Re: [Rd] install.packages and bundles
Warnes, Gregory R wrote:
Hi All,
Since I changed the gregmisc package into a bundle, I almost daily questions
asking how to get the individual packages contained in the bundle.
The standard example arises when someone attempts to install and then use my
'genetics' package which depends on the 'gdata' package contained within the
'gregmisc' bundle. The install succedes, but when the user does
library(genetics) they get the error message:
library(genetics)
Loading required package: gdata
Error: package 'gdata' could not be loaded
The user then attempts to install the package 'gdata' not realizing that it
is part of the (e.g.) gregmisc bundle, and can't find it. For example
install.packages(gdata)
trying URL
`http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 24149 bytes
opened URL
downloaded 23Kb
Warning message:
No package gdata on CRAN. in: download.packages(pkgs, destdir =
tmpd,
available = available,
Now the user is in trouble and sends me an error message asking how to get
the 'gdata' package.
A couple of minor changes to the package installation/listing tools would
help alleviate this and some related problems.
1) Modify install.packages() so that the by default dependencies=TRUE,
since this knows how to find dependencies within bundles.
(Why is this FALSE by default anyway? In normal circumstances, is
there any
reason to install a package without installing its
dependencies?)
2) Modify install.packages() to check if a requested package is contained in
a bundle, and install the bundle if so.
This is already done, at least in R-2.0.1 if dependencies is set to
TRUE.
3) Modify CRAN.packages() to list packages contained within bundles as well
as independent packages, so that the windows install packages from CRAN
menu item will properly show bundled packages.
You already get the packages in bundles in the Contains column with
CRAN.packages()[,Contains]
Uwe
Comments?
Gregory R. Warnes
Associate Director, Non-Clinical Statistics
Pfizer Global Research and Development
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Re: [Rd] Standalone Mathlib, C++ and ISNAN()
On 06/01/2005, at 3:31 PM, John W. Eaton wrote: What I finally decided to do for Octave was to use a C language autoconf test for isnan, then provide a function declared extern C that is a wrapper around the C isnan function (if it exists). I also use this method for other functions that may be easier to call from C than directly from C++. Thanks for confirming my suspicions. As far as I can see that is just what R has done with the R_IsNaN function. I am just asking that it be included in the standalone Rmath library. Bill Northcott __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Standalone Mathlib, C++ and ISNAN()
On Thu, 2005-01-06 at 08:29 +1100, Bill Northcott wrote: On 06/01/2005, at 6:53 AM, Thomas Lumley wrote: I believe (with a little Googling) the suggested C++ approach is to use std::isnan if cmath is included. I tried that too, but without any success. I even tried __gnu_cxx::isnan. It was suggested by one of the gcc people, but I could find no documentation about it. The ISO C++ docs do not include isnan as a symbol provided by cmath within the std namespace. I looked at the gcc source code and could see no reason why it should work. I think the workaround is supposed to look like this: #define _GLIBCPP_USE_C99 1 #include cmath #undef _GLIBCPP_USE_C99 #include iostream using __gnu_cxx::isnan; I don't know whether this solves the problem on MacOs X but it is valid on Linux. But do you really want to write code that is specific to gcc? I don't. Martyn __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Broken Link for gregmisc_2.0.0.zip
On Thu, 06 Jan 2005 08:50:44 +0100, Uwe Ligges (UL) wrote: Peter Dalgaard wrote: Warnes, Gregory R [EMAIL PROTECTED] writes: The link from http://cran.r-project.org/src/contrib/Descriptions/gregmisc.html to the windows package gregmisc_2.0.0.zip is broken. Looks like a generic errors in mirroring the windows packages. Has happened before. Not quite, Windows packages are mirrored correctly, but all (?) links to Windows *and* Mac OS X binary packages in the packages' Descriptions on CRAN are broken. Sorry, my fault. I included the index building in a cron job and that was broken. Should work now. Uwe Also, could the appropriate email address for reporting web site problems please be added to the website in some conspicous place? Good idea. Not really ... we had the webmaster address on almost all pages of CRAN until 2 or 3 years ago. I removed it deliberately from most places because way too many people confused it with r-help. And I doubt that people like Greg really have problems finding out how to contact Kurt or me ;-) Best. Fritz __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Broken Link for gregmisc_2.0.0.zip
On Thu, 6 Jan 2005 13:06:51 +0100, [EMAIL PROTECTED] wrote Not really ... we had the webmaster address on almost all pages of CRAN until 2 or 3 years ago. I removed it deliberately from most places because way too many people confused it with r-help. How about a Contact Us link on each page, which goes to a page that lists the various possible contact addresses, with r-help first? We wouldn't want to put in the r-help submission address there; it should be a link to http://www.stat.math.ethz.ch/mailman/listinfo/r-help or some other page that tells people what to expect, and lets them search the archives. Duncan Murdoch __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R 2.1 dies when some text() arguments are NULL (PR#7477)
[My very deepest apologies in advance if this is not plain text; I am recently at a new job in a windows-based environment and have not yet set up my favorite old (pine) system. I have tried my best to strip all formatting from the message..] I'm overlaying plots of tree locations mapped before and after logging activities and checking my matched individuals using several arguments to text() which plot tree attributes by or near their (x,y) locations. R 2.1 dies when a coding error on my part results in a null data.frame... Example: plot(1) text(NULL ~ NULL, label=NULL) This happens for me under Windows 98 and XP. Andrew Robinson was kind enough to try it for me on FreeBSD with the same result. The code returns nothing for me under R 1.9 on Windows 98 and XP (same win. machines). The version details of the three are as follows: # FreeBSD: version _ platform i386-portbld-freebsd5.3 arch i386 os freebsd5.3 system i386, freebsd5.3 status major2 minor0.1 year 2004 month11 day 15 language R # Windows XP: version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor0.1 year 2004 month11 day 15 language R # Windows 98: version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor0.1 year 2004 month11 day 15 language R Please let me know if I can add any more details- Thank you, Rob _ Rob Keefe Cooperative Forestry Research Unit University of Maine __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 2.1 dies when some text() arguments are NULL (PR#7477)
On Fri, 2005-01-07 at 04:44 +0100, [EMAIL PROTECTED] wrote: [My very deepest apologies in advance if this is not plain text; I am recently at a new job in a windows-based environment and have not yet set up my favorite old (pine) system. I have tried my best to strip all formatting from the message..] I'm overlaying plots of tree locations mapped before and after logging activities and checking my matched individuals using several arguments to text() which plot tree attributes by or near their (x,y) locations. R 2.1 dies when a coding error on my part results in a null data.frame... Example: plot(1) text(NULL ~ NULL, label=NULL) This happens for me under Windows 98 and XP. Andrew Robinson was kind enough to try it for me on FreeBSD with the same result. The code returns nothing for me under R 1.9 on Windows 98 and XP (same win. machines). The version details of the three are as follows: # FreeBSD: version _ platform i386-portbld-freebsd5.3 arch i386 os freebsd5.3 system i386, freebsd5.3 status major2 minor0.1 year 2004 month11 day 15 language R # Windows XP: version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor0.1 year 2004 month11 day 15 language R # Windows 98: version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor0.1 year 2004 month11 day 15 language R Please let me know if I can add any more details- Thank you, Rob Your subject line and body refer to R version 2.1, which technically does not exist as 2.1.0 is the current development version. However, your output above indicates that R version 2.0.1 is what you have installed on the three platforms. That is the current released version. In either case, using: Version 2.0.1 Patched (2005-01-02) I get the following: plot(1) text(NULL ~ NULL, label=NULL) Error in text(xy.coords(x, y, recycle = TRUE), labels, adj, pos, offset, : no coordinates were supplied Same thing with: plot(1) text(NULL, NULL, label = NULL) Error in text.default(NULL, NULL, label = NULL) : x and y lengths differ in text(). No crash. There is the following note in the NEWS file for 2.0.1 patched: text()'s default method could segfault if passed 0-length coordinates. So I believe that this fixes the issue that you have posted about. A patched version for Windows is available via CRAN: http://www.cran.mirrors.pair.com/bin/windows/base/rpatched.html and a source code tarball is available for the *nix versions via the FTP link under the R Sources link: ftp://ftp.stat.math.ethz.ch/Software/R/ HTH, Marc Schwartz __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
