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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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windows(linux)R与bioconductor包的安装  

2009-11-04 18:35:56|  分类: R&Bioconductor |  标签: |举报 |字号 订阅

  下载LOFTER 我的照片书  |
http://www.r-project.org/
http://www.bioconductor.org/

R2.10.1在linux下安装 
解压r.2.10.1的tar文件,然后进入这个目录
# ./configure
# make
#make install
# R(即可运行)

安装R package的2种方法

http://i.azpala.com/2008/05/01/install-r-packages/

1. 自动安装

在R的控制台,输入

install.packages(”stepNorm”, dependencies = TRUE)

这种方法可能找不到需要的package,那么可以用方法2

2. 手动安装

Windows:

下载package.zip文件

打开R的菜单栏->Packages->“Install package from local zip file…”

选择package.zip文件

Linux:

下载package.tar.gz文件

在Shell终端(注意不是R)输入:

sudo R CMD INSTALL package.tar.gz

有人说要用 sudo R CMD INSTALL –build package.tar.gz 没试过。。


  本 地 安 装 两 个 包, XML_0.99-5.tar.gz, RSPerl_0.8-0.tar.gz
install.packages(
    c("XML_0.99-5.tar.gz",
    "../../Interfaces/Perl/RSPerl_0.8-0.tar.gz")
或者:
sudo R CMD INSTALL rgl\_0.81.tar.gz

         升级更新包

  update.packages()



How to install an R package?

http://wiki.r-project.org/rwiki/doku.php?id=getting-started:installation:packages

The official documentation for such a task is included in the R Installation and Administration, a PDF manual installed with each R version. Here is a quick mini ‘HowTo’ summarizing the operations for the easiest way, that is, by using de>install.packages()de>.

Linux/Unix

Look at CRAN to determine if a binary version exists for your system.

Otherwise, you still can compile packages from sources. The simplest way to download a package from CRAN and to install it is by using the de>install.packages()de> function (make sure you install also all required dependencies). For example, to download and install the package called “mypkg”:

install.packages("mypkg", dependencies = TRUE)

Of course, this only works if your computer is connected to the Internet and if all tools required to compile packages are installed (see the manual if it fails).

Another way of installing a package is in de>batch modede> that is, without starting R you should download the package tarball (i.e. package-name.tar.gz) file you want to install and then issue as root from your usual shell (bash, csh, sh,etc.) and under the same directory in which the tarball is:

R CMD INSTALL package-name.tar.gz

Windows

Using Rgui, the default R front-end under Windows, you can install packages from the menu: de>Packages -> Install package(s)...de>. The first time, R asks for a mirror. Choose the one nearest to you in the list. Then, select the package(s) you want to install in the list. If the operation fails, look at the manual and the de>RW-FAQde> for more information.

MacOS X

You can use de>install.packages()de> or de>R CMD INSTALLde> the same way as for Linux/Unix. The Mac GUI also provides a Package Installer for convenient point-and-click installation and updating of packages from various repositories.

Unix users should be aware that the default package type for de>install.packages()de> on Mac OS X is binary unlike on other unix systems.





bioconductor包的安装

R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R是自由软件软件,不带任何担保。
在某些条件下你可以将其自由散布。
用'license()'或'licence()'来看散布的详细条件。

R是个合作计划,有许多人为之做出了贡献.
用'contributors()'来看合作者的详细情况
用'citation()'会告诉你如何在出版物中正确地引用R或R程序包。

用'demo()'来看一些示范程序,用'help()'来阅读在线帮助文件,或
用'help.start()'通过HTML浏览器来看帮助文件。
用'q()'退出R.

> source("http://bioconductor.org/biocLite.R")
> biocLite()
Using R version 2.10.0 (R-devel), biocinstall version 2.5.5.
Installing Bioconductor version 2.5 packages:
[1] "affy" "affydata" "affyPLM" "annaffy"
[5] "annotate" "Biobase" "biomaRt" "Biostrings"
[9] "DynDoc" "gcrma" "genefilter" "geneplotter"
[13] "hgu95av2.db" "limma" "marray" "multtest"
[17] "vsn" "xtable" "affyQCReport"
Please wait...

also installing the dependencies ‘DBI’, ‘RSQLite’, ‘bitops’, ‘affyio’, ‘preprocessCore’, ‘GO.db’, ‘KEGG.db’, ‘AnnotationDbi’, ‘XML’, ‘RCurl’, ‘IRanges’, ‘RColorBrewer’, ‘org.Hs.eg.db’, ‘simpleaffy’

试开URL’http://cran.fhcrc.org/bin/windows/contrib/2.10/DBI_0.2-4.zip'
Content type 'application/zip' length 375508 bytes (366 Kb)
打开了URL
downloaded 366 Kb

试开URL’http://cran.fhcrc.org/bin/windows/contrib/2.10/RSQLite_0.7-3.zip'
Content type 'application/zip' length 544274 bytes (531 Kb)
打开了URL
downloaded 531 Kb

试开URL’http://cran.fhcrc.org/bin/windows/contrib/2.10/bitops_1.0-4.1.zip'
Content type 'application/zip' length 17325 bytes (16 Kb)
打开了URL
downloaded 16 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/affyio_1.13.5.zip'
Content type 'application/zip' length 82858 bytes (80 Kb)
打开了URL
downloaded 80 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/preprocessCore_1.7.9.zip'
Content type 'application/zip' length 118603 bytes (115 Kb)
打开了URL
downloaded 115 Kb

试开URL’http://bioconductor.org/packages/2.5/data/annotation/bin/windows/contrib/2.10/GO.db_2.3.5.zip'
Content type 'application/zip' length 15170627 bytes (14.5 Mb)
打开了URL
downloaded 14.5 Mb

试开URL’http://bioconductor.org/packages/2.5/data/annotation/bin/windows/contrib/2.10/KEGG.db_2.3.5.zip'
Content type 'application/zip' length 1608188 bytes (1.5 Mb)
打开了URL
downloaded 1.5 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/AnnotationDbi_1.7.20.zip'
Content type 'application/zip' length 5035348 bytes (4.8 Mb)
打开了URL
downloaded 4.8 Mb

试开URL’http://bioconductor.org/packages/2.5/extra/bin/windows/contrib/2.10/XML_2.6-0.zip'
Content type 'application/zip' length 2229321 bytes (2.1 Mb)
打开了URL
downloaded 2.1 Mb

试开URL’http://bioconductor.org/packages/2.5/extra/bin/windows/contrib/2.10/RCurl_1.2-1.zip'
Content type 'application/zip' length 1789923 bytes (1.7 Mb)
打开了URL
downloaded 1.7 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/IRanges_1.3.99.zip'
Content type 'application/zip' length 1521672 bytes (1.5 Mb)
打开了URL
downloaded 1.5 Mb

试开URL’http://cran.fhcrc.org/bin/windows/contrib/2.10/RColorBrewer_1.0-2.zip'
Content type 'application/zip' length 23811 bytes (23 Kb)
打开了URL
downloaded 23 Kb

试开URL’http://bioconductor.org/packages/2.5/data/annotation/bin/windows/contrib/2.10/org.Hs.eg.db_2.3.6.zip'
Content type 'application/zip' length 37316242 bytes (35.6 Mb)
打开了URL
downloaded 35.6 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/simpleaffy_2.21.3.zip'
Content type 'application/zip' length 794649 bytes (776 Kb)
打开了URL
downloaded 776 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/affy_1.23.12.zip'
Content type 'application/zip' length 2033590 bytes (1.9 Mb)
打开了URL
downloaded 1.9 Mb

试开URL’http://bioconductor.org/packages/2.5/data/experiment/bin/windows/contrib/2.10/affydata_1.11.10.zip'
Content type 'application/zip' length 12756979 bytes (12.2 Mb)
打开了URL
downloaded 12.2 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/affyPLM_1.21.4.zip'
Content type 'application/zip' length 3968938 bytes (3.8 Mb)
打开了URL
downloaded 3.8 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/annaffy_1.17.2.zip'
Content type 'application/zip' length 371140 bytes (362 Kb)
打开了URL
downloaded 362 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/annotate_1.23.4.zip'
Content type 'application/zip' length 2202749 bytes (2.1 Mb)
打开了URL
downloaded 2.1 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/Biobase_2.5.8.zip'
Content type 'application/zip' length 2378491 bytes (2.3 Mb)
打开了URL
downloaded 2.3 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/biomaRt_2.1.0.zip'
Content type 'application/zip' length 315686 bytes (308 Kb)
打开了URL
downloaded 308 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/Biostrings_2.13.54.zip'
Content type 'application/zip' length 2149067 bytes (2.0 Mb)
打开了URL
downloaded 2.0 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/DynDoc_1.23.1.zip'
Content type 'application/zip' length 99928 bytes (97 Kb)
打开了URL
downloaded 97 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/gcrma_2.17.4.zip'
Content type 'application/zip' length 222812 bytes (217 Kb)
打开了URL
downloaded 217 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/genefilter_1.26.4.zip'
Content type 'application/zip' length 705409 bytes (688 Kb)
打开了URL
downloaded 688 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/geneplotter_1.23.3.zip'
Content type 'application/zip' length 1784562 bytes (1.7 Mb)
打开了URL
downloaded 1.7 Mb

试开URL’http://bioconductor.org/packages/2.5/data/annotation/bin/windows/contrib/2.10/hgu95av2.db_2.3.5.zip'
Content type 'application/zip' length 549126 bytes (536 Kb)
打开了URL
downloaded 536 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/limma_3.0.3.zip'
Content type 'application/zip' length 1205953 bytes (1.2 Mb)
打开了URL
downloaded 1.2 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/marray_1.23.0.zip'
Content type 'application/zip' length 5275041 bytes (5.0 Mb)
打开了URL
downloaded 5.0 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/multtest_2.1.3.zip'
Content type 'application/zip' length 1642453 bytes (1.6 Mb)
打开了URL
downloaded 1.6 Mb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/vsn_3.13.7.zip'
Content type 'application/zip' length 1494717 bytes (1.4 Mb)
打开了URL
downloaded 1.4 Mb

试开URL’http://cran.fhcrc.org/bin/windows/contrib/2.10/xtable_1.5-5.zip'
Content type 'application/zip' length 177954 bytes (173 Kb)
打开了URL
downloaded 173 Kb

试开URL’http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/affyQCReport_1.23.1.zip'
Content type 'application/zip' length 229539 bytes (224 Kb)
打开了URL
downloaded 224 Kb

package 'DBI' successfully unpacked and MD5 sums checked
package 'RSQLite' successfully unpacked and MD5 sums checked
package 'bitops' successfully unpacked and MD5 sums checked
package 'affyio' successfully unpacked and MD5 sums checked
package 'preprocessCore' successfully unpacked and MD5 sums checked
package 'GO.db' successfully unpacked and MD5 sums checked
package 'KEGG.db' successfully unpacked and MD5 sums checked
package 'AnnotationDbi' successfully unpacked and MD5 sums checked
package 'XML' successfully unpacked and MD5 sums checked
package 'RCurl' successfully unpacked and MD5 sums checked
package 'IRanges' successfully unpacked and MD5 sums checked
package 'RColorBrewer' successfully unpacked and MD5 sums checked
package 'org.Hs.eg.db' successfully unpacked and MD5 sums checked
package 'simpleaffy' successfully unpacked and MD5 sums checked
package 'affy' successfully unpacked and MD5 sums checked
package 'affydata' successfully unpacked and MD5 sums checked
package 'affyPLM' successfully unpacked and MD5 sums checked
package 'annaffy' successfully unpacked and MD5 sums checked
package 'annotate' successfully unpacked and MD5 sums checked
package 'Biobase' successfully unpacked and MD5 sums checked
package 'biomaRt' successfully unpacked and MD5 sums checked
package 'Biostrings' successfully unpacked and MD5 sums checked
package 'DynDoc' successfully unpacked and MD5 sums checked
package 'gcrma' successfully unpacked and MD5 sums checked
package 'genefilter' successfully unpacked and MD5 sums checked
package 'geneplotter' successfully unpacked and MD5 sums checked
package 'hgu95av2.db' successfully unpacked and MD5 sums checked
package 'limma' successfully unpacked and MD5 sums checked
package 'marray' successfully unpacked and MD5 sums checked
package 'multtest' successfully unpacked and MD5 sums checked
package 'vsn' successfully unpacked and MD5 sums checked
package 'xtable' successfully unpacked and MD5 sums checked
package 'affyQCReport' successfully unpacked and MD5 sums checked

The downloaded packages are in
C:\Documents and Settings\Administrator\Local Settings\Temp\RtmpCDatG2\downloaded_packages
>

另外,一个网址的R包:

http://www.braju.com/R/

install.packages(c("affxparser","aroma","aroma.apd","aroma.Base","aroma.light","R.audio","R.basic","R.batch","R.cache","R.colors","R.graphics","R.huge","R.image","R.io","R.matlab","R.rsp","R.oo", "R.utils"), contriburl="http://www.braju.com/R/repos/")


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