load AnnBuilder and install XML
3
0
Entering edit mode
zhihua li ▴ 120
@zhihua-li-1129
Last seen 9.6 years ago
Hi netters I've downloaded and installed AnnBuilder. When I loaded it, I was told that the dependent package XML had not been installed. According to the manual of AnnBuilder, the XML package can be found in CRAN. But I can't find a windows binary there. Instead, I went to http://www.omegahat.org/RSXML/index.html and downloaded XML_0.97-0.zip there. I used the menu of "install packages from local zip file" and it seemed that I've installed XML sucessfully: package 'XML' successfully unpacked and MD5 sums checked updating HTML package descriptions But then when I loaded AnnBuilder, I still got: > library(AnnBuilder) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: XML Error in library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) : 'XML' is not a valid package -- installed < 2.0.0? I'm using R 2.0.1 actually. Is there something wrong with windows version of XML? Thanks a lot!
AnnBuilder AnnBuilder • 1.0k views
ADD COMMENT
0
Entering edit mode
John Zhang ★ 2.9k
@john-zhang-6
Last seen 9.6 years ago
>I've downloaded and installed AnnBuilder. When I loaded it, I was told that >the dependent package XML had not been installed. >According to the manual of AnnBuilder, the XML package can be found in >CRAN. But I can't find a windows binary there. Instead, I went to >http://www.omegahat.org/RSXML/index.html and downloaded XML_0.97-0.zip >there. >I used the menu of "install packages from local zip file" and it seemed >that I've installed XML sucessfully: >package 'XML' successfully unpacked and MD5 sums checked >updating HTML package descriptions > >But then when I loaded AnnBuilder, I still got: >> library(AnnBuilder) >Loading required package: Biobase >Loading required package: tools >Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. >Loading required package: XML >Error in library(pkg, character.only = TRUE, logical = TRUE, lib.loc = >lib.loc) : > 'XML' is not a valid package -- installed < 2.0.0? > >I'm using R 2.0.1 actually. > >Is there something wrong with windows version of XML? The XML package was built using an earlier version of R. You may have to rebuild it under R 2.0.1. > >Thanks a lot! > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 3 hours ago
United States
zhihua li wrote: > Hi netters > > I've downloaded and installed AnnBuilder. When I loaded it, I was told > that the dependent package XML had not been installed. > According to the manual of AnnBuilder, the XML package can be found in > CRAN. But I can't find a windows binary there. Instead, I went to > http://www.omegahat.org/RSXML/index.html and downloaded XML_0.97-0.zip > there. I used the menu of "install packages from local zip file" and it > seemed that I've installed XML sucessfully: > package 'XML' successfully unpacked and MD5 sums checked > updating HTML package descriptions > > But then when I loaded AnnBuilder, I still got: > >> library(AnnBuilder) > > Loading required package: Biobase Loading required package: tools > Welcome to Bioconductor Vignettes contain introductory > material. To view, simply type: openVignette() For > details on reading vignettes, see > the openVignette help page. > Loading required package: XML Error in library(pkg, character.only = > TRUE, logical = TRUE, lib.loc = lib.loc) : 'XML' is not a valid > package -- installed < 2.0.0? > > I'm using R 2.0.1 actually. > > Is there something wrong with windows version of XML? No, you just did things in an unnecessarily difficult way. install.packages("XML") will get you what you need. > > Thanks a lot! > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD COMMENT
0
Entering edit mode
Actually I've tried to install XML directly from CRAN. But it failed. > install.packages("XML") trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 27110 bytes opened URL downloaded 26Kb Warning message: No package "XML" on CRAN. in: download.packages(pkgs, destdir = tmpd, available = available, I also tried this: > library(reposTools) Loading required package: tools > > install.packages2("XML") Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users Unable to locate the requested package(s) in any known repository As a lot of documentation and mailing responses suggest installing XML directly from CRAN, it seems that the windows version of XML has ever existed in CRAN repository, but later been removed (for copyright issues)? >From: "James W. MacDonald" <jmacdon@med.umich.edu> >To: zhihua li <lzhtom@hotmail.com> >CC: bioconductor@stat.math.ethz.ch >Subject: Re: [BioC] load AnnBuilder and install XML >Date: Thu, 17 Mar 2005 09:32:21 -0500 > >zhihua li wrote: > > Hi netters > > > > I've downloaded and installed AnnBuilder. When I loaded it, I was told > > that the dependent package XML had not been installed. > > According to the manual of AnnBuilder, the XML package can be found in > > CRAN. But I can't find a windows binary there. Instead, I went to > > http://www.omegahat.org/RSXML/index.html and downloaded XML_0.97-0.zip > > there. I used the menu of "install packages from local zip file" and it > > seemed that I've installed XML sucessfully: > > package 'XML' successfully unpacked and MD5 sums checked > > updating HTML package descriptions > > > > But then when I loaded AnnBuilder, I still got: > > > >> library(AnnBuilder) > > > > Loading required package: Biobase Loading required package: tools > > Welcome to Bioconductor Vignettes contain introductory > > material. To view, simply type: openVignette() For > > details on reading vignettes, see > > the openVignette help page. > > Loading required package: XML Error in library(pkg, character.only = > > TRUE, logical = TRUE, lib.loc = lib.loc) : 'XML' is not a valid > > package -- installed < 2.0.0? > > > > I'm using R 2.0.1 actually. > > > > Is there something wrong with windows version of XML? > >No, you just did things in an unnecessarily difficult way. > >install.packages("XML") > >will get you what you need. > > > > > > Thanks a lot! > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >-- >James W. MacDonald >Affymetrix and cDNA Microarray Core >University of Michigan Cancer Center >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109 >734-647-5623
ADD REPLY
0
Entering edit mode
Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
"James W. MacDonald" <jmacdon@med.umich.edu> writes: >> I'm using R 2.0.1 actually. >> >> Is there something wrong with windows version of XML? > > No, you just did things in an unnecessarily difficult way. > > install.packages("XML") > > will get you what you need. With R 2.0.1 that should work because the default is for install.packages to use the main CRAN site. If you use a CRAN mirror, you _might_ not be able to find the Windows binary XML package. It is a special case I think because it isn't as easy as other packages to build on Windows. And to clarify the error message: The binary version you found was built with an older version of R and so isn't compatible with your R. Best, + seth
ADD COMMENT
0
Entering edit mode
Seth Falcon wrote: > "James W. MacDonald" <jmacdon@med.umich.edu> writes: > >>>I'm using R 2.0.1 actually. >>> >>>Is there something wrong with windows version of XML? >> >>No, you just did things in an unnecessarily difficult way. >> >>install.packages("XML") >> >>will get you what you need. > > > With R 2.0.1 that should work because the default is for > install.packages to use the main CRAN site. > > If you use a CRAN mirror, you _might_ not be able to find the Windows > binary XML package. It is a special case I think because it isn't as > easy as other packages to build on Windows. Yep, you are correct. On R-2.0.1 install.packages("XML") doesn't work out of the box. On R-2.1.0, install.packages() finds the correct version at BDR's website. A version that will work with R-2.0.1 can be found here: http://www.stats.ox.ac.uk/pub/RWin/2.0.0/XML_0.97-0.zip Jim > > And to clarify the error message: The binary version you found was > built with an older version of R and so isn't compatible with your R. > > Best, > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD REPLY

Login before adding your answer.

Traffic: 904 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6