[Rd] R 2.7.2 for Windows fails to install local zip package (PR#12612)
R version 2.7.2 for Windows fails to install local (zipped) packages with following messages: > utils:::menuInstallLocal() updating HTML package descriptions Error in .readRDS(pfile) : error reading from connection > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 2.7.2 for Windows fails to install local zip package (PR#12612)
[EMAIL PROTECTED] wrote: R version 2.7.2 for Windows fails to install local (zipped) packages with following messages: utils:::menuInstallLocal() updating HTML package descriptions Error in .readRDS(pfile) : error reading from connection It works for me. I suspect you have permissions problems. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] S4 coercion
I am extending a DBI connection by
setClass("TSPostgreSQLConnection",
contains=c("PostgreSQLConnection","TSdbOptions"))
but the first time I use this I am getting a warning when it tries to
coerce the TSPostgreSQLConnection to a PostgreSQLConnection. After the
first use the warning stops, but the first warning is causing me
problems when I do automatic checks and set my tests to stop on
warnings. (I think there should be a correct way to do this that does
not produce a warning.) I can trace it back by setting options(warn=2)
as below. Do I need to be more specific about how the coercion
happens? If so, what is the correct way to coerce the
TSPostgreSQLConnection into a PostgreSQLConnection? If not, how to a get
rid of the warning?
Paul Gilbert
> TSdelete("vec", con)
Error: (converted from warning) Ambiguous method selection for "coerce",
target "TSPostgreSQLConnection#integer" (the first of the signatures
shown will be used)
PostgreSQLConnection#integer
dbObjectId#integer
> traceback()
15: doWithOneRestart(return(expr), restart)
14: withOneRestart(expr, restarts[[1]])
13: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
12: .signalSimpleWarning("Ambiguous method selection for \"coerce\",
target \"TSPostgreSQLConnection#integer\" (the first of the signatures
shown will be used)\nPostgreSQLConnection#integer\n
dbObjectId#integer\n",
quote(NULL))
11: warning(gettextf(paste("Ambiguous method selection for \"%s\",
target \"%s\"",
"(the first of the signatures shown will be used)\n%s\n"),
[EMAIL PROTECTED], .sigLabel(classes), paste(" ", names(methods),
collapse = "\n")), domain = NA, call. = FALSE)
10: .findInheritedMethods(signature, fdef, mtable = allmethods, table =
mlist,
useInherited = useInherited, verbose = verbose)
9: selectMethod("coerce", sig, optional = TRUE, c(from = TRUE, to = FALSE),
fdef = coerceFun, mlist = coerceMethods)
8: as(obj, "integer")
7: isIdCurrent(con)
6: postgresqlQuickSQL(conn, statement, ...)
5: dbGetQuery(con, paste("SELECT tbl FROM Meta ", where, ";"))
4: dbGetQuery(con, paste("SELECT tbl FROM Meta ", where, ";"))
3: TSdbi:::TSdeleteSQL(serIDs = serIDs, con = con, ...)
2: TSdelete("vec", con)
1: TSdelete("vec", con)
> str(con)
Formal class 'TSPostgreSQLConnection' [package "TSPostgreSQL"] with 4 slots
..@ Id : int [1:2] 21795 1
..@ dbname : chr "test"
..@ vintage: logi FALSE
..@ panel : logi FALSE
La version française suit le texte anglais.
This email may contain privileged and/or confidential in...{{dropped:26}}
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Re: [Rd] S4 coercion
Hi Paul -- does this make the problem more explicit?
> ## class hierarchy
> setClass("A", representation=representation(a="numeric"))
[1] "A"
> setClass("B", representation=representation(b="numeric"))
[1] "B"
> setClass("C", contains=c("A", "B"))
[1] "C"
> ## coerce methods -- in some instances implicitly created
> setAs("A", "numeric", function(from) slot(from, "a"))
> setAs("B", "numeric", function(from) slot(from, "b"))
> ## trouble: C equidistant from A, B so no unambiguous nearest 'coerce'
> ## method
> as(new("C"), "numeric")
numeric(0)
Warning message:
Ambiguous method selection for "coerce", target "C#numeric" (the first
of the signatures shown will be used)
A#numeric
B#numeric
The solution is to define a method to resolve the conflict, e.g.,
setAs("C", "numeric", function(from) {
## avoid breaking the class abstraction
as(as(from, "A"), "numeric") *
as(as(from, "B"), "numeric")
})
I don't know how you want to break your particular tie; that has to do
with the classes you're extending.
Martin
Paul Gilbert <[EMAIL PROTECTED]> writes:
> I am extending a DBI connection by
>
> setClass("TSPostgreSQLConnection",
> contains=c("PostgreSQLConnection","TSdbOptions"))
>
> but the first time I use this I am getting a warning when it tries to
> coerce the TSPostgreSQLConnection to a PostgreSQLConnection. After
> the first use the warning stops, but the first warning is causing me
> problems when I do automatic checks and set my tests to stop on
> warnings. (I think there should be a correct way to do this that does
> not produce a warning.) I can trace it back by setting
> options(warn=2) as below. Do I need to be more specific about how the
> coercion happens? If so, what is the correct way to coerce the
> TSPostgreSQLConnection into a PostgreSQLConnection? If not, how to a
> get rid of the warning?
>
> Paul Gilbert
>
>
> > TSdelete("vec", con)
> Error: (converted from warning) Ambiguous method selection for
> "coerce", target "TSPostgreSQLConnection#integer" (the first of the
> signatures shown will be used)
>PostgreSQLConnection#integer
>dbObjectId#integer
> > traceback()
> 15: doWithOneRestart(return(expr), restart)
> 14: withOneRestart(expr, restarts[[1]])
> 13: withRestarts({
>.Internal(.signalCondition(simpleWarning(msg, call), msg,
>call))
>.Internal(.dfltWarn(msg, call))
>}, muffleWarning = function() NULL)
> 12: .signalSimpleWarning("Ambiguous method selection for \"coerce\",
> target \"TSPostgreSQLConnection#integer\" (the first of the signatures
> shown will be used)\nPostgreSQLConnection#integer\n
> dbObjectId#integer\n",
>quote(NULL))
> 11: warning(gettextf(paste("Ambiguous method selection for \"%s\",
> target \"%s\"",
>"(the first of the signatures shown will be used)\n%s\n"),
>[EMAIL PROTECTED], .sigLabel(classes), paste(" ", names(methods),
>collapse = "\n")), domain = NA, call. = FALSE)
> 10: .findInheritedMethods(signature, fdef, mtable = allmethods, table
> = mlist,
>useInherited = useInherited, verbose = verbose)
> 9: selectMethod("coerce", sig, optional = TRUE, c(from = TRUE, to = FALSE),
> fdef = coerceFun, mlist = coerceMethods)
> 8: as(obj, "integer")
> 7: isIdCurrent(con)
> 6: postgresqlQuickSQL(conn, statement, ...)
> 5: dbGetQuery(con, paste("SELECT tbl FROM Meta ", where, ";"))
> 4: dbGetQuery(con, paste("SELECT tbl FROM Meta ", where, ";"))
> 3: TSdbi:::TSdeleteSQL(serIDs = serIDs, con = con, ...)
> 2: TSdelete("vec", con)
> 1: TSdelete("vec", con)
> > str(con)
> Formal class 'TSPostgreSQLConnection' [package "TSPostgreSQL"] with 4 slots
> ..@ Id : int [1:2] 21795 1
> ..@ dbname : chr "test"
> ..@ vintage: logi FALSE
> ..@ panel : logi FALSE
>
>
> La version française suit le texte anglais.
>
>
>
> This email may contain privileged and/or confidential in...{{dropped:26}}
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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[Rd] format.data.frame handles names in nested data frames badly (PR#12624)
> d <- data.frame(x=1:3, y=2:4) > d[["r"]] <- d[1]/d[2] > d x y x 1 1 2 0.500 2 2 3 0.667 3 3 4 0.750 It appears that the name "x" was given instead of "r". That is not correct: > names(d) [1] "x" "y" "r" > showStructure(d) # from package splus2R list[3,3] S3 class: data.frame &row.names numeric[ length 3] class: integer $x numeric[ length 3] class: integer $y numeric[ length 3] class: integer $r list[3,1] S3 class: data.frame &row.names numeric[ length 3] class: integer $x numeric[ length 3] class: numeric print.data.frame calls format.data.frame, which loses the name "r" and substitutes the name "x". I suggest that format.data.frame (or print.data.frame) paste together the names, e.g. x y r.x 1 1 2 0.500 2 2 3 0.667 3 3 4 0.750 This generalizes to the case that an included data frame includes two columns. It is also consistent with the behavior for a data frame containing a matrix. > d <- data.frame(x=1:3, y=2:4, A = I(cbind(a=3:5,b=4:6))) > d x y A.a A.b 1 1 2 3 4 2 2 3 4 5 3 3 4 5 6 > showStructure(d) list[3,3] S3 class: data.frame &row.names numeric[ length 3] class: integer $x numeric[ length 3] class: integer $y numeric[ length 3] class: integer $A numeric[3,2] S3 class: AsIs attributes: dimnames --please do not edit the information below-- Version: platform = i486-pc-linux-gnu arch = i486 os = linux-gnu system = i486, linux-gnu status = major = 2 minor = 7.1 year = 2008 month = 06 day = 23 svn rev = 45970 language = R version.string = R version 2.7.1 (2008-06-23) Locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C Search Path: .GlobalEnv, package:Rfixes, package:Rcode, package:aggregate, package:stats, package:graphics, package:grDevices, package:utils, package:datasets, package:showStructure, package:splus2R, package:methods, Autoloads, package:base [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] standard errors for glm
Hi, I'm currently using biglm package to compute GLM outputs on a very large dataset. But no function computes standard erros of predictions. I look in what is done in R, namely in the function predict.glm.R in stats package. In this function, we call predict.lm to compute the standard errors (line 51). The code of predict.lm (in lm.R) is very hard to understand. I wonder if there is any good reference and / documentation on this topic? the manual at http://www.nag.co.uk/numeric/cl/Manual/pdf/G02/g02gbc.pdfprovides a good overview of the method used in R, but there is no reference to standard errors... I suppose this topic have already raised in the past, but I found only this http://tolstoy.newcastle.edu.au/R/help/04/08/1762.html Thanks in advance Christophe [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] specifying compiler path in configure
I'm having trouble building some packages while running Debian Lenny (testing) and suspect that the issues are related to the default use of gcc-4.3. With Lenny, build-essentials depends on 4.3, so I'd like to leave it installed but have also installed 4.2.1. How do I tell ./configure the path to 4.2.1 ? I"m sure it's an option, but I don't see it documented in the R-admin manual. Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] specifying compiler path in configure
On Wed, 27 Aug 2008, Mark Kimpel wrote: I'm having trouble building some packages while running Debian Lenny (testing) and suspect that the issues are related to the default use of gcc-4.3. You might want to compare your problems with the CRAN checks at http://cran.r-project.org/web/checks/check_summary.html as those are run with gcc 4.3.x on Debian testing. From memory, the problems are confined to C++-(mis)using packages. With Lenny, build-essentials depends on 4.3, so I'd like to leave it installed but have also installed 4.2.1. How do I tell ./configure the path to 4.2.1 ? I"m sure it's an option, but I don't see it documented in the R-admin manual. From configure --help: CC C compiler command CFLAGS C compiler flags There are many examples of setting CC in the R-admin manual, and the first para of 'Essential Programs' seems to me to tell you that as well. -- Brian D. Ripley, [EMAIL PROTECTED] 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] specifying compiler path in configure
Mark, On 27 August 2008 at 16:21, Mark Kimpel wrote: | I'm having trouble building some packages while running Debian Lenny | (testing) and suspect that the issues are related to the default use | of gcc-4.3. With Lenny, build-essentials depends on 4.3, so I'd like | to leave it installed but have also installed 4.2.1. How do I tell | ./configure the path to 4.2.1 ? I"m sure it's an option, but I don't | see it documented in the R-admin manual. a) That's an r-sig-debian question, so please post there. As a quick hint a.1) solve it the Debian way via alternatives: man update-alternatives a.2) solve it the standard Unix/GNU way by telling configure what to use for CC, CXX, ... The GNU tools respect those choices. but b) All of Debian's r-cran-* package are built using the most current (ie now 4.3) compiler; other had done complete archive rebuilds before 4.3 was released. The low-hanging fruits (ie easy errors of missing headers etc) have all been addressed. c) Just to lift the lid a little here, but our Google Summer of Code project is coming along just fine, thanks to outstanding work by Charles (the student) and now with hardware support from WU Wien which is letting us hammer away on Xen instance. As of right now: [EMAIL PROTECTED]:~$ sqlite3 /var/cache/cran2deb/cran2deb.db "select count(package),success from builds group by success;" 157|0 1340|1 [EMAIL PROTECTED]:~$ r -e'print(1340/(157+1340)*100)' [1] 89.51236 [EMAIL PROTECTED]:~$ 89.9% autobuild and we're not quite done yet in terms of adding manual translations of SystemRequirements into Debian's Depends: I suspect a local mishap at your end and invite you to post some details at r-sig-debian -- I'm sure we get that sorted out. Dirk -- Three out of two people have difficulties with fractions. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
