trying to install a package containing C code and requiring non-default configure argument settings the incantation (this has worked for R <= 2.8.1 on the same architectures) R CMD INSTALL --configure-args="--with-opt1 --with-opt2" packname does always result in a warning Warning: unknown option '--with-opt2' and consequently the option is ignored. Reverting the order of options results in the now last option to be ignored. Alternative quoting has not provided a solution. Using R CMD INSTALL --configure-args=--with-opt1 --configure-args=--with-opt2 packname does provide a workaround, though. Is this the (new to me) and only intended way to provide more than one configure argument? I checked ?INSTALL and the referenced R-admin sec. 'Configuration variables' but still am not clear on this. Regards, Matthias R version 2.9.0 Under development (unstable) (2009-03-02 r48041) on Ubuntu 8.04, 8.10 -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-0fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] methods package
Terry Therneau wrote:
> I'm working on the next version of coxme, one step of which is converting
> the bdsmatrix library from Splus to R. Actually, it is a conversion from
> S4 methods as first described in the Green book to S4 methods as they
> currently exist. Mostly it's going ok, but not entirely.
>
> 1. The biggest issue is lack of documentation. The online help pages have
> not been a help; they keep saying it's "as found in the green book - almost".
> I've looked for the package on CRAN in the hopes for more there, but can't
> find it. Perchance there is something obvious that I am missing?
>
> 2. The changes are small but numerous. The current one that has me puzzled
> is a method for addition:
>setMethod(Ops, signature=c('numeric', 'bdsmatrix'),
>
> Let xmat be ordinary and bmat be a bdsmatrix. In the old code "xmat + bmat"
> fell to this method (which knows what to do), in the current R I get
> failure due to no method found. is.numeric(xmat) is TRUE.
>What is the fix?
Assuming xmat to be a numeric matrix e.g. diag(n).
S4 inheritance will be determined by is() and
is(xmat, "numeric") will be FALSE
So one solution is to provide explicit methods for signature 'matrix' i.e.
setMethod(Ops, signature=c('matrix', 'bdsmatrix'),
setMethod(Ops, signature=c('bdsmatrix', 'matrix'),
Matthias
> 3. In the green book the examples used .Dim and .Dimnames slots, the Matrix
> library uses Dim and Dimnames. Is there a good reason to choose one or the
> other?
>
> I'll be out of town for the next few days (son's wedding) so instant
> response
> is not necessary.
>
> Terry Therneau
>
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>
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Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany
phone:+49-30-24345-0fax:+49-30-24345-555
http://www.epigenomics.com matthias.bur...@epigenomics.com
--
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Vorstand: Geert Nygaard (CEO/Vorsitzender)
Oliver Schacht PhD (CFO)
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Re: [Rd] R 2.9.0 devel: package installation with configure-args option
Prof Brian Ripley wrote: > I think this should now work (one of several 'FIXME' issues addressed in > the latest commit -- there are still some to go, but 2.9.0 is not due > for 6 weeks). tested and confirmed with R devel revision r48059; more than one configure arguments are now handled correctly. Thank you for the fix! Regards, Matthias > It is always useful to have a real test example, though. (I used rgl in > relation to some discussion about paths on r-sig-mac.) > > On Tue, 3 Mar 2009, Prof Brian Ripley wrote: > >> That version of R is 'under development' and the INSTALL file says >> >> ## FIXME: this loses quotes, so filepaths with spaces in get broken up >> >> so it is I think the same as a known issue. >> >> The whole package installation process has been completely >> reconstructed for R-devel, and the process is not quite finished. >> And this is a low priority as there are effective workarounds. >> >> On Tue, 3 Mar 2009, ml-it-r-de...@epigenomics.com wrote: >> >>> >>> Hi, >>> >>> trying >>> to install a package containing C code and requiring non-default >>> configure argument >>> settings the incantation (this has worked for R <= 2.8.1 on the same >>> architectures) >>> >>> R CMD INSTALL --configure-args="--with-opt1 --with-opt2" packname >>> >>> does always result in a warning >>> Warning: unknown option '--with-opt2' >>> >>> and consequently the option is ignored. Reverting the order of >>> options results in the now >>> last option to be ignored. Alternative quoting has not provided a >>> solution. >>> >>> Using >>> >>> R CMD INSTALL --configure-args=--with-opt1 >>> --configure-args=--with-opt2 packname >>> >>> does provide a workaround, though. Is this the (new to me) and only >>> intended way to >>> provide more than one configure argument? >>> I checked ?INSTALL and the referenced R-admin sec. 'Configuration >>> variables' but still am >>> not clear on this. >>> >>> Regards, Matthias >>> >>> >>> R version 2.9.0 Under development (unstable) (2009-03-02 r48041) >>> on Ubuntu 8.04, 8.10 >>> >>> -- >>> Matthias Burger Project Manager/ Biostatistician >>> Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany >>> phone:+49-30-24345-0fax:+49-30-24345-555 >>> http://www.epigenomics.com matthias.bur...@epigenomics.com >>> -- >>> Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 >>> Vorstand: Geert Nygaard (CEO/Vorsitzender) >>> Oliver Schacht PhD (CFO) >>> Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) >>> >>> __ >>> 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 >> > -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-0fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R (2.9.0 rc) CMD INSTALL will leave OOLOCK folder even if installation succeeded
Hi, since a couple of days ago I see failures when using R CMD INSTALL -l lib path-to-src/pkg.tar.gz This occurs in automated library updating via a shell script and is caused by the immediate preceding call to leave an 00LOCK folder even though the package installation of that call succeeded. This occurs at random (no obvious/systematic correlation to package name or or such) and only for packages where an earlier version has been installed into the same library location. e.g. ~/R/hardy$ R-2.9.0/bin/R CMD INSTALL -l R-2.9.x-libs R-2.9.x-libsSrc/CRAN/feature_1.2.3.tar.gz ... ** building package indices ... * DONE (feature) but ~/R/hardy$ ls -al R-2.9.x-libs/00LOCK/feature/ total 0 lrwxrwxrwx 1 XXX epiR 39 Mar 27 05:56 feature -> /mnt/local/R/hardy/R-2.9.x-libs/feature/ ?INSTALL tells me of a workaround via --unsafe or --no-lock but I would prefer to use the default incantation. Any insights what the cause could be? Regards, Matthias R version 2.9.0 RC (2009-04-10 r48321) on Ubuntu hardy -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-0fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
