Re: [Rd] MacOS X: update.packages(type="mac.binary") fails (PR#7836)
On Wed, 2005-05-04 at 09:01 +0100, Prof Brian Ripley wrote:
>
> This should not be required. What does .Platform say?
>
I couldn't let it be:
> str(.Platform)
List of 6
$ OS.type : chr "unix"
$ file.sep : chr "/"
$ dynlib.ext: chr ".so"
$ GUI : chr "AQUA"
$ endian: chr "big"
$ pkgType : chr "source"
> R.version.string
[1] "R version 2.1.0, 2005-04-18"
(After removing R.app and R.framework, re-installing from R-2.1.0.dmg,
logging out and in -- the last step helped.)
As this is "CRAN Mac OS X build" this seems to be in conflict with
documentation of 'options' "pkgType".
PS.
download.packages("AMORE", type="source", destdir="/tmp")
works in MacOS X (or this one I have here) with any 'type'.
cheers, jari oksanen
--
Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland
Ph. +358 8 5531526, cell +358 40 5136529, fax +358 8 5531061
email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/
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Re: [Rd] MacOS X: update.packages(type="mac.binary") fails (PR#7836)
On Wed, 2005-05-04 at 09:01 +0100, Prof Brian Ripley wrote:
> >
> > This still requires a fix in passing type in update.packages() that B.
> > Ripley already did for R 2.1.1, or setting
> > options(pkgType="mac.binary").
>
> This should not be required. What does .Platform say?
I don't know: R fails to start again in my Mac ("The application R has
unexpectedly quit.") Re-installation and removing all .RData
and .Rhistory do not help this time either (that was the time between
receiving this message and answering now). However, it was the
R-2.1.0.dmg I got from CRAN, I started it in Mac way (clicking the
icon), it was the Mac graphical window. Further, I had checked ?options
which said that default package type in this case should be
"mac.binary". Still it wasn't, but it was "source". I didn't check
the .Platform that time, only pkgType.
It seems that I'll quit using R in MacOS X for a while, since she quits
me in the startup anyway (fortunately I have Linux as my main
environment).
cheers, jari oksanen
--
Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland
Ph. +358 8 5531526, cell +358 40 5136529, fax +358 8 5531061
email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/
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[Rd] MacOS X: update.packages(type="mac.binary") fails (PR#7831)
Full_Name: Jari Oksanen
Version: R 2.1.0
OS: MacOS 10.3.9
Submission from: (NULL) (130.231.102.145)
For various reasons (which need not be expanded here) I have tried to update my
long neglected R in MacOS X using handy command line tool update.packages()
using readily available binaries of contributed packages at CRAN. However, this
fails with message saying that packages _*_tar.gz is not found at the server
(HTTP error 404). Obviously, the package name is expanded wrongly as the binary
packages for MacOS X have type *.tgz. However, this seems not be the problem,
but there are two other problems:
1. update.packages does not transfer the value of 'type' to the next function
install.packages, but install.packages uses the value of getOption("pkgType")
which seems to be "source" in CRAN binary of MacOS X (contrary to documentation
at ?options).
2. If this is corrected, or first set options(pkgType="mac.binary"), the update
fails for missing function .install.macbinary().
The first problem is easy to correct:
--- update.packages.R 2005-05-03 17:13:36.0 +0300
+++ jarioksa.update.packages.R 2005-05-03 17:13:58.0 +0300
@@ -59,5 +59,5 @@
install.packages(update[, "Package"], instlib, contriburl =
contriburl,
method = method, available = available, destdir = destdir,
-installWithVers = installWithVers, type)
+installWithVers = installWithVers, type = type)
}
}
For the second, problem, I don't know what to do. grepping
R-patched_2005-05-03.tar.gz source found only one instance of
.install.macbinary(): the failed call in
R-patched/src/library/utils/R/packages2.R. I couldn't find the definition of the
function.
Do I really have to use GUI? Uh.
cheers, jari oksanen
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[Rd] citation() chops "Roeland " (PR#7797)
Full_Name: Jari Oksanen
Version: 2.0.1, 2.1.0 beta (2005-04-17)
OS: Linux
Submission from: (NULL) (130.231.102.145)
If name ends with "and", such as "Roeland Lastname", citation() will chop "and"
as a separate word giving "Roel and Lastname". This is the case in the upcoming
release of vegan (1.6-8) just submitted to CRAN. Basically, this seems to happen
in utils:::as.personList.default
> unlist(as.personList("Roeland Lastname"))
name.first name.middle name.last name.first name.middle name.last
"" "" "Roel" "" "" "Lastname"
and the culprit line seems to be:
x <- unlist(strsplit(x, "[[:space:]]?(,|and)[[:space:]]+"))
Fortunately, persons like Anders Andtfolk and Mandalay Grandjean are not
chopped, because they don't have space after "and".
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[Rd] stripchart: doc of add (PR#7787)
Full_Name: Jari Oksanen Version: 2.1.0 and 2.0.1 OS: linux Submission from: (NULL) (130.231.102.145) ?stripchart says: add: logical, if true _add_ boxplot to current plot. However, 'add' does not add a boxplot, but it adds a stripchart to an existing plot (overlays). See: example(stripchart) __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] MASS: isoMDS drops names of points in R-2.1.0 (PR#7786)
Full_Name: Jari Oksanen Version: 2.1.0 OS: Linux & MacOS X Submission from: (NULL) (130.231.102.145) isoMDS (MASS) drops names of points. The reason seems to be that R-2.1.0 abandoned names.dist that isoMDS uses to get the Labels attribute of dist object: points <- matrix(tmp$y, , k) rn <- if (is.matrix(d)) rownames(d) else names(d) # This does not work any longer dimnames(points) <- list(rn, NULL) list(points = points, stress = tmp$val) The solution is obvious but not very elegant. __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
